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123 results on '"McConnell MJ"'

1. A Live Salmonella Vaccine Delivering PcrV through the Type III Secretion System Protects against Pseudomonas aeruginosa

Author: Universidad de Sevilla. Departamento de Genética, Aguilera Herce, Julia, García Quintanilla, Meritxell de Jesús, McConnell, MJ, Ramos Morales, Francisco, Romero Flores, Rocío, Universidad de Sevilla. Departamento de Genética, Aguilera Herce, Julia, García Quintanilla, Meritxell de Jesús, McConnell, MJ, Ramos Morales, Francisco, and Romero Flores, Rocío
Abstract: Pseudomonas aeruginosa is a common Gram-negative opportunistic pathogen that is intrinsically resistant to a wide range of antibiotics. The development of a broadly protective vaccine against P. aeruginosa remains a major challenge. Here, we used an attenuated strain of Salmonella enterica serovar Typhimurium as a vehicle to express P. aeruginosa antigens. A fusion between the S. enterica type III secretion effector protein SseJ and the P. aeruginosa antigen PcrV expressed under the control of the sseA promoter was translocated by Salmonella into host cells in vitro and elicited the generation of specific antibodies in mice. Mice immunized with attenuated Salmonella expressing this fusion had reduced bacterial loads in the spleens and lungs and lower serum levels of proinflammatory cytokines than control mice after P. aeruginosa infection. Importantly, immunized mice also showed significantly enhanced survival in this model. These results suggest that type III secretion effectors of S. enterica are appropriate carriers in the design of a live vaccine to prevent infections caused by P. aeruginosa IMPORTANCE The Gram-negative bacterium Pseudomonas aeruginosa is an important opportunistic pathogen that causes infections in cystic fibrosis and hospitalized patients. Therapeutic treatments are limited due to the emergence and spread of new antibiotic-resistant strains. In this context, the development of a vaccine is a priority. Here, we used an attenuated strain of Salmonella enterica serovar Typhimurium as a vehicle to express and deliver the Pseudomonas antigen PcrV. This vaccine induced the generation of specific antibodies in mice and protected them from lethal infections with P. aeruginosa This is an important step toward the development of an effective vaccine for the prevention of infections caused by P. aeruginosa in humans
Published: 2019

2. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

Author: Mcconnell, Mj, Moran, Jv, Abyzov, A, Akbarian, S, Bae, T, Cortes-Ciriano, I, Erwin, Ja, Fasching, L, Flasch, Da, Freed, D, Ganz, J, Jaffe, Ae, Kwan, Ky, Kwon, M, Lodato, Ma, Mills, Re, Paquola, Acm, Rodin, Re, Rosenbluh, C, Sestan, N, Sherman, Ma, Shin, Jh, Song, S, Straub, Re, Thorpe, J, Weinberger, Dr, Urban, Ae, Zhou, B, Gage, Fh, Lehner, T, Senthil, G, Walsh, Ca, Chess, A, Courchesne, E, Gleeson, Jg, Kidd, Jm, Park, Pj, Pevsner, J, Vaccarino, Fm, Barton, Ar, Bekiranov, S, Bohrson, Cl, Burbulis, Ie, Chronister, W, Coppola, G, Daily, K, D'Gama, Am, Emery, Sb, Frisbie, Tj, Gao, T, Gulyás-Kovács, A, Haakenson, M, Keil, Jm, Kopera, Hc, Lam, Mm, Lee, Ea, Marques-Bonet, T, Mathern, Gw, Moldovan, Jb, Oetjens, Mt, Omberg, L, Peters, Ma, Pochareddy, S, Pramparo, T, Ratan, A, Sanavia, T, Shi, L, Skarica, M, Wang, J, Wang, M, Wang, Y, Wierman, M, Wolpert, M, Woodworth, M, Zhao, X, and Zhou, W
Subjects: DNA Replication, 0301 basic medicine, DNA Repair, Brain Somatic Mosaicism, Somatic cell, DNA Mutational Analysis, Genomics, Disease, Biology, Article, Germline, 03 medical and health sciences, Neural Stem Cells, Humans, Copy-number variation, Neurons, Genetics, Multidisciplinary, Genome, Human, Mosaicism, Mental Disorders, Brain, Phenotype, Germ Cells, 030104 developmental biology, Human genome, Nerve Net, Nervous System Diseases, Cell Division, Neurotypical, DNA Damage
Abstract: BACKGROUND Elucidating the genetic architecture of neuropsychiatric disorders remains a major scientific and medical challenge. Emerging genomic technologies now permit the analysis of somatic mosaicism in human tissues. The measured frequencies of single-nucleotide variants (SNVs), small insertion/deletion (indel) mutations, structural variants [including copy number variants (CNVs), inversions, translocations, and whole-chromosome gains or losses], and mobile genetic element insertions (MEIs) indicate that each neuron may harbor hundreds of somatic mutations. Given the long life span of neurons and their central role in neural circuits and behavior, somatic mosaicism represents a potential mechanism that may contribute to neuronal diversity and the etiology of numerous neuropsychiatric disorders. ADVANCES Somatic mutations that confer cellular proliferative or cellular survival phenotypes have been identified in patients with cortical malformations. These data have led to the hypothesis that somatic mutations may also confer phenotypes to subsets of neurons, which could increase the risk of developing certain neuropsychiatric disorders. Genomic technologies, including advances in long-read, next-generation DNA sequencing technologies, single-cell genomics, and cutting-edge bioinformatics, can now make it possible to determine the types and frequencies of somatic mutations within the human brain. However, a comprehensive understanding of the contribution of somatic mosaicism to neurotypical brain development and neuropsychiatric disease requires a coordinated, multi-institutional effort. The National Institute of Mental Health (NIMH) has formed a network of 18 investigative teams representing 15 institutions called the Brain Somatic Mosaicism Network (BSMN). Each research team will use an array of genomic technologies to exploit well-curated human tissue repositories in an effort to define the frequency and pattern of somatic mutations in neurotypical individuals and in schizophrenia, autism spectrum disorder, bipolar disorder, Tourette syndrome, and epilepsy patient populations. Collectively, these efforts are estimated to generate a community resource of more than 10,000 DNA-sequencing data sets and will enable a cross-platform integrated analysis with other NIMH initiatives, such as the PsychENCODE project and the CommonMind Consortium. OUTLOOK A fundamental open question in neurodevelopmental genetics is whether and how somatic mosaicism may contribute to neuronal diversity within the neurotypical spectrum and in diseased brains. Healthy individuals may harbor known pathogenic somatic mutations at subclinical frequencies, and the local composition of neural cell types may be altered by mutations conferring prosurvival phenotypes in subsets of neurons. By extension, the neurotypical architecture of somatic mutations may confer circuit-level differences that would not be present if every neuron had an identical genome. Given the apparent abundance of somatic mutations within neurons, an in-depth understanding of how different types of somatic mosaicism affect neural function could yield mechanistic insight into the etiology of neurodevelopmental and neuropsychiatric disorders. The BSMN will examine large collections of postmortem brain tissue from neurotypical individuals and patients with neuropsychiatric disorders. By sequencing brain DNA and single neuronal genomes directly, rather than genomic DNA derived from peripheral blood or other somatic tissues, the BSMN will test the hypothesis that brain somatic variants contribute to neuropsychiatric disease. Notably, it is also possible that some inherited germline variants confer susceptibility to disease, which is later exacerbated by somatic mutations. Confirming such a scenario could increase our understanding of the genetic risk architecture of neuropsychiatric disease and may, in part, explain discordant neuropsychiatric phenotypes between identical twins. Results from these studies may lead to the discovery of biomarkers and genetic targets to improve the treatment of neuropsychiatric disease and may offer hope for improving the lives of patients and their families.
Published: 2017

3. Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles

Author: Connor, LM, Tang, S-C, Cognard, E, Ochiai, S, Hilligan, KL, Old, SI, Pellefigues, C, White, RF, Patel, D, Smith, AAT, Eccles, DA, Lamiable, O, McConnell, MJ, Ronchese, F, Connor, LM, Tang, S-C, Cognard, E, Ochiai, S, Hilligan, KL, Old, SI, Pellefigues, C, White, RF, Patel, D, Smith, AAT, Eccles, DA, Lamiable, O, McConnell, MJ, and Ronchese, F
Abstract: The dendritic cell signals required for the in vivo priming of IL-4-producing T cells are unknown. We used RNA sequencing to characterize DCs from skin LN of mice exposed to two different Th2 stimuli: the helminth parasite Nippostrongylus brasiliensis (Nb) and the contact sensitizer dibutyl phthalate (DBP)-FITC. Both Nb and DBP-FITC induced extensive transcriptional changes that involved multiple DC subsets. Surprisingly, these transcriptional changes were highly distinct in the two models, with only a small number of genes being similarly regulated in both conditions. Pathway analysis of expressed genes identified no shared pathways between Nb and DBP-FITC, but revealed a type-I IFN (IFN-I) signature unique to DCs from Nb-primed mice. Blocking the IFN-I receptor at the time of Nb treatment had little effect on DC migration and antigen transport to the LN, but inhibited the up-regulation of IFN-I-induced markers on DCs and effectively blunted Th2 development. In contrast, the response to DBP-FITC was not affected by IFN-I receptor blockade, a finding consistent with the known dependence of this response on the innate cytokine TSLP. Thus, the priming of Th2 responses is associated with distinct transcriptional signatures in DCs in vivo, reflecting the diverse environments in which Th2 immune responses are initiated.
Published: 2017

4. Iterative sorting reveals CD133+and CD133-melanoma cells as phenotypically distinct populations

Author: Grasso, C, Anaka, M, Hofmann, O, Sompallae, R, Broadley, K, Hide, W, Berridge, MV, Cebon, J, Behren, A, McConnell, MJ, Grasso, C, Anaka, M, Hofmann, O, Sompallae, R, Broadley, K, Hide, W, Berridge, MV, Cebon, J, Behren, A, and McConnell, MJ
Abstract: BACKGROUND: The heterogeneity and tumourigenicity of metastatic melanoma is attributed to a cancer stem cell model, with CD133 considered to be a cancer stem cell marker in melanoma as well as other tumours, but its role has remained controversial. METHODS: We iteratively sorted CD133+ and CD133- cells from 3 metastatic melanoma cell lines, and observed tumourigenicity and phenotypic characteristics over 7 generations of serial xeno-transplantation in NOD/SCID mice. RESULTS: We demonstrate that iterative sorting is required to make highly pure populations of CD133+ and CD133- cells from metastatic melanoma, and that these two populations have distinct characteristics not related to the cancer stem cell phenotype. In vitro, gene set enrichment analysis indicated CD133+ cells were related to a proliferative phenotype, whereas CD133- cells were of an invasive phenotype. However, in vivo, serial transplantation of CD133+ and CD133- tumours over 7 generations showed that both populations were equally able to initiate and propagate tumours. Despite this, both populations remained phenotypically distinct, with CD133- cells only able to express CD133 in vivo and not in vitro. Loss of CD133 from the surface of a CD133+ cell was observed in vitro and in vivo, however CD133- cells derived from CD133+ retained the CD133+ phenotype, even in the presence of signals from the tumour microenvironment. CONCLUSION: We show for the first time the necessity of iterative sorting to isolate pure marker-positive and marker-negative populations for comparative studies, and present evidence that despite CD133+ and CD133- cells being equally tumourigenic, they display distinct phenotypic differences, suggesting CD133 may define a distinct lineage in melanoma.
Published: 2016

5. Immunization with Lipopolysaccharide-Deficient Whole Cells Provides Protective Immunity in an Experimental Mouse Model of Acinetobacter baumannii Infection

Author: García Quintanilla, Meritxell de Jesús, Pulido, Marina R., Pachón Díaz, Jerónimo, McConnell, MJ, Universidad de Sevilla. Departamento de Microbiología, Universidad de Sevilla. Departamento de Medicina, and Universidad de Sevilla. CTS-203: Estudio de las Enfermedades Infecciosas
Subjects: Acinetobacter baumannii, Vaccines, Gram-negative bacteria, Morbidity, Mortality
Abstract: Editor: Gunnar F. Kaufmann The increasing clinical importance of infections caused by multidrug resistant Acinetobacter baumannii warrants the development of novel approaches for prevention and treatment. In this context, vaccination of certain patient populations may contribute to reducing the morbidity and mortality caused by this pathogen. Vaccines against Gram-negative bacteria based on inactivated bacterial cells are highly immunogenic and have been shown to produce protective immunity against a number of bacterial species. However, the high endotoxin levels present in these vaccines due to the presence of lipopolysaccharide complicates their use in human vaccination. In the present study, we used a laboratory-derived strain of A. baumannii that completely lacks lipopolysaccharide due to a mutation in the lpxD gene (IB010), one of the genes involved in the first steps of lipopolysaccharide biosynthesis, for vaccination. We demonstrate that IB010 has greatly reduced endotoxin content (,1.0 endotoxin unit/106 cells) compared to wild type cells. Immunization with formalin inactivated IB010 produced a robust antibody response consisting of both IgG1 and IgG2c subtypes. Mice immunized with IB010 had significantly lower post-infection tissue bacterial loads and significantly lower serum levels of the pro-inflammatory cytokines IL-1b, TNF-a and IL-6 compared to control mice in a mouse model of disseminated A. baumannii infection. Importantly, immunized mice were protected from infection with the ATCC 19606 strain and an A. baumannii clinical isolate. These data suggest that immunization with inactivated A. baumannii whole cells deficient in lipopolysaccharide could serve as the basis for a vaccine for the prevention of infection caused by A. baumannii. REIPI REIPI RD06/0008/0000 Consejería de Salud de la Junta de Andalucía (PI-0046-2011) Ministerio de Economía y Competitividad, Subprograma Miguel Servet (CP11/00314)
Published: 2014

6. Measurement of the bottom-strange meson mixing phase in the full CDF data set

Author: Aaltonen, T., Alvarez, González, Amerio, B., Amidei, S., Anastassov, D., Annovi, A., Antos, A., Apollinari, J., Appel, G., J. A., Arisawa, Artikov, T., Asaadi, A., Ashmanskas, J., Auerbach, W., Aurisano, B., Azfar, A., Badgett, F., Bae, W., Barbaro, Galtieri, Barnes, A., V. E., Barnett, B. A., Barria, Bartos, P., Bauce, P., Bedeschi, M., Behari, F., Bellettini, S., Bellinger, G., Benjamin, J., Beretvas, D., Bhatti, A., Bisello, A., Bizjak, D., Bland, I., K. R., Blumenfeld, Bocci, B., Bodek, A., Bortoletto, A., Boudreau, D., Boveia, J., Brigliadori, A., Bromberg, L., Brucken, C., Budagov, E., Budd, J., H. S., Burkett, Busetto, K., Bussey, G., Buzatu, P., Calamba, A., Calancha, A., Camarda, C., Campanelli, S., Campbell, M., Canelli, M., Carls, F., Carlsmith, B., Carosi, D., Carrillo, R., Carron, S., Casal, S., Casarsa, B., Castro, M., Catastini, A., Cauz, P., Cavaliere, D., Cavalli, Sforza, Cerri, M., Cerrito, A., Chen, L., Y. C., Chertok, Chiarelli, M., Chlachidze, G., Chlebana, G., Cho, F., Chokheli, K., Chung, D., W. H., Chung, Y. S., Ciocci, M. A., Clark, Clarke, A., Compostella, C., Convery, G., M. E., Conway, Corbo, J., Cordelli, M., Cox, M., C. A., Cox, D. J., Crescioli, Cuevas, F., Culbertson, J., Dagenhart, R., D'Ascenzo, D., Datta, N., Barbaro, De, Dell'Orso, Mauro, Demortier, M., Deninno, L., Devoto, M., D'Errico, F., Canto, Di, Ruzza, Di, Dittmann, B., J. R., D'Onofrio, Donati, Simone, Dong, P., Dorigo, M., Dorigo, T., Ebina, K., Elagin, A., Eppig, A., Erbacher, R., Errede, S., Ershaidat, N., Eusebi, R., Farrington, S., Feindt, M., Fernandez, J. P., Field, R., Flanagan, G., Forrest, R., Frank, M. J., Franklin, M., Freeman, J. C., Funakoshi, Y., Furic, I., Gallinaro, M., Garcia, J. E., Garfinkel, A. F., Garosi, P., Gerberich, H., Gerchtein, E., Giagu, S., Giakoumopoulou, V., Giannetti, P., Gibson, K., Ginsburg, C. M., Giokaris, N., Giromini, P., Giurgiu, G., Glagolev, V., Glenzinski, D., Gold, M., Goldin, D., Goldschmidt, N., Golossanov, A., Gomez, G., Gomez, Ceballos, Goncharov, G., González, M., Gorelov, O., Goshaw, I., A. T., Goulianos, Grillo, K., Grinstein, L., Grosso, Pilcher, Group, C., R. C., Guimaraes Da Costa, Hahn, J., S. R., Halkiadakis, Hamaguchi, E., Han, A., J. Y., Happacher, Hara, F., Hare, K., Hare, D., Harr, M., R. F., Hatakeyama, Hays, K., Heck, C., Heinrich, M., Herndon, J., Hewamanage, M., Hocker, S., Hopkins, A., Horn, W., Hou, D., Hughes, S., R. E., Hurwitz, Husemann, M., Hussain, U., Hussein, N., Huston, M., Introzzi, J., Iori, G., Ivanov, M., James, A., Jang, E., Jayatilaka, D., Jeon, B., E. J., Jindariani, Jones, S., Joo, M., K. K., Jun, S. Y., Junk, T. R., Kamon, Karchin, T., P. E., Kasmi, Kato, A., Ketchum, Y., Keung, W., Khotilovich, J., Kilminster, V., Kim, B., D. H., Kim, H. S., Kim, J. E., Kim, M. J., Kim, S. B., Kim, S. H., Kim, Y. K., Kim, Y. J., Kimura, Kirby, N., Klimenko, M., Knoepfel, S., Kondo, K., Kong, K., D. J., Konigsberg, Kotwal, J., A. V., Kreps, Kroll, M., Krop, J., Kruse, D., Krutelyov, M., Kuhr, V., Kurata, T., Kwang, M., Laasanen, S., A. T., Lami, Lammel, S., Lancaster, S., Lander, M., R. L., Lannon, Lath, K., Latino, A., Lecompte, G., Lee, T., Lee, E., H. S., Lee, J. S., Lee, S. W., Leo, Leone, S., Lewis, S., J. D., Limosani, Lin, A., C. J., Lindgren, Lipeles, M., Lister, E., Litvintsev, A., D. O., Liu, Liu, C., Liu, H., Liu, Q., Lockwitz, T., Loginov, S., Lucchesi, A., Lueck, D., Lujan, J., Lukens, P., Lungu, P., Lys, G., Lysak, J., Madrak, R., Maeshima, R., Maestro, K., Malik, P., Manca, S., Manousakis, Katsikakis, Margaroli, A., Marino, F., Martínez, C., Mastrandrea, M., Matera, P., Mattson, K., M. E., Mazzacane, Mazzanti, A., Mcfarland, P., K. S., Mcintyre, Mcnulty, P., Mehta, R., Mehtala, A., Mesropian, P., Miao, C., Mietlicki, T., Mitra, D., Miyake, A., Moed, H., Moggi, S., Mondragon, N., M. N., Moon, C. S., Moore, Morello, R., M. J., Morlock, Movilla, Fernandez, Mukherjee, P., Muller, A., Murat, T., Mussini, P., Nachtman, M., Nagai, J., Naganoma, Y., Nakano, J., Napier, I., Nett, A., Neu, J., Neubauer, C., M. S., Nielsen, Nodulman, J., Noh, L., S. Y., Norniella, Oakes, O., Oh, L., S. H., Oh, Y. D., Oksuzian, Okusawa, I., Orava, T., Ortolan, R., Pagan, Griso, Pagliarone, S., Palencia, C., Papadimitriou, E., Paramonov, V., A. A., Patrick, Pauletta, J., Paulini, G., Paus, M., Pellett, C., D. E., Penzo, Phillips, A., T. J., Piacentino, Pianori, G., Pilot, E., Pitts, J., Plager, K., Pondrom, C., Poprocki, L., Potamianos, S., Prokoshin, K., Pranko, F., Ptohos, A., Punzi, Giovanni, Rahaman, G., Ramakrishnan, A., Ranjan, V., Redondo, N., Renton, I., Rescigno, P., Riddick, M., Rimondi, T., Ristori, F., Robson, L., Rodrigo, A., Rodriguez, T., Rogers, T., Rolli, E., Roser, S., Ruffini, R., Ruiz, F., Russ, A., Rusu, J., Safonov, V., Sakumoto, A., W. K., Sakurai, Santi, Y., Sato, L., Saveliev, K., Savoy, Navarro, Schlabach, A., Schmidt, P., Schmidt, A., E. E., Schwarz, Scodellaro, T., Scribano, L., Scuri, A., Seidel, F., Seiya, S., Semenov, Y., Sforza, A., Shalhout, F., S. Z., Shears, Shepard, T., P. F., Shimojima, Shochet, M., Shreyber, Tecker, Simonenko, I., Sinervo, A., Sliwa, P., Smith, K., J. R., Snider, F. D., Soha, Sorin, A., Song, V., Squillacioti, H., Stancari, P., Denis, S. t., Stelzer, R., Stelzer, Chilton, Stentz, O., Strologas, D., Strycker, J., G. L., Sudo, Sukhanov, Y., Suslov, A., Takemasa, I., Takeuchi, K., Tang, Y., Tecchio, J., Teng, M., P. K., Thom, Thome, J., Thompson, J., G. A., Thomson, Toback, E., Tokar, D., Tollefson, S., Tomura, K., Tonelli, T., Torre, D., Torretta, S., Totaro, D., Trovato, P., Ukegawa, M., Uozumi, F., Varganov, S., Vázquez, A., Velev, F., Vellidis, G., Vidal, C., Vila, M., Vilar, I., Vizán, R., Vogel, J., Volpi, M., Wagner, G., Wagner, P., R. L., Wakisaka, Wallny, T., Wang, R., S. M., Warburton, Waters, A., Wester, D., W. C., Whiteson, Wicklund, D., A. B., Wicklund, Wilbur, E., Wick, S., Williams, F., H. H., Wilson, J. S., Wilson, Winer, P., B. L., Wittich, Wolbers, P., Wolfe, S., Wright, H., Wu, T., Wu, X., Yamamoto, Z., Yamato, K., Yang, D., Yang, T., U. K., Yang, Y. C., Yao, W. M., Yeh, G. P., Yi, Yoh, K., Yorita, J., Yoshida, K., Yu, T., G. B., Yu, Yu, I., S. S., Yun, J. C., Zanetti, Zeng, A., Zhou, Y., Zucchelli, C., Jy, S., Koh, Yh, Koike, M, Komatsu, M, Kominami, E, Kong, Hj, Kong, Wj, Korolchuk, Vi, Kotake, Y, Koukourakis, Mi, Kouri Flores JB, Kovács, Al, Kraft, C, Krainc, D, Krämer, H, Kretz Remy, C, Krichevsky, Am, Kroemer, G, Krüger, R, Krut, O, Ktistakis, Nt, Kuan, Cy, Kucharczyk, R, Kumar, A, Kumar, R, Kumar, S, Kundu, M, Kung, Hj, Kurz, T, Kwon, Hj, La Spada AR, Lafont, F, Lamark, T, Landry, J, Lane, Jd, Lapaquette, P, Laporte, Jf, László, L, Lavandero, S, Lavoie, Jn, Layfield, R, Lazo, Pa, Le, W, Le Cam, L, Ledbetter, Dj, Lee, Aj, Lee, Bw, Lee, Gm, Lee, J, Lee, Jh, Lee, M, Lee, Ms, Lee, Sh, Leeuwenburgh, C, Legembre, P, Legouis, R, Lehmann, M, Lei, Hy, Lei, Qy, Leib, Da, Leiro, J, Lemasters, Jj, Lemoine, A, Lesniak, Ms, Lev, D, Levenson, Vv, Levine, B, Levy, E, Li, F, Li, Jl, Li, L, Li, S, Li, W, Li, Xj, Li, Yb, Li, Yp, Liang, C, Liang, Q, Liao, Yf, Liberski, Pp, Lieberman, A, Lim, Hj, Lim, Kl, Lim, K, Lin, Cf, Lin, Fc, Lin, J, Lin, Jd, Lin, K, Lin, Ww, Lin, Wc, Lin, Yl, Linden, R, Lingor, P, Lippincott Schwartz, J, Lisanti, Mp, Liton, Pb, Liu, B, Liu, Cf, Liu, K, Liu, L, Liu, Qa, Liu, W, Liu, Yc, Liu, Y, Lockshin, Ra, Lok, Cn, Lonial, S, Loos, B, Lopez Berestein, G, López Otín, C, Lossi, L, Lotze, Mt, Lőw, P, Lu, B, Lu, Z, Luciano, F, Lukacs, Nw, Lund, Ah, Lynch Day MA, Ma, Y, Macian, F, Mackeigan, Jp, Macleod, Kf, Madeo, F, Maiuri, L, Maiuri, Mc, Malagoli, D, Malicdan, Mc, Malorni, W, Man, N, Mandelkow, Em, Manon, S, Manov, I, Mao, K, Mao, X, Mao, Z, Marambaud, P, Marazziti, D, Marcel, Yl, Marchbank, K, Marchetti, P, Marciniak, Sj, Marcondes, M, Mardi, M, Marfe, G, Mariño, G, Markaki, M, Marten, Mr, Martin, Sj, Martinand Mari, C, Martinet, W, Martinez Vicente, M, Masini, M, Matarrese, P, Matsuo, S, Matteoni, R, Mayer, A, Mazure, Nm, Mcconkey, Dj, Mcconnell, Mj, Mcdermott, C, Mcdonald, C, Mcinerney, Gm, Mckenna, Sl, Mclaughlin, B, Mclean, Pj, Mcmaster, Cr, Mcquibban, Ga, Meijer, Aj, Meisler, Mh, Meléndez, A, Melia, Tj, 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Rahaman, V. Ramakrishnan, N. Ranjan, I. Redondo, P. Renton, M. Rescigno, T. Riddick, F. Rimondi, L. Ristori, A. Robson, T. Rodrigo, T. Rodriguez, E. Roger, S. Rolli, R. Roser, F. Ruffini, A. Ruiz, J. Ru, V. Rusu, A. Safonov, W. Sakumoto, Y. Sakurai, L. Santi, K. Sato, V. Saveliev, A. Savoy-Navarro, P. Schlabach, A. Schmidt, E. Schmidt, T. Schwarz, L. Scodellaro, A. Scribano, F. Scuri, S. Seidel, Y. Seiya, A. Semenov, F. Sforza, S. Shalhout, T. Shear, P. Shepard, M. Shimojima, M. Shochet, I. Shreyber-Tecker, A. Simonenko, P. Sinervo, K. Sliwa, J. Smith, F. Snider, A. Soha, V. Sorin, H. Song, P. Squillacioti, M. Stancari, R. St. Deni, B. Stelzer, O. Stelzer-Chilton, D. Stentz, J. Strologa, G. Strycker, Y. Sudo, A. Sukhanov, I. Suslov, K. Takemasa, Y. Takeuchi, J. Tang, M. Tecchio, P. Teng, J. Thom, J. Thome, G. Thompson, E. Thomson, D. Toback, S. Tokar, K. Tollefson, T. Tomura, D. Tonelli, S. Torre, D. Torretta, P. Totaro, M. Trovato, F. Ukegawa, S. Uozumi, A. Varganov, F. Vázquez, G. Velev, C. Vellidi, M. Vidal, I. Vila, R. Vilar, J. Vizán, M. Vogel, G. Volpi, P. Wagner, R. Wagner, T. Wakisaka, R. Wallny, S. Wang, A. Warburton, D. Water, W. Wester, D. Whiteson, A. Wicklund, E. Wicklund, S. Wilbur, F. Wick, H. William, J. Wilson, P. Wilson, B. Winer, P. Wittich, S. Wolber, H. Wolfe, T. Wright, X. Wu, Z. Wu, K. Yamamoto, D. Yamato, T. Yang, U. Yang, Y. Yang, W.-M. Yao, G. Yeh, K. Yi, J. Yoh, K. Yorita, T. Yoshida, G. Yu, I. Yu, S. Yu, J. Yun, A. Zanetti, Y. Zeng, C. Zhou, S. Zucchelli, and Universidad de Cantabria
Subjects: FERMILAB TEVATRON COLLIDER, Particle physics, CP-violating asymmetries, Meson, B physic, General Physics and Astronomy, FOS: Physical sciences, B physics, Angle distribution, Branching ratio, CDF experiments, CP violations, CP-violating asymmetries, Data sample, Fermilab Tevatron collider, Integrated luminosity, Longitudinal polarization, Vector meson, Longitudinal polarization, 7. Clean energy, 01 natural sciences, High Energy Physics - Experiment, Vector meson, Physics and Astronomy (all), High Energy Physics - Experiment (hep-ex), High Energy Physics - Phenomenology (hep-ph), Mixing (mathematics), Strange b mesons, Phase (matter), 0103 physical sciences, STRANGE QUARK, mixing, Bottom-Strange Meson Mixing Phase, proton antiproton collisions, 010306 general physics, TEVATRON, Nuclear Experiment, BOTTOM QUARK, Physics, Integrated luminosity, 010308 nuclear & particles physics, Branching ratio, High Energy Physics - Phenomenology, CDF experiments, CP violations, Full data, Content (measure theory), Angle distribution, CDF, Production (computer science), High Energy Physics::Experiment, Data sample
Abstract: We report a measurement of the bottom-strange meson mixing phase βs using the time evolution of Bs0→J/ψ(→μ+μ-)ϕ(→K+K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at s=1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of βs and the Bs0 decay-width difference ΔΓs and measure βs∈[-π/2,-1.51]∪[-0.06,0.30]∪[1.26,π/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of βs, we also determine ΔΓs=0.068±0.026(stat)±0.009(syst) ps-1 and the mean Bs0 lifetime τs=1.528±0.019(stat)±0.009(syst) ps, which are consistent and competitive with determinations by other experiments., This work was supported by the U.S. Department of Energy and National Science Foundation; the Italian Istituto Nazionale di Fisica Nucleare; the Ministry of Education, Culture, Sports, Science and Technology of Japan; the Natural Sciences and Engineering Research Council of Canada; the National Science Council of the Republic of China; the Swiss National Science Foundation; the A. P. Sloan Foundation; the Bundesministerium für Bildung und Forschung, Germany; the Korean World Class University Program, the National Research Foundation of Korea; the Science and Technology Facilities Council and the Royal Society, UK; the Russian Foundation for Basic Research; the Ministerio de Ciencia e Innovación, and Programa Consolider-Ingenio 2010, Spain; the Slovak R&D Agency; the Academy of Finland; and the Australian Research Council (ARC).
Published: 2012

7. Immunization with Lipopolysaccharide-Deficient Whole Cells Provides Protective Immunity in an Experimental Mouse Model of Acinetobacter baumannii Infection

Author: Universidad de Sevilla. Departamento de Microbiología, Universidad de Sevilla. Departamento de Medicina, Universidad de Sevilla. CTS-203: Estudio de las Enfermedades Infecciosas, García Quintanilla, Meritxell de Jesús, Pulido, Marina R., Pachón Díaz, Jerónimo, McConnell, MJ, Universidad de Sevilla. Departamento de Microbiología, Universidad de Sevilla. Departamento de Medicina, Universidad de Sevilla. CTS-203: Estudio de las Enfermedades Infecciosas, García Quintanilla, Meritxell de Jesús, Pulido, Marina R., Pachón Díaz, Jerónimo, and McConnell, MJ
Abstract: The increasing clinical importance of infections caused by multidrug resistant Acinetobacter baumannii warrants the development of novel approaches for prevention and treatment. In this context, vaccination of certain patient populations may contribute to reducing the morbidity and mortality caused by this pathogen. Vaccines against Gram-negative bacteria based on inactivated bacterial cells are highly immunogenic and have been shown to produce protective immunity against a number of bacterial species. However, the high endotoxin levels present in these vaccines due to the presence of lipopolysaccharide complicates their use in human vaccination. In the present study, we used a laboratory-derived strain of A. baumannii that completely lacks lipopolysaccharide due to a mutation in the lpxD gene (IB010), one of the genes involved in the first steps of lipopolysaccharide biosynthesis, for vaccination. We demonstrate that IB010 has greatly reduced endotoxin content (,1.0 endotoxin unit/106 cells) compared to wild type cells. Immunization with formalin inactivated IB010 produced a robust antibody response consisting of both IgG1 and IgG2c subtypes. Mice immunized with IB010 had significantly lower post-infection tissue bacterial loads and significantly lower serum levels of the pro-inflammatory cytokines IL-1b, TNF-a and IL-6 compared to control mice in a mouse model of disseminated A. baumannii infection. Importantly, immunized mice were protected from infection with the ATCC 19606 strain and an A. baumannii clinical isolate. These data suggest that immunization with inactivated A. baumannii whole cells deficient in lipopolysaccharide could serve as the basis for a vaccine for the prevention of infection caused by A. baumannii.
Published: 2014

8. Guidelines for the use and interpretation of assays for monitoring autophagy.

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Macian, F, Mackeigan, Jp, Macleod, Kf, Madeo, F, Maiuri, L, Maiuri, Mc, Malagoli, D, Malicdan, Mc, Malorni, W, Man, N, Mandelkow, Em, Manon, S, Manov, I, Mao, K, Mao, X, Mao, Z, Marambaud, P, Marazziti, D, Marcel, Yl, Marchbank, K, Marchetti, P, Marciniak, Sj, Marcondes, M, Mardi, M, Marfe, G, Mariño, G, Markaki, M, Marten, Mr, Martin, Sj, Martinand-Mari, C, Martinet, W, Martinez-Vicente, M, Masini, M, Matarrese, P, Matsuo, S, Matteoni, R, Mayer, A, Mazure, Nm, Mcconkey, Dj, Mcconnell, Mj, Mcdermott, C, Mcdonald, C, Mcinerney, Gm, Mckenna, Sl, Mclaughlin, B, Mclean, Pj, Mcmaster, Cr, Mcquibban, Ga, Meijer, Aj, Meisler, Mh, Meléndez, A, Melia, Tj, Melino, G, Mena, Ma, Menendez, Ja, Menna-Barreto, Rf, Menon, Mb, Menzies, Fm, Mercer, Ca, Merighi, A, Merry, De, Meschini, S, Meyer, Cg, Meyer, Tf, Miao, Cy, Miao, Jy, Michels, Pa, Michiels, C, Mijaljica, D, Milojkovic, A, Minucci, S, Miracco, C, Miranti, Ck, Mitroulis, I, Miyazawa, K, Mizushima, N, Mograbi, B, Mohseni, S, Molero, X, Mollereau, B, Mollinedo, F, Momoi, T, Monastyrska, I, Monick, Mm, Monteiro, Mj, Moore, Mn, Mora, R, Moreau, K, Moreira, Pi, Moriyasu, Y, Moscat, J, Mostowy, S, Mottram, Jc, Motyl, T, Moussa, Ce, Müller, S, Muller, S, Münger, K, Münz, C, Murphy, Lo, Murphy, Me, Musarò, A, Mysorekar, I, Nagata, E, Nagata, K, Nahimana, A, Nair, U, Nakagawa, T, Nakahira, K, Nakano, H, Nakatogawa, H, Nanjundan, M, Naqvi, Ni, Narendra, Dp, Narita, M, Navarro, M, Nawrocki, St, Nazarko, Ty, Nemchenko, A, Netea, Mg, Neufeld, Tp, Ney, Pa, Nezis, Ip, Nguyen, Hp, Nie, D, Nishino, I, Nislow, C, Nixon, Ra, Noda, T, Noegel, Aa, Nogalska, A, Noguchi, S, Notterpek, L, Novak, I, Nozaki, T, Nukina, N, Nürnberger, T, Nyfeler, B, Obara, K, Oberley, Td, Oddo, S, Ogawa, M, Ohashi, T, Okamoto, K, Oleinick, Nl, Oliver, Fj, Olsen, Lj, Olsson, S, Opota, O, Osborne, Tf, Ostrander, Gk, Otsu, K, Ou, Jh, Ouimet, M, Overholtzer, M, Ozpolat, B, Paganetti, P, Pagnini, U, Pallet, N, Palmer, Ge, Palumbo, C, Pan, T, Panaretakis, T, Pandey, Ub, Papackova, Z, Papassideri, I, Paris, I, Park, J, Park, Ok, Parys, Jb, Parzych, Kr, Patschan, S, Patterson, C, Pattingre, S, Pawelek, Jm, Peng, J, Perlmutter, Dh, Perrotta, I, Perry, G, Pervaiz, S, Peter, M, Peters, Gj, Petersen, M, Petrovski, G, Phang, Jm, Piacentini, M, Pierre, P, Pierrefite-Carle, V, Pierron, G, Pinkas-Kramarski, R, Piras, A, Piri, N, Platanias, Lc, Pöggeler, S, Poirot, M, Poletti, A, Poüs, C, Pozuelo-Rubio, M, Prætorius-Ibba, M, Prasad, A, Prescott, M, Priault, M, Produit-Zengaffinen, N, Progulske-Fox, A, Proikas-Cezanne, T, Przedborski, S, Przyklenk, K, Puertollano, R, Puyal, J, Qian, Sb, Qin, L, Qin, Zh, Quaggin, Se, Raben, N, Rabinowich, H, Rabkin, Sw, Rahman, I, Rami, A, Ramm, G, Randall, G, Randow, F, Rao, Va, Rathmell, Jc, Ravikumar, B, Ray, Sk, Reed, Bh, Reed, Jc, Reggiori, F, Régnier-Vigouroux, A, Reichert, A, Reiners JJ, Jr, Reiter, Rj, Ren, J, Revuelta, Jl, Rhodes, Cj, Ritis, K, Rizzo, E, Robbins, J, Roberge, M, Roca, H, Roccheri, Mc, Rocchi, S, Rodemann, Hp, Rodríguez de Córdoba, S, Rohrer, B, Roninson, Ib, Rosen, K, Rost-Roszkowska, Mm, Rouis, M, Rouschop, Km, Rovetta, F, Rubin, Bp, Rubinsztein, Dc, Ruckdeschel, K, Rucker EB, 3rd, Rudich, A, Rudolf, E, Ruiz-Opazo, N, Russo, R, Rusten, Te, Ryan, Km, Ryter, Sw, Sabatini, Dm, Sadoshima, J, Saha, T, Saitoh, T, Sakagami, H, Sakai, Y, Salekdeh, Gh, Salomoni, P, Salvaterra, Pm, Salvesen, G, Salvioli, R, Sanchez, Am, Sánchez-Alcázar, Ja, Sánchez-Prieto, R, Sandri, M, Sankar, U, Sansanwal, P, Santambrogio, L, Saran, S, Sarkar, S, Sarwal, M, Sasakawa, C, Sasnauskiene, A, Sass, M, Sato, K, Sato, M, Schapira, Ah, Scharl, M, Schätzl, Hm, Scheper, W, Schiaffino, S, Schneider, C, Schneider, Me, Schneider-Stock, R, Schoenlein, Pv, Schorderet, Df, Schüller, C, Schwartz, Gk, Scorrano, L, Sealy, L, Seglen, Po, Segura-Aguilar, J, Seiliez, I, Seleverstov, O, Sell, C, Seo, Jb, Separovic, D, Setaluri, V, Setoguchi, T, Settembre, C, Shacka, Jj, Shanmugam, M, Shapiro, Im, Shaulian, E, Shaw, Rj, Shelhamer, Jh, Shen, Hm, Shen, Wc, Sheng, Zh, Shi, Y, Shibuya, K, Shidoji, Y, Shieh, Jj, Shih, Cm, Shimada, Y, Shimizu, S, Shintani, T, Shirihai, O, Shore, Gc, Sibirny, Aa, Sidhu, Sb, Sikorska, B, Silva-Zacarin, Ec, Simmons, A, Simon, Ak, Simon, Hu, Simone, C, Simonsen, A, Sinclair, Da, Singh, R, Sinha, D, Sinicrope, Fa, Sirko, A, Siu, Pm, Sivridis, E, Skop, V, Skulachev, Vp, Slack, R, Smaili, S, Smith, Dr, Soengas, M, Soldati, T, Song, X, Sood, Ak, Soong, Tw, Sotgia, F, Spector, Sa, Spies, Cd, Springer, W, Srinivasula, Sm, Stefanis, L, Steffan, J, Stendel, R, Stenmark, H, Stephanou, A, Stern, St, Sternberg, C, Stork, B, Strålfors, P, Subauste, C, Sui, X, Sulzer, D, Sun, J, Sun, Sy, Sun, Zj, Sung, Jj, Suzuki, K, Suzuki, T, Swanson, M, Swanton, C, Sweeney, St, Sy, Lk, Szabadkai, G, Tabas, I, Taegtmeyer, H, Tafani, M, Takács-Vellai, K, Takano, Y, Takegawa, K, Takemura, G, Takeshita, F, Talbot, Nj, Tan, K, Tanaka, K, Tang, D, Tanida, I, Tannous, Ba, Tavernarakis, N, Taylor, G, Taylor, Ga, Taylor, Jp, Terada, L, Terman, A, Tettamanti, G, Thevissen, K, Thompson, Cb, Thorburn, A, Thumm, M, Tian, F, Tian, Y, Tocchini-Valentini, G, Tolkovsky, Am, Tomino, Y, Tönges, L, Tooze, Sa, Tournier, C, Tower, J, Towns, R, Trajkovic, V, Travassos, Lh, Tsai, Tf, Tschan, Mp, Tsubata, T, Tsung, A, Turk, B, Turner, L, Tyagi, Sc, Uchiyama, Y, Ueno, T, Umekawa, M, Umemiya-Shirafuji, R, Unni, Vk, Vaccaro, Mi, Valente, Em, Van den Berghe, G, van der Klei, Ij, van Doorn, W, van Dyk, Lf, van Egmond, M, van Grunsven, La, Vandenabeele, P, Vandenberghe, Wp, Vanhorebeek, I, Vaquero, Ec, Velasco, G, Vellai, T, Vicencio, Jm, Vierstra, Rd, Vila, M, Vindis, C, Viola, G, Viscomi, Maria Teresa, Voitsekhovskaja, Ov, von Haefen, C, Votruba, M, Wada, K, Wade-Martins, R, Walker, Cl, Walsh, Cm, Walter, J, Wan, Xb, Wang, A, Wang, C, Wang, D, Wang, F, Wang, G, Wang, H, Wang, Hg, Wang, Hd, Wang, J, Wang, K, Wang, M, Wang, Rc, Wang, X, Wang, Yj, Wang, Y, Wang, Z, Wang, Zc, Wansink, Dg, Ward, Dm, Watada, H, Waters, Sl, Webster, P, Wei, L, Weihl, Cc, Weiss, Wa, Welford, Sm, Wen, Lp, Whitehouse, Ca, Whitton, Jl, Whitworth, Aj, Wileman, T, Wiley, Jw, Wilkinson, S, Willbold, D, Williams, Rl, Williamson, Pr, Wouters, Bg, Wu, C, Wu, Dc, Wu, Wk, Wyttenbach, A, Xavier, Rj, Xi, Z, Xia, P, Xiao, G, Xie, Z, Xu, Dz, Xu, J, Xu, L, Xu, X, Yamamoto, A, Yamashina, S, Yamashita, M, Yan, X, Yanagida, M, Yang, D, Yang, E, Yang, Jm, Yang, Sy, Yang, W, Yang, Wy, Yang, Z, Yao, Mc, Yao, Tp, Yeganeh, B, Yen, Wl, Yin, Jj, Yin, Xm, Yoo, Oj, Yoon, G, Yoon, Sy, Yorimitsu, T, Yoshikawa, Y, Yoshimori, T, Yoshimoto, K, You, Hj, Youle, Rj, Younes, A, Yu, L, Yu, Sw, Yu, Wh, Yuan, Zm, Yue, Z, Yun, Ch, Yuzaki, M, Zabirnyk, O, Silva-Zacarin, E, Zacks, D, Zacksenhaus, E, Zaffaroni, N, Zakeri, Z, Zeh HJ, 3rd, Zeitlin, So, Zhang, H, Zhang, Hl, Zhang, J, Zhang, Jp, Zhang, L, Zhang, My, Zhang, Xd, Zhao, M, Zhao, Yf, Zhao, Y, Zhao, Zj, Zheng, X, Zhivotovsky, B, Zhong, Q, Zhou, Cz, Zhu, C, Zhu, Wg, Zhu, Xf, Zhu, X, Zhu, Y, Zoladek, T, Zong, Wx, Zorzano, A, Zschocke, J, Zuckerbraun, B., and Viscomi M. T. (ORCID:0000-0002-9096-4967)
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused o
Published: 2012

9. Deep Intraclonal Analysis for the Development of Vaccines against Drug-Resistant Klebsiella pneumoniae Lineages.

Author: Tajuelo A, Gato E, Oteo-Iglesias J, Pérez-Vázquez M, McConnell MJ, Martín-Galiano AJ, and Pérez A
Subjects: Humans, Drug Resistance, Multiple, Bacterial genetics, Antigens, Bacterial immunology, Antigens, Bacterial genetics, Vaccine Development, Bacterial Proteins immunology, Bacterial Proteins genetics, Epitopes, B-Lymphocyte immunology, Klebsiella pneumoniae immunology, Klebsiella pneumoniae genetics, Bacterial Vaccines immunology, Klebsiella Infections prevention & control, Klebsiella Infections microbiology, Klebsiella Infections immunology
Abstract: Despite its medical relevance, there is no commercial vaccine that protects the population at risk from multidrug-resistant (MDR) Klebsiella pneumoniae infections. The availability of massive omic data and novel algorithms may improve antigen selection to develop effective prophylactic strategies. Up to 133 exposed proteins in the core proteomes, between 516 and 8666 genome samples, of the six most relevant MDR clonal groups (CGs) carried conserved B-cell epitopes, suggesting minimized future evasion if utilized for vaccination. Antigens showed a range of epitopicity, functional constraints, and potential side effects. Eleven antigens, including three sugar porins, were represented in all MDR-CGs, constitutively expressed, and showed limited reactivity with gut microbiota. Some of these antigens had important interactomic interactions and may elicit adhesion-neutralizing antibodies. Synergistic bivalent to pentavalent combinations that address expression conditions, interactome location, virulence activities, and clone-specific proteins may overcome the limiting protection of univalent vaccines. The combination of five central antigens accounted for 41% of all non-redundant interacting partners of the antigen dataset. Specific antigen mixtures represented in a few or just one MDR-CG further reduced the chance of microbiota interference. Rational antigen selection schemes facilitate the design of high-coverage and "magic bullet" multivalent vaccines against recalcitrant K. pneumoniae lineages.
Published: 2024
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10. Loss of Lipooligosaccharide Synthesis in Acinetobacter baumannii Produces Changes in Outer Membrane Vesicle Protein Content.

Author: Cano-Castaño B, Corral-Lugo A, Gato E, Terrón MC, Martín-Galiano AJ, Sotillo J, Pérez A, and McConnell MJ
Subjects: Acinetobacter Infections microbiology, Animals, Mice, Tandem Mass Spectrometry, Bacterial Outer Membrane metabolism, Acinetobacter baumannii metabolism, Acinetobacter baumannii genetics, Lipopolysaccharides biosynthesis, Bacterial Outer Membrane Proteins metabolism, Bacterial Outer Membrane Proteins genetics
Abstract: Outer membrane vesicles (OMVs) are nanostructures derived from the outer membrane of Gram-negative bacteria. We previously demonstrated that vaccination with endotoxin-free OMVs isolated from an Acinetobacter baumannii strain lacking lipooligosaccharide (LOS) biosynthesis, due to a mutation in lpxD , provides full protection in a murine sepsis model. The present study characterizes the protein content of highly-purified OMVs isolated from LOS-replete and LOS-deficient strains. Four purification methods were evaluated to obtain highly purified OMV preparations: ultracentrifugation, size exclusion chromatography (SEC), ultracentrifugation followed by SEC, and Optiprep™. OMVs from each method were characterized using nanoparticle tracking analysis and electron microscopy. OMVs from LOS-deficient and LOS-replete strains purified using the Optiprep™ method were subjected to LC-MS/MS analysis to determine protein content. Significant differences in protein composition between OMVs from LOS-deficient and LOS-replete strains were found. Computational analyses using Bepipred 3.0 and SEMA 2.0 indicated that the lack of LOS led to the overexpression of immunogenic proteins found in LOS-containing OMVs and the presence of immune-stimulating proteins absent in LOS-replete OMVs. These findings have important implications for developing OMV-based vaccines against A. baumannii , using both LOS-containing and LOS-free OMVs preparations.
Published: 2024
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11. Mapping recurrent mosaic copy number variation in human neurons.

Author: Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, and McConnell MJ
Subjects: Humans, Alleles, DNA Copy Number Variations, Neurons metabolism, Mosaicism
Abstract: When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes., (© 2024. The Author(s).)
Published: 2024
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12. Interleukin-7-based identification of liver lymphatic endothelial cells reveals their unique structural features.

Author: Yang Y, Jeong J, Su T, Lai S, Zhang P, Garcia-Milian R, Graham M, Liu X, McConnell MJ, Utsumi T, Pereira J, and Iwakiri Y
Abstract: Background & Aims: The lymphatic system plays crucial roles in maintaining fluid balance and immune regulation. Studying the liver lymphatics has been considered challenging, as common lymphatic endothelial cell (LyEC) markers are expressed by other liver cells. Additionally, isolation of sufficient numbers of LyECs has been challenging because of their extremely low abundance (<0.01% of entire liver cell population) in a normal liver., Methods: Potential LyEC markers was identified using our published single-cell RNA sequencing (scRNA-seq) dataset (GSE147581) in mouse livers. Interleukin-7 (IL7) promoter-driven green fluorescent protein knock-in heterozygous mice were used for the validation of IL7 expression in LyECs in the liver, for the development of liver LyEC isolation protocol, and generating liver ischemia/reperfusion (I/R) injury. Scanning electron microscopy was used for the structural analysis of LyECs. Changes in LyEC phenotypes in livers of mice with I/R were determined by RNA-seq analysis., Results: Through scRNA-seq analysis, we have identified IL7 as an exclusive marker for liver LyECs, with no overlap with other liver cell types. Based on IL7 expression in liver LyECs, we have established an LyEC isolation method and observed distinct cell surface structures of LyECs with fenestrae and cellular pores (ranging from 100 to 400 nm in diameter). Furthermore, we identified LyEC genes that undergo alterations during I/R liver injuries., Conclusions: This study not only identified IL7 as an exclusively expressed gene in liver LyECs, but also enhanced our understanding of LyEC structures and demonstrated transcriptomic changes in injured livers., Impact and Implications: Understanding the lymphatic system in the liver is challenging because of the absence of specific markers for liver LyEC. This study has identified IL7 as a reliable marker for LyECs, enabling the development of an effective method for their isolation, elucidating their unique cell surface structure, and identifying LyEC genes that undergo changes during liver damage. The development of IL7 antibodies for detecting it in human liver specimens will further advance our understanding of the liver lymphatic system in the future., Competing Interests: The authors declare no competing interests. Please refer to the accompanying ICMJE disclosure forms for further details., (© 2024 The Author(s).)
Published: 2024
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13. Special Issue: Vaccines against Antibiotic-Resistant Bacteria: From Bench to Bedside.

Author: López-Siles M, Corral-Lugo A, and McConnell MJ
Abstract: The emergence and global dissemination of bacterial strains from numerous species with resistance to multiple antibiotic classes has increased in recent years, both in the healthcare and the community setting [...].
Published: 2024
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14. The Sympathetic Nervous System Promotes Hepatic Lymphangiogenesis, which Is Protective Against Liver Fibrosis.

Author: Tanaka M, Jeong J, Thomas C, Zhang X, Zhang P, Saruwatari J, Kondo R, McConnell MJ, Utsumi T, and Iwakiri Y
Subjects: Rats, Humans, Animals, Lymphangiogenesis, Rats, Sprague-Dawley, Disease Models, Animal, Liver Cirrhosis pathology, Liver pathology, Sympathetic Nervous System, Vascular Endothelial Growth Factor C, Vascular Diseases pathology
Abstract: Liver is the largest lymph-producing organ. In cirrhotic patients, lymph production significantly increases concomitant with lymphangiogenesis. The aim of this study was to determine the mechanism of lymphangiogenesis in liver and its implication in liver fibrosis. Liver biopsies from portal hypertensive patients with portal-sinusoidal vascular disease (n = 22) and liver cirrhosis (n = 5) were evaluated for lymphangiogenesis and compared with controls (n = 9 and n = 6, respectively). For mechanistic studies, rats with partial portal vein ligation (PPVL) and bile duct ligation (BDL) were used. A gene profile data set (GSE77627), including 14 histologically normal liver, 18 idiopathic noncirrhotic portal hypertension, and 22 cirrhotic patients, was analyzed. Lymphangiogenesis was significantly increased in livers from patients with portal-sinusoidal vascular disease, cirrhotic patients, as well as PPVL and BDL rats. Importantly, Schwann cells of sympathetic nerves highly expressed vascular endothelial growth factor-C in PPVL rats. Vascular endothelial growth factor-C neutralizing antibody or sympathetic denervation significantly decreased lymphangiogenesis in livers of PPVL and BDL rats, which resulted in progression of liver fibrosis. Liver specimens from cirrhotic patients showed a positive correlation between sympathetic nerve/Schwann cell-positive areas and lymphatic vessel numbers, which was supported by gene set analysis from patients with noncirrhotic portal hypertension and cirrhotic patients. Sympathetic nerves promote hepatic lymphangiogenesis in noncirrhotic and cirrhotic livers. Increased hepatic lymphangiogenesis can be protective against liver fibrosis., (Copyright © 2023 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
Published: 2023
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15. An optimized visualization and quantitative protocol for in-depth evaluation of lymphatic vessel architecture in the liver.

Author: Jeong J, Tanaka M, Yang Y, Arefyev N, DiRito J, Tietjen G, Zhang X, McConnell MJ, Utsumi T, and Iwakiri Y
Subjects: Rats, Humans, Mice, Animals, Liver pathology, Bile Ducts, Liver Cirrhosis pathology, Lymphatic Vessels diagnostic imaging, Lymphatic Vessels pathology, Cholestasis pathology
Abstract: The liver lymphatic system is essential for maintaining tissue fluid balance and immune function. The detailed structure of lymphatic vessels (LVs) in the liver remains to be fully demonstrated. The aim of this study is to reveal LV structures in normal and diseased livers by developing a tissue-clearing and coimmunolabeling protocol optimized for the tissue size and the processing time for three-dimensional (3-D) visualization and quantification of LVs in the liver. We showed that our optimized protocol enables in-depth exploration of lymphatic networks in the liver, consisting of LVs along the portal tract (deep lymphatic system) and within the collagenous Glisson's capsule (superficial lymphatic system) in different species. With this protocol, we have shown 3-D LVs configurations in relation to blood vessels and bile ducts in cholestatic mouse livers, in which LVs were highly dilated and predominantly found around highly proliferating bile ducts and peribiliary vascular plexuses in the portal tract. We also established a quantification method using a 3-D volume-rendering approach. We observed a 1.6-fold ( P < 0.05) increase in the average diameter of LVs and a 2.4-fold increase ( P < 0.05) in the average branch number of LVs in cholestatic/fibrotic livers compared with control livers. Furthermore, cholestatic/fibrotic livers showed a 4.3-fold increase ( P < 0.05) in total volume of LVs compared with control livers. Our optimized protocol and quantification method demonstrate an efficient and simple liver tissue-clearing procedure that allows the comprehensive analysis of liver lymphatic system. NEW & NOTEWORTHY This article showed a comprehensive 3-D-structural analysis of liver lymphatic vessel (LV) in normal and diseased livers in relation to blood vessels and bile ducts. In addition to the LVs highly localized at the portal tract, we revealed capsular LVs in mouse, rat, and human livers. In cholestatic livers, LVs are significantly increased and dilated compared with normal livers. Our optimized protocol provides detailed spatial information for LVs remodeling in normal and pathological conditions.
Published: 2023
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16. Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes.

Author: Pérez-Vázquez M, López-Causapé C, Corral-Lugo A, McConnell MJ, Oteo-Iglesias J, Oliver A, and Martín-Galiano AJ
Abstract: Mutations leading to upregulation of efflux pumps can produce multiple drug resistance in the pathogen Pseudomonas aeruginosa . Changes in their DNA binding regions, i.e., palindromic operators, can compromise pump depression and subsequently enhance resistance against several antibacterials and biocides. Here, we have identified (pseudo)palindromic repeats close to promoters of genes encoding 13 core drug-efflux pumps of P. aeruginosa . This framework was applied to detect mutations in these repeats in 17,292 genomes. Eighty-nine percent of isolates carried at least one mutation. Eight binary genetic properties potentially related to expression were calculated for mutations. These included palindromicity reduction, mutation type, positioning within the repeat and DNA-bending shift. High-risk ST298, ST308 and ST357 clones commonly carried four conserved mutations while ST175 and the cystic fibrosis-linked ST649 clones showed none. Remarkably, a T-to-C transition in the fourth position of the upstream repeat for mexEF - oprN was nearly exclusive of the high-risk ST111 clone. Other mutations were associated with high-risk sublineages using sample geotemporal metadata. Moreover, 1.5% of isolates carried five or more mutations suggesting they undergo an alternative program for regulation of their effluxome. Overall, P. aeruginosa shows a wide range of operator mutations with a potential effect on efflux pump expression and antibiotic resistance.
Published: 2023
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17. Editorial: Resistant pathogens: from distribution to emerging therapies.

Author: García-Ríos E, McConnell MJ, Pérez-Romero P, and López-Siles M
Abstract: Competing Interests: MM and PP-R are founders and stockholders of the biotechnology spin-off company Vaxdyn, which develops vaccines for infections caused by MDR bacteria. Vaxdyn had no role in the elaboration of this manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Published: 2023
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18. Fecal carriage of extended-spectrum beta-lactamase-producing Enterobacterales in healthy Spanish schoolchildren.

Author: López-Siles M, Moure Z, Muadica AS, Sánchez S, Cruces R, Ávila A, Lara N, Köster PC, Dashti A, Oteo-Iglesias J, Carmena D, and McConnell MJ
Abstract: Background: Extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) are a serious threat among emerging antibiotic resistant bacteria. Particularly, the number of cases of ESBL-E infections reported in children has been increasing in recent years, and approved antibiotic treatments for this age group are limited. However, information regarding the prevalence of colonization in European children, risk factors associated with colonization, and the characteristics of the colonizing strains is scarce. The aims of this study were to determine the prevalence of ESBL-E colonization in fecal samples of apparently healthy schoolchildren, to identify lifestyle routines associated with colonization, and to characterize clonal relationships and mechanisms of resistance in ESBL-E isolates., Methods: A cohort of 887 healthy children (3-13 years old) from seven primary and secondary schools in the Madrid metropolitan area was recruited between April-June 2018, and sociodemographic information and daily habits were collected. Fecal samples were screened for ESBL-E carriage in selective medium. ESBL-E isolates were further characterized by assessing molecular epidemiology (PFGE and MLST), ESBL gene carriage, and antibiotic resistance profile. This information was analyzed in conjunction with the metadata of the participants in order to identify external factors associated with ESBL-E carriage., Results: Twenty four ESBL-E, all but one Escherichia coli, were detected in 23 children (prevalence: 2.6%; 95% CI: 1.6-3.6%). Of these, seven contained the bla CTX-M-14 allele, five the bla CTX-M-15 , five the bla SHV-12 , three the bla CTX-M-27 , three the bla CTX-M-32 , and one the bla CTX-M-9 . Significant clonal diversity was observed among the isolates that grouped into 22 distinct clusters (at <85% similarity of PFGE profile). ESBL-producing E. coli isolates belonged to 12 different STs, with ST10 (25%) and ST131 (17%) being the most frequent. Apart from ß-lactams, resistance to trimethoprim/sulfamethoxazole (46%), ciprofloxacin (33%), levofloxacin (33%), tobramycin (21%), and gentamicin (8%) were the most frequently detected., Conclusion: The prevalence of ESBL-E in the studied cohort of children was lower than the average colonization rate previously detected in Europe for both children and adults. E. coli was the main ESBL-producing species detected and CTX-M were the most frequently identified ESBLs. High ST diversity suggests polyclonal dissemination. Compared to other STs, ST131 isolates were associated with resistance to various antimicrobials., Competing Interests: MM was founder and stockholder of the biotechnology spin-off company Vaxdyn, which develops vaccines for infections caused by MDR bacteria. Vaxdyn had no role in the elaboration of this manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 López-Siles, Moure, Muadica, Sánchez, Cruces, Ávila, Lara, Köster, Dashti, Oteo-Iglesias, Carmena and McConnell.)
Published: 2023
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19. Mapping the Complex Genetic Landscape of Human Neurons.

Author: Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, and McConnell MJ
Abstract: When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes., Competing Interests: Competing interests J.V.M. is an inventor on patent US6150160, is a paid consultant for Gilead Sciences, serves on the scientific advisory board of Tessera Therapeutics Inc. (where he is paid as a consultant and has equity options), has licensed reagents to Merck Pharmaceutical, and recently served on the American Society of Human Genetics Board of Directors. The other authors do not declare competing interests.
Published: 2023
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20. Role of peptidoglycan recycling enzymes AmpD and AnmK in Acinetobacter baumannii virulence features.

Author: Tajuelo A, Terrón MC, López-Siles M, and McConnell MJ
Subjects: Virulence, Peptidoglycan metabolism, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents metabolism, Biofilms, Drug Resistance, Multiple, Bacterial, Fosfomycin pharmacology, Acinetobacter baumannii metabolism
Abstract: Acinetobacter baumannii is an important causative agent of hospital acquired infections. In addition to acquired resistance to many currently-available antibiotics, it is intrinsically resistant to fosfomycin. It has previously been shown that AmpD and AnmK contribute to intrinsic fosfomycin resistance in A. baumannii due to their involvement in the peptidoglycan recycling pathway. However, the role that these two enzymes play in the fitness and virulence of A. baumannii has not been studied. The aim of this study was to characterize several virulence-related phenotypic traits in A. baumannii mutants lacking AmpD and AnmK. Specifically, cell morphology, peptidoglycan thickness, membrane permeability, growth under iron-limiting conditions, fitness, resistance to disinfectants and antimicrobial agents, twitching motility and biofilm formation of the mutant strains A. baumannii ATCC 17978 Δ ampD ::Kan and Δ anmK ::Kan were compared to the wild type strain. Our results demonstrate that bacterial growth and fitness of both mutants were compromised, especially in the Δ ampD ::Kan mutant. In addition, biofilm formation was decreased by up to 69%, whereas twitching movement was reduced by about 80% in both mutants. These results demonstrate that, in addition to increased susceptibility to fosfomycin, alteration of the peptidoglycan recycling pathway affects multiple aspects related to virulence. Inhibition of these enzymes could be explored as a strategy to develop novel treatments for A. baumannii in the future. Furthermore, this study establishes a link between intrinsic fosfomycin resistance mechanisms and bacterial fitness and virulence traits., Competing Interests: MM is founder and stockholder of the biotechnology spin-off company Vaxdyn, which develops vaccines for infections caused by MDR bacteria. Vaxdyn had no role in the elaboration of this manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Tajuelo, Terrón, López-Siles and McConnell.)
Published: 2023
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21. Unsupervised Machine Learning Organization of the Functional Dark Proteome of Gram-Negative "Superbugs": Six Protein Clusters Amenable for Distinct Scientific Applications.

Author: Sicilia C, Corral-Lugo A, Smialowski P, McConnell MJ, and Martín-Galiano AJ
Abstract: Uncharacterized proteins have been underutilized as targets for the development of novel therapeutics for difficult-to-treat bacterial infections. To facilitate the exploration of these proteins, 2819 predicted, uncharacterized proteins (19.1% of the total) from reference strains of multidrug Acinetobacter baumannii , Klebsiella pneumoniae , and Pseudomonas aeruginosa species were organized using an unsupervised k-means machine learning algorithm. Classification using normalized values for protein length, pI, hydrophobicity, degree of conservation, structural disorder, and %AT of the coding gene rendered six natural clusters. Cluster proteins showed different trends regarding operon membership, expression, presence of unknown function domains, and interactomic relevance. Clusters 2, 4, and 5 were enriched with highly disordered proteins, nonworkable membrane proteins, and likely spurious proteins, respectively. Clusters 1, 3, and 6 showed closer distances to known antigens, antibiotic targets, and virulence factors. Up to 21.8% of proteins in these clusters were structurally covered by modeling, which allowed assessment of druggability and discontinuous B-cell epitopes. Five proteins (4 in Cluster 1) were potential druggable targets for antibiotherapy. Eighteen proteins (11 in Cluster 6) were strong B-cell and T-cell immunogen candidates for vaccine development. Conclusively, we provide a feature-based schema to fractionate the functional dark proteome of critical pathogens for fundamental and biomedical purposes., Competing Interests: The authors declare the following competing financial interest(s): MM is a founder and shareholder in the biotechnology company Vaxdyn, S.L., (© 2022 The Authors. Published by American Chemical Society.)
Published: 2022
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22. Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis.

Author: Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, and McConnell MJ
Subjects: DNA genetics, DNA metabolism, DNA Repair, Humans, Tumor Suppressor Protein p53 genetics, Tumor Suppressor Protein p53 metabolism, DNA Breaks, Double-Stranded, Induced Pluripotent Stem Cells cytology, Induced Pluripotent Stem Cells metabolism, Neurogenesis
Abstract: Neurons are overproduced during cerebral cortical development. Neural progenitor cells (NPCs) divide rapidly and incur frequent DNA double-strand breaks (DSBs) throughout cortical neurogenesis. Although half of the neurons born during neurodevelopment die, many neurons with inaccurate DNA repair survive leading to brain somatic mosaicism. Recurrent DNA DSBs during neurodevelopment are associated with both gene expression level and gene length. We used imaging flow cytometry and a genome-wide DNA DSB capture approach to quantify and map DNA DSBs during human induced pluripotent stem cell (hiPSC)-based neurogenesis. Reduced p53 signaling was brought about by knockdown (p53 KD ); p53 KD led to elevated DNA DSB burden in neurons that was associated with gene expression level but not gene length in neural progenitor cells (NPCs). Furthermore, DNA DSBs incurred from transcriptional, but not replicative, stress lead to p53 activation in neurotypical NPCs. In p53 KD NPCs, DNA DSBs accumulate at transcription start sites of genes that are associated with neurological and psychiatric disorders. These findings add to a growing understanding of how neuronal genome dynamics are engaged by high transcriptional or replicative burden during neurodevelopment., (© 2022. The Author(s).)
Published: 2022
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23. Corrigendum: Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients.

Author: Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, San Juan R, Fernández-Ruiz M, Aguado JM, McConnell MJ, and Pérez-Romero P
Abstract: [This corrects the article DOI: 10.3389/fimmu.2022.878812.]., (Copyright © 2022 Tajuelo, Carretero, García-Ríos, López-Siles, Cano, Vázquez, Más, Rodríguez-Goncer, Lalueza, López-Medrano, San Juan, Fernández-Ruiz, Aguado, McConnell and Pérez-Romero.)
Published: 2022
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24. Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii .

Author: López-Siles M, McConnell MJ, and Martín-Galiano AJ
Abstract: Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with "experimentally verified," "presumed," and "probably irrelevant" degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the IS Aba 1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the "experimentally verified" level was permitted for 42 isolates to 7-8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria., Competing Interests: MM is a founder and shareholder in the biotechnology company Vaxdyn, S.L. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 López-Siles, McConnell and Martín-Galiano.)
Published: 2022
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25. Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients.

Author: Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, Juan RS, Fernández-Ruiz M, Aguado JM, McConnell MJ, and Pérez-Romero P
Subjects: Adult, Antibodies, Neutralizing, Antibodies, Viral, Cross-Sectional Studies, Humans, Immunity, Humoral, Immunoglobulin G, Immunoglobulin M, Oxygen, Prospective Studies, Research Report, SARS-CoV-2, COVID-19, Respiratory Insufficiency
Abstract: Introduction: There is robust evidence indicating that the SARS-CoV-2-specific humoral response is associated with protection against severe disease. However, relatively little data exist regarding how the humoral immune response at the time of hospital admission correlates with disease severity in unimmunized patients. Our goal was toidentify variables of the humoral response that could potentially serve as prognostic markers for COVID-19 progressionin unvaccinated SARS-CoV-2 patients., Methods: A prospective cross-sectional study was carried out in a cohort of 160 unimmunized, adult COVID-19 patients from the Hospital Universitario 12Octubre. Participants were classified into four clinical groups based on disease severity: non-survivors with respiratory failure (RF), RF survivors, patients requiring oxygen therapy and those not receiving oxygen therapy. Serum samples were taken on admission and IgM, IgG, IgG subclass antibody titers were determined by ELISA, and neutralizing antibody titersusing a surrogate neutralization assay. The differences in the antibody titers between groups and the association between the clinical and analytical characteristics of the patients and the antibody titers were analyzed., Results: Patients that developed RF and survived had IgM titers that were 2-fold higher than non-survivors ( p = 0.001), higher levels of total IgG than those who developed RF and succumbed to infection ( p < 0.001), and than patients who required oxygen therapy ( p < 0.05), and had 5-fold higher IgG1 titers than RF non-survivors ( p < 0.001) and those who needed oxygen therapy ( p < 0.001), and 2-fold higher than patients that did not require oxygen therapy during admission ( p < 0.05). In contrast, RF non-survivorshad the lowest neutralizing antibodylevels, which were significantly lower compared those with RF that survived ( p = 0.03). A positive correlation was found between IgM, total IgG, IgG1 and IgG3 titers and neutralizing antibody titers in the total cohort (p ≤ 0.0036)., Conclusions: We demonstrate that patients with RF that survived infection had significantly higher IgM, IgG, IgG1 and neutralizing titers compared to patients with RF that succumb to infection, suggesting that using humoral response variables could be used as a prognostic marker for guiding the clinical management of unimmunized patients admitted to the hospital for SARS-CoV-2 infection., Competing Interests: MJM and PPR are founders and stockholders of the biotech-nology spin-off company Vaxdyn, which develops vaccines for infections caused by MDR bacteria. Vaxdyn had no role in the elaboration of this manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Tajuelo, Carretero, García-Ríos, López-Siles, Cano, Vázquez, Más, Rodríguez-Goncer, Lalueza, López-Medrano, Juan, Fernández-Ruiz, Aguado, McConnell and Pérez-Romero.)
Published: 2022
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26. Cross-Recognition of SARS-CoV-2 B-Cell Epitopes with Other Betacoronavirus Nucleoproteins.

Author: Tajuelo A, López-Siles M, Más V, Pérez-Romero P, Aguado JM, Briz V, McConnell MJ, Martín-Galiano AJ, and López D
Subjects: Adult, Amino Acid Sequence, COVID-19 immunology, COVID-19 virology, Cohort Studies, Coronavirus Nucleocapsid Proteins chemistry, Coronavirus Nucleocapsid Proteins genetics, Coronavirus OC43, Human genetics, Coronavirus OC43, Human physiology, Cross Reactions genetics, Enzyme-Linked Immunosorbent Assay methods, Epitopes, B-Lymphocyte metabolism, HEK293 Cells, Health Personnel statistics & numerical data, Humans, Protein Domains, SARS-CoV-2 genetics, SARS-CoV-2 physiology, Sequence Homology, Amino Acid, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus immunology, Coronavirus Nucleocapsid Proteins immunology, Coronavirus OC43, Human immunology, Cross Reactions immunology, Epitope Mapping methods, Epitopes, B-Lymphocyte immunology, SARS-CoV-2 immunology
Abstract: The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.
Published: 2022
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27. Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.

Author: Foix A, López D, Díez-Fuertes F, McConnell MJ, and Martín-Galiano AJ
Subjects: Epitopes genetics, Epitopes immunology, Gene Frequency, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class I immunology, Humans, Viral Proteins genetics, Viral Proteins immunology, COVID-19 immunology, COVID-19 virology, Genome, Viral genetics, Genome, Viral immunology, Immune Evasion genetics, Immune Evasion immunology, Mutation genetics, Mutation immunology, SARS-CoV-2 genetics, SARS-CoV-2 immunology
Abstract: The massive assessment of immune evasion due to viral mutations that increase COVID-19 susceptibility can be computationally facilitated. The adaptive cytotoxic T response is critical during primary infection and the generation of long-term protection. Here, potential HLA class I epitopes in the SARS-CoV-2 proteome were predicted for 2,915 human alleles of 71 families using the netMHCIpan EL algorithm. Allele families showed extreme epitopic differences, underscoring genetic variability of protective capacity between humans. Up to 1,222 epitopes were associated with any of the twelve supertypes, that is, allele clusters covering 90% population. Next, from all mutations identified in ~118,000 viral NCBI isolates, those causing significant epitope score reduction were considered epitope escape mutations. These mutations mainly involved non-conservative substitutions at the second and C-terminal position of the ligand core, or total ligand removal by large recurrent deletions. Escape mutations affected 47% of supertype epitopes, which in 21% of cases concerned isolates from two or more sub-continental areas. Some of these changes were coupled, but never surpassed 15% of evaded epitopes for the same supertype in the same isolate, except for B27. In contrast to most supertypes, eight allele families mostly contained alleles with few SARS-CoV-2 ligands. Isolates harboring cytotoxic escape mutations for these families co-existed geographically within sub-Saharan and Asian populations enriched in these alleles according to the Allele Frequency Net Database. Collectively, our findings indicate that escape mutation events have already occurred for half of HLA class I supertype epitopes. However, it is presently unlikely that, overall, it poses a threat to the global population. In contrast, single and double mutations for susceptible alleles may be associated with viral selective pressure and alarming local outbreaks. The integration of genomic, geographical and immunoinformatic information eases the surveillance of variants potentially affecting the global population, as well as minority subpopulations., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: MJM is a founder and shareholder in the company Vaxdyn, S.L. Vaxdyn played no role in the present study. No other competing interest is declared for the remaining co-authors.
Published: 2022
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28. Covid-19 and Liver Injury: Role of Inflammatory Endotheliopathy, Platelet Dysfunction, and Thrombosis.

Author: McConnell MJ, Kondo R, Kawaguchi N, and Iwakiri Y
Subjects: Blood Platelet Disorders immunology, Blood Platelet Disorders physiopathology, COVID-19 immunology, Endothelium, Vascular immunology, Endothelium, Vascular physiopathology, Humans, Inflammation immunology, Inflammation physiopathology, Liver Diseases immunology, Liver Diseases physiopathology, Thrombosis immunology, Thrombosis physiopathology, Blood Platelet Disorders virology, COVID-19 physiopathology, Endothelium, Vascular virology, Inflammation virology, Liver Diseases virology, Thrombosis virology
Abstract: Liver injury, characterized predominantly by elevated aspartate aminotransferase and alanine aminotransferase, is a common feature of coronavirus disease 2019 (COVID-19) symptoms caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). Additionally, SARS-CoV-2 infection is associated with acute-on-chronic liver failure in patients with cirrhosis and has a notably elevated mortality in patients with alcohol-related liver disease compared to other etiologies. Direct viral infection of the liver with SARS-CoV-2 remains controversial, and alternative pathophysiologic explanations for its hepatic effects are an area of active investigation. In this review, we discuss the effects of SARS-CoV-2 and the inflammatory environment it creates on endothelial cells and platelets more generally and then with a hepatic focus. In doing this, we present vascular inflammation and thrombosis as a potential mechanism of liver injury and liver-related complications in COVID-19., (© 2021 The Authors. Hepatology Communications published by Wiley Periodicals LLC on behalf of American Association for the Study of Liver Diseases.)
Published: 2022
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29. Subinhibitory Concentrations of Clinically-Relevant Antimicrobials Affect Resistance-Nodulation-Division Family Promoter Activity in Acinetobacter baumannii .

Author: Prieto Martin Gil S, Tajuelo A, López-Siles M, and McConnell MJ
Abstract: Efflux pumps contribute to multidrug resistance in Acinetobacter baumannii due to their ability to expel a wide variety of structurally unrelated compounds. This study aimed to characterize the effect of subinhibitory concentrations of clinically-relevant antibiotics and disinfectants on the promoter activity of members of the Resistance-Nodulation-Division (RND) family in A. baumannii . The promoter regions from three RND efflux pumps (AdeABC, AdeFGH and AdeIJK) and the AdeRS regulatory system from three different A. baumannii strains (ATCC 17961, ATCC 17978, and ATCC 19606) were cloned into a luciferase reporter system (pLPV1Z). Promoter activity was quantitatively assessed in both exponential and stationary phase cultures after exposure to subinhibitory concentrations of four antibiotics from different classes (rifampicin, meropenem, tigecycline and colistin) and two disinfectants (ethanol and chlorhexidine). Subinhibitory concentrations of the compounds tested had variable effects on promoter activity that were highly dependent on the A. baumannii strain, the compound tested and the growth phase. Fold changes in AdeABC promoter activity ranged from 1.97 to 113.7, in AdeFGH from -5.6 to 1.13, in AdeIJK from -2.5 to 2, and in AdeRS from -36.2 to -1.32. Taken together, these results indicate that subinhibitory concentrations of clinically-relevant antibiotics and disinfectants affect the promoter activity of RND family members in A. baumannii in a strain and growth phase dependent manner. These results may have important implications for the treatment of infections caused by A. baumannii ., Competing Interests: MJM is founder and stockholder of the biotechnology spin-off company Vaxdyn, which develops vaccines for infections caused by MDR bacteria. Vaxdyn had no role in the elaboration of this manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Prieto Martin Gil, Tajuelo, López-Siles and McConnell.)
Published: 2021
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30. Predicted Epitope Abundance Supports Vaccine-Induced Cytotoxic Protection Against SARS-CoV-2 Variants of Concern.

Author: Martín-Galiano AJ, Díez-Fuertes F, McConnell MJ, and López D
Subjects: Alleles, COVID-19 prevention & control, COVID-19 virology, Epitopes, B-Lymphocyte metabolism, Epitopes, T-Lymphocyte metabolism, Female, Genes, MHC Class I genetics, Genes, MHC Class I immunology, Humans, Immunogenicity, Vaccine immunology, Mutation, SARS-CoV-2 genetics, SARS-CoV-2 physiology, T-Lymphocytes immunology, T-Lymphocytes metabolism, T-Lymphocytes virology, Vaccination, Vaccine Efficacy, COVID-19 immunology, COVID-19 Vaccines immunology, Epitopes, B-Lymphocyte immunology, Epitopes, T-Lymphocyte immunology, SARS-CoV-2 immunology, Spike Glycoprotein, Coronavirus immunology
Abstract: The effect of emerging SARS-CoV-2 variants on vaccine efficacy is of critical importance. In this study, the potential impact of mutations that facilitate escape from the cytotoxic cellular immune response in these new virus variants for the 551 most abundant HLA class I alleles was analyzed. Computational prediction showed that most of these alleles, that cover >90% of the population, contain enough epitopes without escape mutations in the principal SARS-CoV-2 variants. These data suggest that the cytotoxic cellular immune protection elicited by vaccination is not greatly affected by emerging SARS-CoV-2 variants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Martín-Galiano, Díez-Fuertes, McConnell and López.)
Published: 2021
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31. Effect of Subinhibitory Concentrations of Antibiotics and Disinfectants on IS Aba -Mediated Inactivation of Lipooligosaccharide Biosynthesis Genes in Acinetobacter baumannii .

Author: Olmeda-López H, Corral-Lugo A, and McConnell MJ
Abstract: Inactivation of the lipooligosaccharide (LOS) biosynthesis genes lpxA , lpxC and lpxD by IS Aba insertion elements results in high-level resistance to colistin in A. baumannii . In the present study, we quantify the rate of spontaneous insertional inactivation of LOS biosynthesis genes by IS Aba elements in the ATCC 19606-type strain and two multidrug clinical isolates. Using insertional inactivation of lpxC by IS Aba 11 in the ATCC 19606 strain as a model, we determine the effect of several subinhibitory concentrations of the antibiotics, namely tetracycline, ciprofloxacin, meropenem, kanamycin and rifampicin, as well as the disinfectants ethanol and chlorhexidine on IS Aba 11 insertion frequencies. Notably, subinhibitory concentrations of tetracycline significantly increased IS Aba 11 insertion, and rifampicin completely inhibited the emergence of colistin resistance due to IS Aba 11 inactivation of lpxC . Sequencing of IS Aba 11 insertion sites within the lpxC gene demonstrated that insertions clustered between nucleotides 382 and 618 (58.3% of unique insertions detected), indicating that this may be a hotspot for IS Aba 11 insertion. The alignment of insertion sites revealed a semi-conserved AT-rich consensus sequence upstream of the IS Aba 11 insertion site, suggesting that IS Aba 11 insertion sites may be sequence-dependent. This study explores previously uncharacterized aspects regarding the acquisition of colistin resistance through insertional activation in LOS biosynthesis genes in A. baumannii .
Published: 2021
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32. Optimization of a Lambda-RED Recombination Method for Rapid Gene Deletion in Human Cytomegalovirus.

Author: García-Ríos E, Gata-de-Benito J, López-Siles M, McConnell MJ, and Pérez-Romero P
Subjects: Bacteriophage lambda metabolism, Cell Line, Cloning, Molecular methods, Cytomegalovirus Infections virology, Genome, Viral genetics, HEK293 Cells, Humans, Mutation, Plasmids genetics, Reproducibility of Results, Bacteriophage lambda genetics, Chromosomes, Artificial, Bacterial genetics, Cytomegalovirus genetics, Escherichia coli genetics, Gene Deletion, Recombination, Genetic
Abstract: Human cytomegalovirus (HCMV) continues to be a major cause of morbidity in transplant patients and newborns. However, the functions of many of the more than 282 genes encoded in the HCMV genome remain unknown. The development of bacterial artificial chromosome (BAC) technology contributes to the genetic manipulation of several organisms including HCMV. The maintenance of the HCMV BAC in E. coli cells permits the rapid generation of recombinant viral genomes that can be used to produce viral progeny in cell cultures for the study of gene function. We optimized the Lambda-Red Recombination system to construct HCMV gene deletion mutants rapidly in the complete set of tested genes. This method constitutes a useful tool that allows for the quick generation of a high number of gene deletion mutants, allowing for the analysis of the whole genome to improve our understanding of HCMV gene function. This may also facilitate the development of novel vaccines and therapeutics.
Published: 2021
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33. The Big Picture of Glioblastoma Malignancy: A Meta-Analysis of Glioblastoma Proteomics to Identify Altered Biological Pathways.

Author: Tribe AKW, McConnell MJ, and Teesdale-Spittle PH
Abstract: Glioblastoma is a highly malignant cancer with no effective treatment. It is vital to elucidate the mechanisms which drive glioblastoma in order to identify therapeutic targets. The differences in protein expression between glioblastoma, grade I-III glioma, and normal brain tissue reflect the functional alterations driving malignancy. However, proteomic analysis of glioblastoma has been hampered by the heterogeneity of glioblastoma and the variety of methodology used in its study. To reduce these inconsistencies, we performed a meta-analysis of the literature published since 2015, including 14 datasets from eight papers comparing the whole proteome of glioblastoma to normal brain or grade I-III glioma. We found that 154 proteins were commonly upregulated and 116 proteins were commonly downregulated in glioblastoma compared to normal brain. Meanwhile, 240 proteins were commonly upregulated and 125 proteins were commonly downregulated in glioblastoma compared to grade I-III glioma. Functional enrichment analysis revealed upregulation of proteins involved in mRNA splicing and the immune system and downregulation of proteins involved in synaptic signaling and glucose and glutamine metabolism. The identification of these altered biological pathways provides a basis for deeper investigation in the pursuit of an effective treatment for glioblastoma., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)
Published: 2021
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34. Inhibition of LpxC Increases the Activity of Iron Chelators and Gallium Nitrate in Multidrug-Resistant Acinetobacter baumannii .

Author: Vinuesa V, Cruces R, Nonnoi F, and McConnell MJ
Abstract: Infections caused by multidrug-resistant Acinetobacter baumannii would benefit from the development of novel treatment approaches. Compounds that interfere with bacterial iron metabolism, such as iron chelators and gallium nitrate, have previously been shown to have antimicrobial activity against A. baumannii . In this study, we characterize the effect of LpxC inhibitors on the antimicrobial activity of previously characterized iron chelators, 2,2'-bipyridyl (BIP) and deferiprone (DFP), and gallium nitrate (Ga(NO 3 ) 3 ) against A. baumannii reference strains and multidrug-resistant clinical isolates. The LpxC inhibitor LpxC-2 was synergistic with BIP for 30% of strains tested (FICI values: 0.38-1.02), whereas inhibition with LpxC-4 was synergistic with BIP for 60% of strains tested (FICI values: 0.09-0.75). In time-kill assays, combinations of BIP with both LpxC inhibitors demonstrated synergistic activity, with a more than 3 log 10 reduction in bacterial counts compared to BIP alone. LpxC-2 was synergistic with Ga(NO 3 ) 3 for 50% of strains tested (FICI values: 0.27-1.0), whereas LpxC-4 was synergistic with Ga(NO 3 ) 3 for all strains tested (FICI values: 0.08-≤0.50). In time-kill assays, combinations of Ga(NO 3 ) 3 with LpxC-2 and LpxC-4 decreased the growth of both strains compared to each compound separately; however, only the combination with LpxC-4 met the defined criteria for synergy. These results identify a novel synergy between two antimicrobial classes against A. baumannii strains.
Published: 2021
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35. Vaccines for multidrug resistant Gram negative bacteria: lessons from the past for guiding future success.

Author: López-Siles M, Corral-Lugo A, and McConnell MJ
Subjects: Anti-Bacterial Agents pharmacology, Drug Resistance, Multiple, Bacterial, Gram-Negative Bacteria drug effects, Humans, Bacterial Vaccines, Gram-Negative Bacterial Infections prevention & control
Abstract: Antimicrobial resistance is a major threat to global public health. Vaccination is an effective approach for preventing bacterial infections, however it has not been successfully applied to infections caused by some of the most problematic multidrug resistant pathogens. In this review, the potential for vaccines to contribute to reducing the burden of disease of infections caused by multidrug resistant Gram negative bacteria is presented. Technical, logistical and societal hurdles that have limited successful vaccine development for these infections in the past are identified, and recent advances that can contribute to overcoming these challenges are assessed. A synthesis of vaccine technologies that have been employed in the development of vaccines for key multidrug resistant Gram negative bacteria is included, and emerging technologies that may contribute to future successes are discussed. Finally, a comprehensive review of vaccine development efforts over the last 40 years for three of the most worrisome multidrug resistant Gram negative pathogens, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa is presented, with a focus on recent and ongoing studies. Finally, future directions for the vaccine development field are highlighted., (© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.)
Published: 2021
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36. Single-cell sequencing of the small and AT-skewed genome of malaria parasites.

Author: Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, and Güler JL
Subjects: Computational Biology methods, DNA Copy Number Variations, Erythrocytes parasitology, Humans, Malaria parasitology, Plasmodium falciparum genetics, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Base Composition, Genome, Protozoan, Genomics methods, High-Throughput Nucleotide Sequencing, Plasmodium genetics, Single-Cell Analysis methods
Abstract: Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
Published: 2021
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37. Designing Multi-Antigen Vaccines Against Acinetobacter baumannii Using Systemic Approaches.

Author: McConnell MJ and Martín-Galiano AJ
Subjects: Acinetobacter Infections immunology, Acinetobacter Infections prevention & control, Acinetobacter baumannii genetics, Antigens, Bacterial immunology, Epitopes chemistry, Epitopes genetics, Genes, Bacterial, Genome, Bacterial, Genomics methods, Humans, Acinetobacter baumannii drug effects, Acinetobacter baumannii immunology, Bacterial Vaccines immunology, Drug Resistance, Bacterial immunology, Epitopes immunology
Abstract: Vaccines and monoclonal antibodies are promising approaches for preventing and treating infections caused by multidrug resistant Acinetobacter baumannii . However, only partial protection has been achieved with many previously tested protein antigens, which suggests that vaccines incorporating multiple antigens may be necessary in order to obtain high levels of protection. Several aspects that use the wealth of omic data available for A. baumannii have not been fully exploited for antigen identification. In this study, the use of fractionated proteomic and computational data from ~4,200 genomes increased the number of proteins potentially accessible to the humoral response to 8,824 non-redundant proteins in the A. baumannii panproteome. Among them, 59% carried predicted B-cell epitopes and T-cell epitopes recognized by two or more alleles of the HLA class II DP supertype. Potential cross-reactivity with human proteins was detected for 8.9% of antigens at the protein level and 2.7% at the B-cell epitope level. Individual antigens were associated with different infection types by genomic, transcriptomic or functional analyses. High intra-clonal genome density permitted the identification of international clone II as a "vaccitype", in which 20% of identified antigens were specific to this clone. Network-based centrality measurements were used to identify multiple immunologic nodes. Data were formatted, unified and stored in a data warehouse database, which was subsequently used to identify synergistic antigen combinations for different vaccination strategies. This study supports the idea that integration of multi-omic data and fundamental knowledge of the pathobiology of drug-resistant bacteria can facilitate the development of effective multi-antigen vaccines against these challenging infections., Competing Interests: MM is a founder and shareholder in the company Vaxdyn, S.L. The remaining author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 McConnell and Martín-Galiano.)
Published: 2021
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38. Recent Advances in Iron Chelation and Gallium-Based Therapies for Antibiotic Resistant Bacterial Infections.

Author: Vinuesa V and McConnell MJ
Subjects: Anti-Bacterial Agents adverse effects, Anti-Bacterial Agents therapeutic use, Bacteria drug effects, Bacteria pathogenicity, Bacterial Infections microbiology, Drug Resistance, Bacterial, Humans, Hydroxamic Acids chemistry, Hydroxamic Acids therapeutic use, Iron chemistry, Iron Chelating Agents chemistry, Microbial Sensitivity Tests, Bacterial Infections drug therapy, Gallium therapeutic use, Iron metabolism, Iron Chelating Agents therapeutic use
Abstract: Iron is essential for multiple bacterial processes and is thus required for host colonization and infection. The antimicrobial activity of multiple iron chelators and gallium-based therapies against different bacterial species has been characterized in preclinical studies. In this review, we provide a synthesis of studies characterizing the antimicrobial activity of the major classes of iron chelators (hydroxamates, aminocarboxylates and hydroxypyridinones) and gallium compounds. Special emphasis is placed on recent in-vitro and in-vivo studies with the novel iron chelator DIBI. Limitations associated with iron chelation and gallium-based therapies are presented, with emphasis on limitations of preclinical models, lack of understanding regarding mechanisms of action, and potential host toxicity. Collectively, these studies demonstrate potential for iron chelators and gallium to be used as antimicrobial agents, particularly in combination with existing antibiotics. Additional studies are needed in order to characterize the activity of these compounds under physiologic conditions and address potential limitations associated with their clinical use as antimicrobial agents.
Published: 2021
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39. Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development.

Author: Corral-Lugo A, López-Siles M, López D, McConnell MJ, and Martin-Galiano AJ
Abstract: The efficacy of SARS-CoV-2 nucleic acid-based vaccines may be limited by proteolysis of the translated product due to anomalous protein folding. This may be the case for vaccines employing linear SARS-CoV-2 B-cell epitopes identified in previous studies since most of them participate in secondary structure formation. In contrast, we have employed a consensus of predictors for epitopic zones plus a structural filter for identifying 20 unstructured B-cell epitope-containing loops (uBCELs) in S, M, and N proteins. Phylogenetic comparison suggests epitope switching with respect to SARS-CoV in some of the identified uBCELs. Such events may be associated with the reported lack of serum cross-protection between the 2003 and 2019 pandemic strains. Incipient variability within a sample of 1639 SARS-CoV-2 isolates was also detected for 10 uBCELs which could cause vaccine failure. Intermediate stages of the putative epitope switch events were observed in bat coronaviruses in which additive mutational processes possibly facilitating evasion of the bat immune system appear to have taken place prior to transfer to humans. While there was some overlap between uBCELs and previously validated SARS-CoV B-cell epitopes, multiple uBCELs had not been identified in prior studies. Overall, these uBCELs may facilitate the development of biomedical products for SARS-CoV-2.
Published: 2020
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40. A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat.

Author: Grosenbaugh DK, Joshi S, Fitzgerald MP, Lee KS, Wagley PK, Koeppel AF, Turner SD, McConnell MJ, and Goodkin HP
Subjects: Animals, Cerebral Cortex, Disease Models, Animal, Electroencephalography, Epilepsy genetics, Female, Male, Rats, Seizures genetics, Classical Lissencephalies and Subcortical Band Heterotopias genetics, Malformations of Cortical Development, Group II genetics, Microtubule-Associated Proteins genetics
Abstract: Children with malformations of cortical development (MCD) are at risk for epilepsy, developmental delays, behavioral disorders, and intellectual disabilities. For a subset of these children, antiseizure medications or epilepsy surgery may result in seizure freedom. However, there are limited options for treating or curing the other conditions, and epilepsy surgery is not an option in all cases of pharmacoresistant epilepsy. Understanding the genetic and neurobiological mechanisms underlying MCD is a necessary step in elucidating novel therapeutic targets. The tish (telencephalic internal structural heterotopia) rat is a unique model of MCD with spontaneous seizures, but the underlying genetic mutation(s) have remained unknown. DNA and RNA-sequencing revealed that a deletion encompassing a previously unannotated first exon markedly diminished Eml1 transcript and protein abundance in the tish brain. Developmental electrographic characterization of the tish rat revealed early-onset of spontaneous spike-wave discharge (SWD) bursts beginning at postnatal day (P) 17. A dihybrid cross demonstrated that the mutant Eml1 allele segregates with the observed dysplastic cortex and the early-onset SWD bursts in monogenic autosomal recessive frequencies. Our data link the development of the bilateral, heterotopic dysplastic cortex of the tish rat to a deletion in Eml1., (Copyright © 2020. Published by Elsevier Inc.)
Published: 2020
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41. Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration.

Author: Fragola G, Mabb AM, Taylor-Blake B, Niehaus JK, Chronister WD, Mao H, Simon JM, Yuan H, Li Z, McConnell MJ, and Zylka MJ
Subjects: Animals, Apoptosis drug effects, Cerebral Cortex enzymology, Cerebral Cortex pathology, DNA Damage, DNA Topoisomerases, Type I genetics, Hippocampus enzymology, Hippocampus pathology, Inflammation, Mice, Mice, Knockout, Mortality, Premature, Motor Activity, Mutation, NAD administration & dosage, Neurodegenerative Diseases drug therapy, Neurodegenerative Diseases pathology, Neurodegenerative Diseases physiopathology, Neurons drug effects, Neurons pathology, Niacinamide administration & dosage, Niacinamide analogs & derivatives, Poly (ADP-Ribose) Polymerase-1 metabolism, Pyridinium Compounds, DNA Topoisomerases, Type I deficiency, Genomic Instability, Neurodegenerative Diseases enzymology, Neurons enzymology
Abstract: Topoisomerase 1 (TOP1) relieves torsional stress in DNA during transcription and facilitates the expression of long (>100 kb) genes, many of which are important for neuronal functions. To evaluate how loss of Top1 affected neurons in vivo, we conditionally deleted (cKO) Top1 in postmitotic excitatory neurons in the mouse cerebral cortex and hippocampus. Top1 cKO neurons develop properly, but then show biased transcriptional downregulation of long genes, signs of DNA damage, neuroinflammation, increased poly(ADP-ribose) polymerase-1 (PARP1) activity, single-cell somatic mutations, and ultimately degeneration. Supplementation of nicotinamide adenine dinucleotide (NAD + ) with nicotinamide riboside partially blocked neurodegeneration, and increased the lifespan of Top1 cKO mice by 30%. A reduction of p53 also partially rescued cortical neuron loss. While neurodegeneration was partially rescued, behavioral decline was not prevented. These data indicate that reducing neuronal loss is not sufficient to limit behavioral decline when TOP1 function is disrupted.
Published: 2020
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42. The oncogene BCL6 is up-regulated in glioblastoma in response to DNA damage, and drives survival after therapy.

Author: Fabre MS, Stanton NM, Slatter TL, Lee S, Senanayake D, Gordon RMA, Castro ML, Rowe MR, Taha A, Royds JA, Hung N, Melnick AM, and McConnell MJ
Subjects: Animals, Cell Line, Tumor, Gene Expression Regulation, Neoplastic genetics, Humans, Male, Mice, Mice, Inbred C57BL, Signal Transduction genetics, Transcriptional Activation genetics, Xenograft Model Antitumor Assays methods, Brain Neoplasms genetics, DNA Damage genetics, Glioblastoma genetics, Oncogenes genetics, Proto-Oncogene Proteins c-bcl-6 genetics, Up-Regulation genetics
Abstract: The prognosis for people with the high-grade brain tumor glioblastoma is very poor, due largely to low cell death in response to genotoxic therapy. The transcription factor BCL6, a protein that normally suppresses the DNA damage response during immune cell maturation, and a known driver of B-cell lymphoma, was shown to mediate the survival of glioblastoma cells. Expression was observed in glioblastoma tumor specimens and cell lines. When BCL6 expression or activity was reduced in these lines, increased apoptosis and a profound loss of proliferation was observed, consistent with gene expression signatures suggestive of anti-apoptotic and pro-survival signaling role for BCL6 in glioblastoma. Further, treatment with the standard therapies for glioblastoma-ionizing radiation and temozolomide-both induced BCL6 expression in vitro, and an in vivo orthotopic animal model of glioblastoma. Importantly, inhibition of BCL6 in combination with genotoxic therapies enhanced the therapeutic effect. Together these data demonstrate that BCL6 is an active transcription factor in glioblastoma, that it drives survival of cells, and that it increased with DNA damage, which increased the survival rate of therapy-treated cells. This makes BCL6 an excellent therapeutic target in glioblastoma-by increasing sensitivity to standard DNA damaging therapy, BCL6 inhibitors have real potential to improve the outcome for people with this disease., Competing Interests: The authors have declared that no competing interests exist.
Published: 2020
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43. An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding.

Author: Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, and Paschal BM
Subjects: Amino Acid Sequence, Amino Acid Substitution, CCCTC-Binding Factor metabolism, Cell Nucleus metabolism, Cells, Cultured, Cytoplasm metabolism, Gene Expression, Humans, Protein Binding genetics, Protein Transport genetics, alpha Karyopherins metabolism, beta Karyopherins metabolism, Epilepsy genetics, Mutation genetics, Nuclear Localization Signals genetics, Nuclear Localization Signals metabolism, alpha Karyopherins genetics
Abstract: KPNA7 is a member of the Importin-α family of nuclear import receptors. KPNA7 forms a complex with Importin-β and facilitates the translocation of signal-containing proteins from the cytoplasm to the nucleus. Exome sequencing of siblings with severe neurodevelopmental defects and clinical features of epilepsy identified two amino acid-altering mutations in KPNA7. Here, we show that the E344Q substitution reduces KPNA7 binding to nuclear localization signals, and that this limits KPNA7 nuclear import activity. The P339A substitution, by contrast, has little effect on KPNA7 binding to nuclear localization signals. Given the neuronal phenotype described in the two patients, we used SILAC labeling, affinity enrichment, and mass spectrometry to identify KPNA7-interacting proteins in human induced pluripotent stem cell-derived neurons. We identified heterogeneous nuclear ribonucleoproteins hnRNP R and hnRNP U as KPNA7-interacting proteins. The E344Q substitution reduced binding and KPNA7-mediated import of these cargoes. The c.1030G > C allele which generates E344Q is within a predicted CTCF binding site, and we found that it reduces CTCF binding by approximately 40-fold. Our data support a role for altered neuronal expression and activity of KPNA7 in a rare type of pediatric epilepsy.
Published: 2020
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44. Using Omics Technologies and Systems Biology to Identify Epitope Targets for the Development of Monoclonal Antibodies Against Antibiotic-Resistant Bacteria.

Author: Martín-Galiano AJ and McConnell MJ
Subjects: Antibodies, Monoclonal immunology, Humans, Antibodies, Monoclonal pharmacology, Bacteria drug effects, Bacteria immunology, Drug Resistance, Bacterial, Epitopes immunology, Genomics methods, Systems Biology methods
Abstract: Over the past few decades, antimicrobial resistance has emerged as an important threat to public health due to the global dissemination of multidrug-resistant strains from several bacterial species. This worrisome trend, in addition to the paucity of new antibiotics with novel mechanisms of action in the development pipeline, warrants the development of non-antimicrobial approaches to combating infection caused by these isolates. Monoclonal antibodies (mAbs) have emerged as highly effective molecules for the treatment of multiple diseases. However, in spite of the fact that antibodies play an important role in protective immunity against bacteria, only three mAb therapies have been approved for clinical use in the treatment of bacterial infections. In the present review, we briefly outline the therapeutic potential of mAbs in the treatment of bacterial diseases and discuss how their development can be facilitated when assisted by "omics" technologies and interpreted under a systems biology paradigm. Specifically, methods employing large genomic, transcriptomic, structural, and proteomic datasets allow for the rational identification of epitopes. Ideally, these include those that are present in the majority of circulating isolates, highly conserved at the amino acid level, surface-exposed, located on antigens essential for virulence, and expressed during critical stages of infection. Therefore, these knowledge-based approaches can contribute to the identification of high-value epitopes for the development of effective mAbs against challenging bacterial clones., (Copyright © 2019 Martín-Galiano and McConnell.)
Published: 2019
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45. A Live Salmonella Vaccine Delivering PcrV through the Type III Secretion System Protects against Pseudomonas aeruginosa.

Author: Aguilera-Herce J, García-Quintanilla M, Romero-Flores R, McConnell MJ, and Ramos-Morales F
Subjects: Animals, Antibodies, Bacterial blood, Bacterial Load, Cytokines blood, Female, Lung microbiology, Mice, Mice, Inbred C57BL, Pseudomonas Infections immunology, Pseudomonas aeruginosa, Spleen microbiology, Type III Secretion Systems immunology, Vaccines, Attenuated administration & dosage, Antigens, Bacterial immunology, Bacterial Toxins immunology, Pore Forming Cytotoxic Proteins immunology, Pseudomonas Infections prevention & control, Salmonella Vaccines administration & dosage, Type III Secretion Systems genetics
Abstract: Pseudomonas aeruginosa is a common Gram-negative opportunistic pathogen that is intrinsically resistant to a wide range of antibiotics. The development of a broadly protective vaccine against P. aeruginosa remains a major challenge. Here, we used an attenuated strain of Salmonella enterica serovar Typhimurium as a vehicle to express P. aeruginosa antigens. A fusion between the S. enterica type III secretion effector protein SseJ and the P. aeruginosa antigen PcrV expressed under the control of the sseA promoter was translocated by Salmonella into host cells in vitro and elicited the generation of specific antibodies in mice. Mice immunized with attenuated Salmonella expressing this fusion had reduced bacterial loads in the spleens and lungs and lower serum levels of proinflammatory cytokines than control mice after P. aeruginosa infection. Importantly, immunized mice also showed significantly enhanced survival in this model. These results suggest that type III secretion effectors of S. enterica are appropriate carriers in the design of a live vaccine to prevent infections caused by P. aeruginosa IMPORTANCE The Gram-negative bacterium Pseudomonas aeruginosa is an important opportunistic pathogen that causes infections in cystic fibrosis and hospitalized patients. Therapeutic treatments are limited due to the emergence and spread of new antibiotic-resistant strains. In this context, the development of a vaccine is a priority. Here, we used an attenuated strain of Salmonella enterica serovar Typhimurium as a vehicle to express and deliver the Pseudomonas antigen PcrV. This vaccine induced the generation of specific antibodies in mice and protected them from lethal infections with P. aeruginosa This is an important step toward the development of an effective vaccine for the prevention of infections caused by P. aeruginosa in humans., (Copyright © 2019 Aguilera-Herce et al.)
Published: 2019
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46. Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex.

Author: Chronister WD, Burbulis IE, Wierman MB, Wolpert MJ, Haakenson MF, Smith ACB, Kleinman JE, Hyde TM, Weinberger DR, Bekiranov S, and McConnell MJ
Subjects: Aged, 80 and over, Female, Genome-Wide Association Study, Humans, Male, Aging genetics, Aging metabolism, Aging pathology, DNA Copy Number Variations, Genome, Human, Karyotype, Neocortex metabolism, Neocortex pathology, Neurons metabolism, Neurons pathology
Abstract: A subset of human neocortical neurons harbors complex karyotypes wherein megabase-scale copy-number variants (CNVs) alter allelic diversity. Divergent levels of neurons with complex karyotypes (CNV neurons) are reported in different individuals, yet genome-wide and familial studies implicitly assume a single brain genome when assessing the genetic risk architecture of neurological disease. We assembled a brain CNV atlas using a robust computational approach applied to a new dataset (>800 neurons from 5 neurotypical individuals) and to published data from 10 additional neurotypical individuals. The atlas reveals that the frequency of neocortical neurons with complex karyotypes varies widely among individuals, but this variability is not readily accounted for by tissue quality or CNV detection approach. Rather, the age of the individual is anti-correlated with CNV neuron frequency. Fewer CNV neurons are observed in aged individuals than in young individuals., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)
Published: 2019
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47. Phenotypic changes associated with Colistin resistance due to Lipopolysaccharide loss in Acinetobacter baumannii.

Author: Carretero-Ledesma M, García-Quintanilla M, Martín-Peña R, Pulido MR, Pachón J, and McConnell MJ
Subjects: Acinetobacter Infections metabolism, Acinetobacter baumannii genetics, Acinetobacter baumannii metabolism, Acinetobacter baumannii pathogenicity, Animals, Bacterial Proteins genetics, Bacterial Proteins metabolism, Female, Humans, Interleukin-6 metabolism, Mice, Inbred C57BL, Microbial Sensitivity Tests, Phenotype, Tumor Necrosis Factor-alpha metabolism, Virulence, Acinetobacter Infections microbiology, Acinetobacter baumannii drug effects, Anti-Bacterial Agents pharmacology, Colistin pharmacology, Drug Resistance, Bacterial, Lipopolysaccharides biosynthesis
Abstract: Acinetobacter baumannii can acquire resistance to colistin via complete loss of lipopolysaccharide (LPS) biosynthesis due to mutations in the lpxA, lpxC and lpxD genes. However, although colistin is increasingly being used for the treatment of multidrug resistant infections, very few A. baumannii clinical isolates develop colistin resistance through loss of LPS biosynthesis. This may suggest that LPS loss affects virulence traits that play a role in the transmission and pathogenesis of A. baumannii. In this study we characterize multiple virulence phenotypes of colistin resistant, LPS-deficient derivatives of the ATCC 19606 strain and five multidrug resistant clinical isolates and their colistin resistant, LPS-deficient derivatives. Our results indicate that LPS loss results in growth defects compared to the parental strain in vitro both in laboratory media and human serum (competition indices of 0.58 and 7.0 × 10 -7 , respectively) and reduced ability to grow and disseminate in vivo (competition index 6.7 × 10 -8 ). Infection with the LPS-deficient strain resulted in lower serum levels of pro-inflammatory cytokines TNF-α and IL-6 compared to the parent strain, and was less virulent in a mouse model of disseminated sepsis. LPS loss also significantly affected biofilm production, surface motility, growth under iron limitation and susceptibility to multiple disinfectants used in the clinical setting. These results demonstrate that LPS loss has a significant effect on multiple virulence traits, and may provide insight into the low incidence of colistin resistant strains lacking LPS that have been reported in the clinical setting.
Published: 2018
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48. Application of BioFire FilmArray Blood Culture Identification panel for rapid identification of the causative agents of ventilator-associated pneumonia.

Author: Pulido MR, Moreno-Martínez P, González-Galán V, Fernández Cuenca F, Pascual Á, Garnacho-Montero J, Antonelli M, Dimopoulos G, Lepe JA, McConnell MJ, and Cisneros JM
Subjects: Blood Culture methods, Female, Humans, Male, Bacteria isolation & purification, Bacteriological Techniques methods, Pneumonia, Bacterial microbiology, Pneumonia, Ventilator-Associated diagnosis, Pneumonia, Ventilator-Associated microbiology
Abstract: Objective: To evaluate the ability of the BioFire FilmArray Blood Culture Identification (BCID) panel to rapidly detect pathogens producing late-onset ventilator-associated pneumonia (VAP), a severe infection often produced by Gram-negative bacteria. These microorganisms are frequently multidrug resistant and typically require broad-spectrum empiric treatment., Methods: In the context of an international multicentre clinical trial (MagicBullet), respiratory samples were collected at the time of suspicion of VAP from 165 patients in 32 participating hospitals in Spain, Greece and Italy. Microorganisms were identified using the BCID panel and compared with results obtained by conventional microbiologic techniques., Results: Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae were the most commonly identified species, representing 54.7% (70/128) of microorganisms. The BCID panel showed high global specificity (98.1%; 95% confidence interval, 96-100) and negative predictive values (96.6%) and a global sensitivity and positive predictive value of 78.6% (95% confidence interval, 70-88) and 87.3%, respectively, for these microorganisms. Importantly, the BCID panel provided results in only 1 hour directly from respiratory samples with minimal sample processing times., Conclusions: The BCID panel may have clinical utility in rapidly ruling out microorganisms causing VAP, specifically multidrug-resistant Gram-negative species. This could facilitate the optimization of empiric treatment., (Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)
Published: 2018
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49. Pharmacological reactivation of inactive X-linked Mecp2 in cerebral cortical neurons of living mice.

Author: Przanowski P, Wasko U, Zheng Z, Yu J, Sherman R, Zhu LJ, McConnell MJ, Tushir-Singh J, Green MR, and Bhatnagar S
Subjects: Animals, Cell Line, Cerebral Cortex pathology, Humans, Mice, Mice, Knockout, Neurons pathology, Rett Syndrome drug therapy, Rett Syndrome genetics, Rett Syndrome pathology, Cerebral Cortex metabolism, Methyl-CpG-Binding Protein 2 biosynthesis, Methyl-CpG-Binding Protein 2 genetics, Methyl-CpG-Binding Protein 2 metabolism, Mutation, Neurons metabolism, Rett Syndrome metabolism
Abstract: Rett syndrome (RTT) is a genetic disorder resulting from a loss-of-function mutation in one copy of the X-linked gene methyl-CpG-binding protein 2 ( MECP2 ). Typical RTT patients are females and, due to random X chromosome inactivation (XCI), ∼50% of cells express mutant MECP2 and the other ∼50% express wild-type MECP2. Cells expressing mutant MECP2 retain a wild-type copy of MECP2 on the inactive X chromosome (Xi), the reactivation of which represents a potential therapeutic approach for RTT. Previous studies have demonstrated reactivation of Xi-linked MECP2 in cultured cells by biological or pharmacological inhibition of factors that promote XCI (called "XCI factors" or "XCIFs"). Whether XCIF inhibitors in living animals can reactivate Xi-linked MECP2 in cerebral cortical neurons, the cell type most therapeutically relevant to RTT, remains to be determined. Here, we show that pharmacological inhibitors targeting XCIFs in the PI3K/AKT and bone morphogenetic protein signaling pathways reactivate Xi-linked MECP2 in cultured mouse fibroblasts and human induced pluripotent stem cell-derived postmitotic RTT neurons. Notably, reactivation of Xi-linked MECP2 corrects characteristic defects of human RTT neurons including reduced soma size and branch points. Most importantly, we show that intracerebroventricular injection of the XCIF inhibitors reactivates Xi-linked Mecp2 in cerebral cortical neurons of adult living mice. In support of these pharmacological results, we also demonstrate genetic reactivation of Xi-linked Mecp2 in cerebral cortical neurons of living mice bearing a homozygous XCIF deletion. Collectively, our results further establish the feasibility of pharmacological reactivation of Xi-linked MECP2 as a therapeutic approach for RTT., Competing Interests: The authors declare no conflict of interest.
Published: 2018
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50. Exploring opportunities to prevent cirrhosis admissions in the emergency department: A multicenter multidisciplinary survey.

Author: Siddique SM, Lane-Fall M, McConnell MJ, Jakhete N, Crismale J, Porges S, Khungar V, Mehta SJ, Goldberg D, Li Z, Schiano T, Regan L, Orloski C, and Shea JA
Abstract: Patients with cirrhosis have high admission and readmission rates, and it is estimated that a quarter are potentially preventable. Little data are available regarding nonmedical factors impacting triage decisions in this patient population. This study sought to explore such factors as well as to determine provider perspectives on low-acuity clinical presentations to the emergency department, including ascites and hepatic encephalopathy. A survey was distributed in four liver transplant centers to both emergency medicine and hepatology providers, who included attending physicians, house staff, and advanced practitioners; 196 surveys were returned (estimated response rate 50.6%). Emergency medicine providers identified several influential nonmedical factors impacting inpatient triage decisions, including input from a hepatologist (77.7%), inadequate patient access to outpatient specialty care (68.6%), and patient need for diagnostic testing for a procedure (65.6%). When given patient-based scenarios of low-acuity cases, such as ascites requiring paracentesis, only 7.0% believed patients should be hospitalized while 48.9% said these patients would be hospitalized at their institution ( P < 0.0001). For mild hepatic encephalopathy, the comparable numbers were 19.5% and 55.2%, respectively ( P < 0.001). Several perceived barriers were cited for this discrepancy, including limited resources both in the outpatient setting and emergency department. Most providers believed that an emergency department observation unit protocol would influence triage toward an emergency department observation unit visit instead of inpatient admission for both ascites requiring large volume paracentesis (83.2%) and mild hepatic encephalopathy (79.4%). Conclusion : Many nonmedical factors that influence inpatient triage for patients with cirrhosis could be targeted for quality improvement initiatives. In some scenarios, providers are limited by resource availability, which results in triage to an inpatient admission even when they believe this is not the most appropriate disposition. ( Hepatology Communications 2018;2:237-244).
Published: 2018
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