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Nidogen 1 (NID1) is an important basement membrane protein secreted by many cell types. We previously found that human cytomegalovirus (HCMV) infection rapidly induced chromosome 1 breaks and that the basement membrane protein NID1, encoded near the 1q42 break site, was downregulated. We have now determined that the specific breaks in and of themselves did not regulate NID1, rather interactions between several viral proteins and the cellular machinery and DNA regulated NID1. We screened a battery of viral proteins present by 24 hours postinfection (hpi) when regulation was induced, including components of the incoming virion and immediate early (IE) proteins. Adenovirus (Ad) delivery of the tegument proteins pp71 and UL35 and the IE protein IE1 influenced steady-state (ss) NID1 levels. IE1’s mechanism of regulation was unclear, while UL35 influenced proteasomal regulation of ss NID1. Real-time quantitative PCR (RT-qPCR) experiments determined that pp71 downregulated NID1 transcription. Surprisingly, WF28-71, a fibroblast clone that expresses minute quantities of pp71, suppressed NID1 transcription as efficiently as HCMV infection, resulting in the near absence of ss NID1. Sequence analysis of the region surrounding the 1q42 break sites and NID1 promoter revealed CCCTC-binding factor (CTCF) binding sites. Chromatin immunoprecipitation experiments determined that pp71 and CTCF were both bound at these two sites during HCMV infection. Expression of pp71 alone replicated this binding. Binding was observed as early as 1 hpi, and colocalization of pp71 and CTCF occurred as quickly as 15 min postinfection (pi) in infected cell nuclei. In fibroblasts where CTCF was knocked down, Adpp71 infection did not decrease NID1 transcription nor ss NID1 protein levels. Our results emphasize another aspect of pp71 activity during infection and identify this viral protein as a key contributor to HCMV’s efforts to eliminate NID1. Further, we show, for the first time, direct interaction between pp71 and the cellular genome. IMPORTANCE We have found that human cytomegalovirus (HCMV) utilizes multiple viral proteins in multiple pathways to regulate a ubiquitous cellular basement membrane protein, nidogen-1 (NID1). The extent of the resources and the redundant methods that the virus has evolved to affect this control strongly suggest that its removal provides a life cycle advantage to HCMV. Our discoveries that one of the proteins that HCMV uses to control NID1, pp71, binds directly to the cellular DNA and can exert control when present in vanishingly small quantities may have broad implications in a wide range of infection scenarios. Dysregulation of NID1 in an immunocompetent host is not known to manifest complications during infection; however, in the naive immune system of a developing fetus, disruption of this developmentally critical protein could initiate catastrophic HCMV-induced birth defects.

Funding Acknowledgements Type of funding sources: None. Background The gold standard for the diagnosis of left ventricular hypertrophy is cardiac magnetic resonance (CMR). Nonetheless, electrocardiogram is the most widely used screening test due to convenience, availability and low cost. There are more than 35 electrocardiographic indices to diagnose left ventricular hypertrophy among them stand out: Cornell, Sokolow-Lyon and the Index of Peguero- Lo Presti. Methods Retrospective cohort study that included 190 cardiovascular patients from January 2015 to December 2019 in a National Cardiology Center. We described demographic and electrocardiographic indices and correlate them with CMR information. A bivariate analysis was performed with association tests as Pearson, Chi square and Fisher’s exact 2x2 test. Results Our population included predominantly males (64.6%), with median age of 52 years, ischemic heart disease (74%), diabetes mellitus 2 (74%), dyslipidemia (67.9%), valvular heart disease (62.6%) and hypertension (51.6%.). Ventricular mass average140 grams, with a mean LVEF 52%. Electrocardiographic indices: Peguero Lo-Presti (75.3%) positive for left ventricular hypertrophy, Cornell Index ( 51.6%), Sokolow index (41.1%), RaVL (27.9%) and RDI (21.1%). Quantitative analysis: Peguero Lo-Presti index average 35.1 mm, Sokolow index: 30.9 mm, Cornel index: 25 mm. The most sensitive criteria to determine left ventricular hypertrophy was Peguero Lo-Presti 59.3% (95 CI 41.4% - 55.5%), followed by Cornell 51.6% (95% CI 44.5% - 58.6%), Sokolow Lyon 41.1% (95% CI34.3% to 48.2%). Conclusion Peguero- Lo Presti criteria are more sensitive than other electrocardiographic criteria for the diagnosis of left ventricular hypertrophy

The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.

The effects SARS-CoV-2 inflicts on human physiology, especially in patients who developed COVID-19, can range from flu-like symptoms to death, and although many lives have been lost during the pandemic, others have faced the resolution of aggressive neoplasms that once proclaimed a poor prognosis following traditional treatments. The purpose of this review was to analyze several fortunate case reports and their associated biomolecular pathways to further explore new avenues that might provide oncological treatments in the future of medicine. We included papers that discussed cases in which patients affected by COVID-19 suffered beneficial changes in their cancer status. Multiple mechanisms which elicited a reactivation of the host’s immune system included cross-reactivity with viral antigens and downregulation of neoplastic cells. We were able to identify important cases presenting the resolution/remission of different aggressive neoplasms, for which most of the time, standard-of-care treatments offered little to no prospect towards a cure. The intricacy of the defense mechanisms humans have adopted against cancer cells through the millennia are still not well understood, but SARS-CoV-2 has demonstrated that the same ruinous cytokine storm which has taken so many lives can paradoxically be the answer we have been looking for to recalibrate the immunological system to retarget and vanquish malignancies.

El quiste periapical se deriva del epitelio de revestimiento por una proliferación de pequeños residuos epiteliales de Malassez, el presente reporte señala características clínico-patológicas de un quiste periapical y la incorporación del uso de la tomografía computarizada de haz cónico (CBCT) como método de diagnóstico y el procedimiento de biopsia para descartar malignidad. Por lo general, en el protocolo de intervención, el odontólogo no emplea la realización de biopsia ni estudios histopatológicos a lesiones que aparentan ser benignas, con base en la literatura y experiencia del caso clíni- co, se pretende que el estudiante de pregrado, odontólogo general y especialista incorpore la CBCT y biopsia en el diagnóstico. Paciente femenina de 45 años, acudió a las clínicas estomatológicas de la Carrera de Odontología de la Universidad Nacional Autónoma de Honduras en el Valle de Sula (UNAH-VS). En el exámen intraoral se observó fracturas de coronas fijas de cerá- mica en el incisivo central e incisivo lateral superior izquierdo, presencia de tumefacción fluctuante en el rafe palatino medio, dolor a la palpación y presencia de fístula activa. Se realizó una CBCT para elaboración del plan de tratamiento; el abordaje clínico fue terapia endodóntica convencional, apicectomía con obturación retrógrada en los dientes involucrados, remoción del quiste, realización de biopsia y estudios anatomopatológicos que corroboran el diagnóstico presuntivo de epitelio escamoso típico densamente infiltrado de linfocitos, el corion muestra infiltrados linfoplasmocitarios de un quiste periapical. La paciente evolucionó sin complicaciones permaneciendo asintomática; en 12 meses radiografía periapical evidenció formación de tejido óseo en el área tratada.

Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.

Background. Urinary tract infections (UTIs) affect up to 150 million individuals annually worldwide, mainly due to Escherichia coli (E. coli) and Klebsiella. The emergence and spread of multidrug-resistant (MDR) bacteria are increasing, representing one of the biggest threats for human health. The objective of our study was to describe antimicrobial patterns of resistance and identify risk factors associated with MDR uropathogens. Methods. We conducted a cross-sectional study in 296 patients with community-acquired UTI who underwent clinical and microbiologic analysis, and clinical associations to MDR uropathogens were investigated. Findings. Microbiological analysis included E. coli (55%), ESBL-E. coli (26%), Enterococcus (6%), Klebsiella (5%), and others (8%). Higher frequencies of MDR bacteria were found among ESBL-E. coli, with resistance to ampicillin (100%), ceftriaxone (96%), gentamicin (57%), ciprofloxacin (89%), and TMP/SMX (53%). However, they were sensitive to fosfomycin (6.6%), nitrofurantoin (1.3%), and carbapenems (0%). Fosfomycin MIC90 for ESBL-E. coli was 5.78 μg/mL. The only clinical variable with significant association to ESBL producers was the presence of comorbidities: hypertension and type 2 diabetes mellitus with an OR (95%CI) of 2.51.3−4.9p<0.01 and 2.81.2−6.7p<0.05, respectively. Conclusions. In the majority of cases, resistance rates to commonly prescribed antimicrobials in UTIs were high, except for fosfomycin, nitrofurantoin, and carbapenems. To provide appropriate treatment, both the identification of risk factors and the uropathogen would be important. An active surveillance in UTIs in the community is required since the proportion of ESBL producers is increasing.

We compared the activity of the integrase inhibitor bictegravir against HIV-1 and HIV-2 using a culture-based, single-cycle assay. Values of 50% effective concentrations ranged from 1.2 to 2.5 nM for 9 HIV-1 isolates and 1.4 to 5.6 nM for 15 HIV-2 isolates. HIV-2 integrase mutants G140S/Q148R and G140S/Q148H were 34- and 110-fold resistant to bictegravir, respectively; other resistance-associated mutations conferred ≤5-fold changes in bictegravir susceptibility. Our findings indicate that bictegravir-based antiretroviral therapy should be evaluated in HIV-2-infected individuals.

pH variations influence the delivery of essential nutrients and CO2 solubility, which impact algae metabolism. In this study the microalgal growth and chlorophyll, lipid, and fatty acids content; along with the expression of some genes implicated in the biosynthesis of lipids were examined in Chlamydomonas reinhardtii subjected to pH values of 7.0, 7.8, and 8.5. At pH 7.8 an increase in cell growth was observed with a significant accumulation of chlorophyll (1.75-fold) when compared with growth at pH 7, while at pH 8.5 a sharp decrease in both parameters was observed when compared with the other pH values tested. Lipid content increased 3.0 (14.81% of dry cell weight, dcw) and 2.3 times (11.43% dcw) at pH 7.8 and 8.5, respectively, when compared with the experiment at pH 7 (4.97% dcw). The compositions of major fatty acids in the strains growing at pH 7.0, 7.8, or 8.5 were 25.7, 28.0, and 32.1% for palmitic acid; 17.3, 14.7, and 25.7% for oleic acid; and 9.8, 12.1, and 4.6% for linoleic acid; respectively. qRT-PCR analysis showed that the transcripts of s-carboxyltransferase, Acyl carrier protein 1, acyl-ACP thiolase 1, acyl-sn-glycerol-3-phosphate acyltransferase, and diacylglycerol acyl transferase isoform 3 were significantly induced at pH 7.8 when compared with the other two pH conditions. These results indicate that the induction of genes implicated in the early and final steps of lipid biosynthesis contributes to their accumulation in the stationary phase. Our research suggests that a pH of 7.8 might be ideal to maximize growth and lipid accumulation.

Colletotrichum lindemuthianum is the etiological agent of anthracnose, one of the main diseases of bean (Phaseolus vulgaris). In this study, the complete cDNAs of two endo-β-1,4-xylanase genes (xyl1) from non-pathogenic (0) and pathogenic (1472) races of C. lindemuthianum were isolated and characterized. To get an insight into the role of endo-β-1,4-xylanases in their different lifestyles, xyl1 gene expression and enzyme activity in mycelia of both races grown in the presence of xylan or P. vulgaris cell walls were investigated. The xyl1 sequence analysis and Clustal alignment revealed the characteristic elements of genes coding for endo-β-1,4-xylanases of the GH11 family. The growth of the two races with glucose as the sole carbon source showed both basal transcription levels of xyl1 and endoxylanase activity. When glucose was substituted with xylan or plant cell walls, xyl1 transcription, and enzyme activity significantly increased in race 1472 as compared to race 0. The pathogenic race degraded xylan faster and grew better than the non-pathogenic counterpart. Seemingly, the regulation of xylanolytic gene expression, enzyme production and the nature of the assimilatory carbon substrates processed by these organisms play a determinant role in their lifestyle. Phylogenetic analyses of XYL1 and endo-β-1,4-xylanases from other fungi revealed a diversification process and separation of proteins from the same fungal species into different lineages. Key words: Colletotrichum lindemuthianum, Phaseolus vulgaris, endo-β-1,4-xylanase, gene expression, phylogeny.

In this work, X-ray diffraction and Mossbauer spectroscopy techniques were used to characterise and carry out a comparison of the corrosion products obtained during the pigging activities in two sour-hydrocarbon-transporting pipelines located in the Gulf of Mexico: the first one being a gas pipeline and the other one a crude oil pipeline. The results indicate that for these specific conditions, there are differences between the corrosion products formed in each pipeline. Iron sulphides and oxides were the main corrosion products and their presence is directly related to the operating conditions prevailing in the pipelines as well as to the hydrocarbon quality. As for the sour gas pipeline, higher concentrations of greigite and pyrite were observed, whereas more proportions of magnetite, mackinawite and marcasite were found in the sour crude oil pipeline. The most important parameters in the formation of the different types of corrosion products are the water content, hydrogen sulphide concentration and ox...

Background & Aim Traumatic events leading to focal lesions in articular cartilage are an important cause of joint functionality deterioration, leading to physical inactivity and osteoarthritis. Although restorative and regenerative strategies utilizing different scaffolds seeded with chondrocytes or progenitor cells have been tested with partial success. Their indication is limited for small lesions and their mechanical insufficiency of the fibrocartilage can result in their degeneration overtime, requiring patients to be re-operated within two years. Treatment modalities that favor the application of rapidly-crosslinking biopolymeric solutions to reconstruct cartilage lesions via an arthroscopic approach are highly desirable to reduce risk, surgery time and post-operative recovery times. The desired features of the alternative materials for lesion restoration should match the mechanical properties of cartilage, mimic its mechanical behavior and exhibit satisfactory chondro-inductive capacity. Methods, Results & Conclusion In this work, a new methacrylamide-functionalized gelatin extracted from a cold-adapted species was evaluated as the principal biopolymer for a photo-curable and injectable formulation for cartilage restoration. Unlike using mammalian gelatin, the cold-adapted nature allowed the formulation of highly concentrated biopolymeric solutions (>35 % W/V), while maintaining arthroscopic extrudability and avoiding sol-gel transition at room temperature. The dense and interconnected network of biopolymers after photo-crosslinking showed similar stiffness to human cartilage (∼ 1 MPa), whereas the chondrocyte-laden biopolymeric network was capable to induce formation of cartilage tissue in vitro, presenting similar values to human cartilage in glycosaminoglycan (GAG) (∼ 2 µg/mg), mRNA collagen(Col)2A/Col1A mRNA ratio (∼7) and similar distribution of GAG and Col staining across the scaffold. Finally, precise arthroscopic restoration of a cartilage lesion has been proven in a 3D simulation model. The developed Injectable functionalized-gelatin formulation respond to all the suitability criteria for using the regeneration of functional hyaline cartilage of patients through minimally invasive procedures.

This corrects the article DOI: 10.1103/PhysRevLett.116.071802.

We examined the antiviral activity of the integrase inhibitor (INI) cabotegravir against HIV-2 isolates from INI-naive individuals. HIV-2 was sensitive to cabotegravir in single-cycle and spreading-infection assays, with 50% effective concentrations (EC(50)s) in the low to subnanomolar range; comparable results were obtained for HIV-1 in both assay formats. Our findings suggest that cabotegravir should be evaluated in clinical trials as a potential option for antiretroviral therapy and preexposure prophylaxis in HIV-2-prevalent settings.

Neoplasms exhibits a high incidence and mortality rates due to their complex and commonly overlapping clinical, biochemical, and morphologic profiles influenced by acquired or inherited molecular abnormalities, cell of origin, and level of differentiation. Obesity appears related to ~20% of cancers including endometrial, esophageal, colorectal, postmenopausal breast, prostate, and renal. Several factors other than obesity, i.e., insulin, insulin-like growth factor, sexual hormones, and adipokines may play a potential role in neoplasia. Cancer-associated hypercoagulable and thrombotic states are influenced by abnormalities in the vascular wall and susceptibility to invasion, interference in blood flow and increase in circulating tissue factor and thrombin, activation of cell growth factors, the presence of a central catheter, chemotherapies, neoplasm type, and surgery. In cancer, thromboembolic complications are the second most frequent cause of death with pulmonary thromboembolism in ~50% of cases postmortem. Thrombosis worsens prognosis as demonstrated with a survival rate as low as 12% per year vs 36% in nonthrombic patients. Deep vein thrombosis is the most frequent thromboembolic complication in cancer. It is usually detected at diagnosis and within the first 3 months of chemotherapy. The underlining mechanisms of this association should be further studied to identify patients at higher risk and develop adequate prevention, diagnostic, and treatment measures. The D-dimer test can be successfully used to assess the fibrinolytic phase of coagulation and as such is routinely used in suspected cases of deep vein thrombosis and pulmonary thromboembolism. In addition, significant advances have been made in understanding the composition and functional capabilities of the gut microbiota in the inflammatory process, obesity, and its roles in cancer; however, the intricate balance that exists within the microbiota may not only affect the host directly, it can also disrupt the entire microbial community.Cancer is a prothrombotic and inflammatory state in which the activation of coagulation is related to tumor growth, angiogenesis, and metastasis. It is important to identify the relationship between body mass index with these processes and clarify their importance in cancer prognosis. Future research should answer the question if manipulation of resident microbial communities could potentially improve prognosis and treatment outcome.

Much progress with respect to congenital Zika virus (ZIKV) pathogenesis has been achieved after the 2015 outbreak in Brazil. It is now accepted that ZIKV is vertically transmitted, infects cells of the developing central nervous system and the placenta, yet it is unclear to what extent placental affection contributes to the development of congenital ZIKV. The association between fulminant villitis and severe fetal involvement emerges as a possibility. ZIKV is unique among the Flaviviruses in its ability to be sexually transmitted, possibly responsible for its teratogenicity. Furthermore, there is controversy over the participation of antibody dependent enhancement (ADE) in patients with non-neutralizing anti-Flavivirus antibodies, a phenomenon previously recognized in serious DENV infections. Our aim was to analyze information regarding the contribution of the placental barrier as an actual player in neonatal ZIKV. Therefore, we underwent a systematic review with keywords "Zika virus" and "ZIKV". Articles were screened for relevance concerning the topics of microcephaly, transplacental transmission, sexual transmission, and ADE. We identified variables that affect the severity of congenital Zika syndrome: age of gestation at maternal infection, the extent of placental disruption (villitis), sexual transmission, initial viral replication at the uterine wall, anti-DENV antibodies, and the possibility of antibody-mediated transcytosis of ZIKV through the placenta. These questions may not seem relevant when Zika becomes endemic, and we are no longer witness to the extreme clinical sequelae seen when the virus moves through an immunologically naive population; however, characterizing the pathogenesis of congenital Zika syndrome will continue to further our understanding.

Single neutral pion production via muon antineutrino charged-current interactions in plastic scintillator (CH) is studied using the MINERvA detector exposed to the NuMI low-energy, wideband antineutrino beam at Fermilab. Measurement of this process constrains models of neutral pion production in nuclei, which is important because the neutral-current analog is a background for ν ¯ e appearance oscillation experiments. The differential cross sections for π 0 momentum and production angle, for events with a single observed π 0 and no charged pions, are presented and compared to model predictions. These results comprise the first measurement of the π 0 kinematics for this process.

Loss-of-function mutations in the WRN helicase gene cause Werner syndrome- a progeroid syndrome with an elevated risk of cancer and other age-associated diseases. Large numbers of single nucleotide polymorphisms have been identified in WRN. We report here the organismal, cellular, and molecular phenotypes of variant rs3087425 (c. 2500C > T) that results in an arginine to cysteine substitution at residue 834 (R834C) and up to 90% reduction of WRN helicase activity. This variant is present at a high (5%) frequency in Mexico, where we identified 153 heterozygous and three homozygous individuals among 3,130 genotyped subjects. Family studies of probands identified ten additional TT homozygotes. Biochemical analysis of WRN protein purified from TT lymphoblast cell lines confirmed that the R834C substitution strongly and selectively reduces WRN helicase, but not exonuclease activity. Replication track analyses showed reduced replication fork progression in some homozygous cells following DNA replication stress. Among the thirteen TT homozygotes, we identified a previously unreported and statistically significant gender bias in favor of males (p = 0.0016), but none of the clinical findings associated with Werner syndrome. Our results indicate that WRN helicase activity alone is not rate-limiting for the development of clinical WS.

Background. Cytomegalovirus (CMV) pulmonary involvement is rarely associated with IRIS; therefore, limited information is available. Case Presentation. Here, we describe the case of a 43-year-old HIV-infected male who developed an unusual case of IRIS after cytomegalovirus (CMV) pneumonia. Clinically there was a progressive and paradoxical worsening of respiratory distress, despite being treated for CMV after initiation with antiretroviral therapy. Chest X-ray revealed disseminated infiltrates in both lungs; chest CT-scan showed generalized lung involvement and mediastinal adenopathy. Pulmonary biopsy confirmed CMV pneumonia with the observation of typical viral inclusions on pneumocytes. Conclusions. CMV pneumonia can be associated with the development of IRIS requiring treatment with immunosuppressant’s and immunomodulatory drugs.

Previous studies have demonstrated that the machinery for sulfate assimilation influences the capacity of pathogenic microorganisms to invade a minor or major range of hosts, and this machinery appears to be dispensable when the lifestyle of the organism allows it. Colletotrichum lindemuthianum is the etiological agent of anthracnose, which is an important disease of beans (Phaseolus vulgaris) and an interesting model of study due to its hemibiotrophic lifestyle. We report the isolation, sequence and analysis of a 442 bp DNA fragment from the Clsir gene, which encodes the β subunit of sulfite reductase from C. lindemuthianum. The Clsir nucleotide sequence showed an identity of 97% with Trichoderma atroviride, 81% with Gibberella zeae, 77% with Penicillium chrysogenum, Arthroderma otae and 74% with Leptosphaeria maculans. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clsir and 48 reported SiR sequences from fungi with different lifestyles. The distance tree showed diverse clusters of fungi related with different lifestyles and host types: pathogens of animals, saprophytic/opportunistic, phytopathogens, endophytes and mycoparasites/saprophytes. The deduced amino acid sequence of ClSiR from C. lindemuthianum was grouped with the sequences of SiRs from T. atroviride, Trichoderma virens and Trichoderma reesei. Based on the fact that T. atroviride is a mycoparasite, this result suggests horizontal gene transfer. Key words: Colletotrichum lindemuthianum, sulfite reductase, pathogen, lifestyle, host type.

This report describes the development of a novel dual color Southern protocol to visualize two distinct genomes or genic regions simultaneously on a single Southern blot. The blot is developed with IRDye-conjugated antibody (Ab) and streptavidin that recognize digoxigenin (Dig)- or biotin-labeled probes, respectively and visualized on an infrared imager. This protocol was validated by visualizing viral and host genomes of human cytomegalovirus (HCMV)-infected human fibroblasts. This technique utilizes extremely sensitive fluorescent imaging, allowing the detection of nanogram quantities of DNA, as opposed to microgram quantities needed in Southerns using radioactively labeled probes, and eliminates the inherent loss in signal after stripping and reprobing a Southern blot. The probes are labeled with non-radioactive Dig and biotin and can be stored for extended periods of time. This protocol will aid in studies of any system with two genomes, such as cells infected with numerous types of microorganisms (virus/parasites/bacteria), or studies of mitochondrial and nuclear DNA within the same cells.

Background: Urinary tract infections (UTIs) are a major public health problem worldwide. In Latin America, most UTIs are treated without bacteriological identifiation. Our aim was to examine resistance rates to commonly prescribed antibiotics, focusing on cases from Jalisco, Mexico; and additionally to conduct a review of the literature to search for resistance patterns in other countries of Latin America. Methods: Retrospective analysis of urine cultures from ambulatory and hospitalized patients taken from Nov 2012-Nov 2013; susceptibi lity testing and minimal inhibitory concentration (MIC) was done by microdilution methodology. For literature search, we reviewed diffe rent data bases and included papers in English and Spanish, published from 2007-2014, representative from the Latin America region. Results: We obtained 1.206 consecutive samples from outpatient and inpatient facilities, including adult and pediatric subjects. The most frequent isolate in all groups was ESBL-producing E. coli with high resistance rates for ampicillin, TMP-SMX, and ciproflxacin. In the literature review we found 15 papers related to resistance rates of commonly prescribed antibiotics. Conclusions: The information summarized in this article supports the fiding that resistance rates to commonly prescribed antimicrobial agents are increasing worldwide. As such, this study challenges the rationale behind empiric use of antibiotics, emphasizing the need, whenever possible, to perform urine cultures before initiating antimi crobial treatment.

Repair of DNA lesions must occur within the chromatin landscape and is associated with alterations in histone modifications and nucleosome rearrangement. To directly associate these chromatin features with DNA damage and repair, it is necessary to be able to map DNA adducts. We have developed a cyclobutane pyrimidine dimer (CPD)-specific immunoprecipitation method and mapped ultraviolet damage hotspots across human chromosomes 1 and 6. CPD hotspots occur almost equally in genic and intergenic regions. However, these hotspots are significantly more prevalent adjacent to repeat elements, especially Alu repeats. Nucleosome mapping studies indicate that nucleosomes are consistently positioned at Alu elements where CPD hotspots form, but by 2 h post-irradiation, these same regions are significantly depleted of nucleosomes. These results indicate that nucleosomes associated with hotspots of CPD formation are readily rearranged, potentially making them accessible to DNA repair machinery. Our results represent the first chromosome scale map of ultraviolet-induced DNA lesions in the human genome, and reveal the sequence features and dynamic chromatin changes associated with CPD hotspots.

Between 30% and 50% of patients with non-small-cell lung cancer (NSCLC) will develop cerebral metastases in the course of their illness. As improvements are made in the local brain treatment, the question arises on how to manage patients with NSCLC who have solely stable brain metastatic disease and if treatment should be considered for the primary lung lesion. The present article will review published series of patients with NSCLC and with brain metastases treated with aggressive thoracic management, with either lung tumor resection or thoracic radiation with or without chemotherapy as definitive treatment. We will also assess which prognostic factors may be useful in the identification of the subset of patients who could benefit from this more aggressive approach. For patients treated with surgical resection for the primary lung tumor, median survival ranged from 19 to 27 months, and the 1-, 2-, and 5-year survival reached 56%-69%, 28%-54%, and 11%-24%, respectively. Patients treated with aggressive radiotherapy with or without chemotherapy, achieved a median survival of 15.5-31.8 months, with a 1-year survival of 50%-71%, and a 2-year survival of 16%-60%. Well-selected patients with NSCLC and with exclusively oligometastatic cerebral disease represent a subgroup of patients with stage IV NSCLC that might achieve long-term survival after treatment directed to the brain and lung tumor lesions. Patients with N0 or N1 disease may be selected for surgical thoracic treatment, whereas those with N2 or N3 disease may benefit from combined chemoradiotherapy in the absence of progression after induction chemotherapy.

Neutrino-induced charged-current coherent kaon production, $\nu_{\mu}A\rightarrow\mu^{-}K^{+}A$, is a rare, inelastic electroweak process that brings a $K^+$ on shell and leaves the target nucleus intact in its ground state. This process is significantly lower in rate than neutrino-induced charged-current coherent pion production, because of Cabibbo suppression and a kinematic suppression due to the larger kaon mass. We search for such events in the scintillator tracker of MINERvA by observing the final state $K^+$, $\mu^-$ and no other detector activity, and by using the kinematics of the final state particles to reconstruct the small momentum transfer to the nucleus, which is a model-independent characteristic of coherent scattering. We find the first experimental evidence for the process at $3\sigma$ significance., Comment: added ancillary file with information about the six kaon candidates

Muon-neutrino elastic scattering on electrons is an observable neutrino process whose cross section is precisely known. Consequently a measurement of this process in an accelerator-based $\nu_\mu$ beam can improve the knowledge of the absolute neutrino flux impinging upon the detector; typically this knowledge is limited to $\sim$ 10% due to uncertainties in hadron production and focusing. We have isolated a sample of 135 $\pm$ 17 neutrino-electron elastic scattering candidates in the segmented scintillator detector of MINERvA, after subtracting backgrounds and correcting for efficiency. We show how this sample can be used to reduce the total uncertainty on the NuMI $\nu_\mu$ flux from 9% to 6%. Our measurement provides a flux constraint that is useful to other experiments using the NuMI beam, and this technique is applicable to future neutrino beams operating at multi-GeV energies., Comment: 11 pages, 11 figures

Here, the MINERvA Collaboration reports a novel study of neutrino-nucleus charged-current deep inelastic scattering (DIS) using the same neutrino beam incident on targets of polystyrene, graphite, iron, and lead. Results are presented as ratios of C, Fe, and Pb to CH. The ratios of total DIS cross sections as a function of neutrino energy and flux-integrated differential cross sections as a function of the Bjorken scaling variable x are presented in the neutrino-energy range of 5–50 GeV. Based on the predictions of charged-lepton scattering ratios, good agreement is found between the data and prediction at medium x and low neutrino energy. However, the ratios appear to be below predictions in the vicinity of the nuclear shadowing region, x < 0.1. This apparent deficit, reflected in the DIS cross-section ratio at high Eν, is consistent with previous MINERvA observations [B. Tice (MINERvA Collaboration), Phys. Rev. Lett. 112, 231801 (2014).] and with the predicted onset of nuclear shadowing with the axial-vector current in neutrino scattering.

Previously, we reported that the absence of the ataxia telangiectasia mutated (ATM) kinase, a critical DNA damage response (DDR) signaling component for double-strand breaks, caused no change in HCMV Towne virion production. Later, others reported decreased AD169 viral titers in the absence of ATM. To address this discrepancy, human foreskin fibroblasts (HFF) and three ATM − lines (GM02530, GM05823, and GM03395) were infected with both Towne and AD169. Two additional ATM − lines (GM02052 and GM03487) were infected with Towne. Remarkably, both previous studies' results were confirmed. However, the increased number of cell lines and infections with both lab-adapted strains confirmed that ATM was not necessary to produce wild-type-level titers in fibroblasts. Instead, interactions between individual virus strains and the cellular microenvironment of the individual ATM − line determined efficiency of virion production. Surprisingly, these two commonly used lab-adapted strains produced drastically different titers in one ATM − cell line, GM05823. The differences in titer suggested a rapid method for identifying genes involved in differential virion production. In silico comparison of the Towne and AD169 genomes determined a list of 28 probable candidates responsible for the difference. Using serial iterations of an experiment involving virion entry and input genome nuclear trafficking with a panel of related strains, we reduced this list to four (UL129, UL145, UL147, and UL148). As a proof of principle, reintroduction of UL148 largely rescued genome trafficking. Therefore, use of a battery of related strains offers an efficient method to narrow lists of candidate genes affecting various virus life cycle checkpoints. IMPORTANCE Human cytomegalovirus (HCMV) infection of multiple cell lines lacking ataxia telangiectasia mutated (ATM) protein produced wild-type levels of infectious virus. Interactions between virus strains and the microenvironment of individual ATM − lines determined the efficiency of virion production. Infection of one ATM − cell line, GM05823, produced large titer differentials dependent on the strain used, Towne or AD169. This discrepancy resolved a disagreement in the literature of a requirement for ATM expression and HCMV reproduction. The titer differentials in GM08523 cells were due, in part, to a decreased capacity of AD169 virions to enter the cell and traffic genomes to the nucleus. In silico comparison of the Towne, AD169, and related variant strains' genomes was coupled with serial iterations of a virus entry experiment, narrowing 28 candidate proteins responsible for the phenotype down to 4. Reintroduction of UL148 significantly rescued genome trafficking. Differential behavior of virus strains can be exploited to elucidate gene function.