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Coiled-coil domain containing 3 (CCDC3) was previously shown to regulate liver lipid metabolism as a secretory protein. Here, we report an unexpected intracellular role of CCDC3 as a tumor suppressor in breast cancer (BrC). Bioinformatics datasets analysis showed that CCDC3 is under-expressed in BrCs, while its higher levels are correlated with higher overall survival and lower relapse of cancer patients, and CCDC3 is positively correlated with p53 and its target genes. Ectopic CCDC3 markedly suppressed proliferation, colony formation, and xenograft tumor growth by augmenting p53 activity in BrC cells. Depletion of endogenous CCDC3 by CRISPR-Cas9 increased proliferation and drug resistance of BrC cells by alleviating 5-Fluorouracil (5-FU)-induced p53 level and activity. Mechanistically, CCDC3 bound to the C-termini of p53 and MDM2, consequently stabilizing p53 in the nucleus and impairing MDM2 recruitment of p53 to the 26S proteosome without inhibiting p53 ubiquitination. p53 induced CCDC3 expression by binding to its promoter in BrC cells. Our results unveil a unique mechanism underlying CCDC3 activation of p53 in a positive feedback fashion to suppress BrC growth.

One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain, but more importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the originalin-frameamino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. Here we present the first machine-learning based method to detect and predict the presence of PRFs in all types of coding genes and taxa with an accuracy exceding 90%.

Bacteroidota are the most common bacteria in the human gut and are responsible for degrading complex polysaccharides that would otherwise remain undigested. The abundance of Bacteroides in the gut is shaped by phages such as crAssphages that infect and kill them. While close to 600 genomes have been identified computationally, only four have been successfully cultured. Here, we identify and characterize three novel crAssphage species isolated from wastewater and infecting the bacterial hostBacteroides cellulosilyticusWH2. We named the novel species,Kehishuvirus winsdale(Bc01),Kolpuevirus frurule(Bc03), andRudgehvirus redwords(Bc11) which span two different families and three genera. These phages may not have co-evolved with their respective bacterial hosts. The phages had a conserved gene arrangement with known crAssphages, but gene similarity within phages belonging to the same taxa was highly variable. Across the three species, only two structural genes encoding a hypothetical protein and a tail spike protein were similar. Evolutionary analysis revealed the tail spike protein is undergoing purifying selection and was predicted to bind to a TonB-dependent transporter on the host cell surface, suggesting a role for host specificity. This study expands the known crAssphage isolates and reveals insights into the crAssphage infection mechanism. The availability of pure cultures of multiple crAssphage infecting the same host provides an opportunity to perform controlled experiments on one of the most dominant members of the human enteric virome.

PURPOSE: To determine the variance and correlation with tumor viability of fluorine 18 ((18)F) fluoromisonidazole (FMISO) uptake in hepatocellular carcinoma (HCC) prior to and after embolization treatment. MATERIALS AND METHODS: In this single-arm, single-center, prospective pilot study between September 2016 and March 2017, participants with at least one tumor measuring 1.5 cm or larger with imaging or histologic findings diagnostic for HCC were enrolled (five men; mean age, 68 years; age range, 61–76 years). Participants underwent (18)F-FMISO PET/CT before and after bland embolization of HCC. A tumor-to-liver ratio (TLR) was calculated by using standardized uptake values of tumor and liver. The difference in mean TLR before and after treatment was compared by using a Wilcoxon rank sum test, and correlation between TLR and tumor viability was assessed by using the Spearman rank correlation coefficient. RESULTS: Four participants with five tumors were included in the final analysis. The median tumor diameter was 3.2 cm (IQR, 3.0–3.9 cm). The median TLR before treatment was 0.97 (IQR, 0.88–0.98), with a variance of 0.02, and the median TLR after treatment was 0.85 (IQR, 0.79–1), with a variance of 0.01; both findings indicate a narrow range of (18)F-FMISO uptake in HCC. The Spearman rank correlation coefficient was 0.87, indicating a high correlation between change in TLR and nonviable tumor. CONCLUSION: Although there was a correlation between change in TLR and response to treatment, the low signal-to-noise ratio of (18)F-FMISO in the liver limited its use in HCC. Keywords: Molecular Imaging-Clinical Translation, Embolization, Abdomen/Gastrointestinal, Liver Clinical trial registration no. NCT02695628 © RSNA, 2022

Coiled-coil domain containing 3 (CCDC3) was previously shown to regulate liver lipid metabolism as a secretory protein. Our recent studies revealed an intracellular role of CCDC3 as a tumor suppressor in breast cancer (BrC). Bioinformatics datasets analysis showed that CCDC3 is under-expressed in BrCs, while its higher levels are correlated with higher overall survival and lower relapse of cancer patients. CCDC3 is positively correlated with p53 and its target genes. Ectopic CCDC3 markedly suppressed proliferation, colony formation, and xenograft tumor growth by augmenting p53 activity in BrC cells. In contrast, knockdown of endogenous CCDC3 using CRISPR led to reduction of p53 level and activity, consequently promoting the proliferation of BrC cells. Mechanistically, CCDC3 bound to the C-termini of p53 and MDM2, consequently stabilizing p53 in the nucleus and impairing MDM2 recruitment of p53 to the 26S proteosome without inhibiting p53 ubiquitination. Also, knockdown of CCDC3 caused the resistance of BrC cells to 5-FU to some degrees by alleviating p53 response to this drug. p53 induced CCDC3 expression by binding to its promoter specifically in BrC cells. Our results unveil a unique mechanism underlying CCDC3 activation of p53 in a positive feedback fashion to suppress BrC growth and suggest that CCDC3 deficiency could be a factor for drug resistance of BrCs. Citation Format: Hyemin Lee, Caiyue Li, Ji Hoon Jung, Yiwei Zhang, Jieqiong Wang, Chang Liu, Allyson M. Segall, Roger L. Sheffmaker, Shelya X. Zeng, Hua Lu. Coiled-coil domain containing 3 suppresses breast cancer growth by protecting p53 from proteasome-mediated degradation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 856.

Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere., eLife digest When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.

Increasingly, clinical infections are becoming recalcitrant or completely resistant to antibiotics treatment and multidrug resistance is rising alarmingly. Patients suffering from infections that used to be treated successfully by antibiotic regimens are running out of the treatment options. Bacteriophage (phage) therapy, long practiced in parts of Eastern Europe and the states of the former Soviet Union, is now being reevaluated as a treatment option complementary to and synergistic with antibiotic treatments. We discuss some current studies that have addressed synergistic killing activity between phages and antibiotics, the issues of treatment order and antibiotic class, and point to considerations that will have to be addressed by future studies. Overall, co-treatments with phages and antibiotics promise to extend the utility of antibiotics in current use. Nevertheless, a lot of work, both basic and clinical, remains to be done before such co-treatments become routine options in the hospital setting.

Author(s): Schooley, Robert T; Biswas, Biswajit; Gill, Jason J; Hernandez-Morales, Adriana; Lancaster, Jacob; Lessor, Lauren; Barr, Jeremy J; Reed, Sharon L; Rohwer, Forest; Benler, Sean; Segall, Anca M; Taplitz, Randy; Smith, Davey M; Kerr, Kim; Kumaraswamy, Monika; Nizet, Victor; Lin, Leo; McCauley, Melanie D; Strathdee, Steffanie A; Benson, Constance A; Pope, Robert K; Leroux, Brian M; Picel, Andrew C; Mateczun, Alfred J; Cilwa, Katherine E; Regeimbal, James M; Estrella, Luis A; Wolfe, David M; Henry, Matthew S; Quinones, Javier; Salka, Scott; Bishop-Lilly, Kimberly A; Young, Ry; Hamilton, Theron | Abstract: Volume 61, no. 10, e00954-17, 2017, https://doi.org/10.1128/AAC.00954-17. Materials and Methods, 2nd paragraph, 2nd sentence: “Phages provided by the Biological Defense Research Directorate (BDRD) of the Naval Medical Research Center (AB-Navy1, AB-Navy4, AB-Navy71, AB-Navy97, and AbTP31) were isolated from various environmental samples by using routine isolation techniques, as previously described (9)” should read “Phages provided by the Biological Defense Research Directorate (BDRD) of the Naval Medical Research Center (AB-Navy1, AB-Navy4, AB-Navy97, and AbTP31) were isolated from various environmental samples by using routine isolation techniques, as previously described (9), except for one phage (AB-Navy71, also known as phage vB_Ab-M-G7, DSM strain no. 25639), which was purchased from Liebniz Institute DSMZ (Germany).”

Cardiovascular disease (CVD) currently claims nearly one million lives yearly in the US, accounting for nearly 40% of all deaths. Coronary artery disease (CAD) accounts for the largest number of these deaths. While efforts aimed at treating CAD in recent decades have concentrated on surgical and catheter-based interventions, limited resources have been directed toward prevention and rehabilitation. CAD is commonly treated using percutaneous coronary intervention (PCI), and this treatment has increased exponentially since its adoption over three decades ago. Recent questions have been raised regarding the cost-effectiveness of PCI, the extent to which PCI is overused, and whether selected patients may benefit from optimal medical therapy in lieu of PCI. One alternative therapy that has been shown to improve outcomes in CAD is exercise therapy; exercise programs have been shown to have numerous physiological benefits, and a growing number of studies have demonstrated reductions in mortality. Given the high volume of PCI, its high cost, its lack of effect on survival and the potential for alternative treatments including exercise, the current study is termed "PCI Alternative Using Sustained Exercise" (PAUSE). The primary aim of PAUSE is to determine whether patients randomized to exercise and lifestyle intervention have greater improvement in coronary function and anatomy compared to those randomized to PCI. Coronary function and anatomy is determined using positron emission tomography combined with computed tomographic angiography (PET/CTA). Our objective is to demonstrate the utility of a non-invasive technology to document the efficacy of exercise as an alternative treatment strategy to PCI.

585 Objectives: The degree to which a single metabolic pattern is present (pattern expression score, PES) has recently been evaluated as a powerful predictor of conversion to Alzheimer9s disease (AD) in patients with mild cognitive impairment (MCI). We recently proposed controls-based denoising (CODE), a novel approach to improve PES-based image analysis by identifying patterns of physiological variance in a separate control sample using principal component analysis and removing them from patient data. Our aim was to improve prediction of conversion to AD from FDG-PET with CODE and to compare classification performances between various classification algorithms (including clinical features and machine learning based on multiple ROI). Methods: Multi-center FDG-PET from 110 patients with MCI (80 non-converters with follow-up > 4 years and 30 AD-converters with time to conversion < 4 years) were obtained from the ADNI-database. 243 healthy controls were used to determine the patterns of physiological variance. Classification performance was calculated for classification based on PES only and PES combined with neuropsychological and ApoE4 genotype (support-vector machine, cross-validated). Classification performance was compared between standard analysis (without CODE), improved analysis (using CODE) and a state-of-the-art machine learning approach (support vector machine) based on multiple ROIs. Results: With CODE, applied in its basic form (optimizations are possible), we were able to significantly improve the area under curve from 0.78 to 0.87 (p=0.03, DeLong’s method) and accuracy from 69% to 82% using PES only and from 83% to 88% when combining PES with clinical features. The state-of-the-art approach based on multiple ROIs yielded an accuracy of 74%. Conclusions: In our sample, we could significantly improve classification based on PES. When combined with CODE, classification based on PES was superior to a state-of-the-art machine learning algorithm based on multiple ROI data, presumably owing to the fact that including healthy controls in the analysis allowed us to use a much larger data set as compared to the limited number of MCI subjects available for training in machine learning. We conclude that the proposed method is a powerful tool to improve image analysis and offers a wide spectrum of biomedical applications, even beyond image analysis.

The traditional connection between rate constants and free energy landscapes is extended to define effective free energy landscapes relevant on any chosen timescale. Although the Eyring–Polanyi transition state theory specifies a fixed timescale of τ = h / k B T ${\tau =h/k_{\mathrm {B}}T}$ , we introduce instead the timescale of interest for the system in question, e.g. the observation time. The utility of drawing such landscapes using a variety of timescales is illustrated by the example of Holliday junction resolution. The resulting free energy landscapes are easier to interpret, clearly reveal observation time dependent effects like coalescence of short-lived states, and reveal features of interest for the specific system more clearly.

Gene amplification is a phenotype-causing form of chromosome instability and is initiated by DNA double-strand breaks (DSBs). Cells with mutant p53 lose G1/S checkpoint and are permissive to gene amplification. In this study we show that mammalian cells become proficient for spontaneous gene amplification when the function of the DSB repair protein complex MRN (Mre11/Rad50/Nbs1) is impaired. Cells with impaired MRN complex experienced severe replication stress and gained substrates for gene amplification during replication, as evidenced by the increase of replication-associated single-stranded breaks that were converted to DSBs most likely through replication fork reversal. Impaired MRN complex directly compromised ATM/ATR-mediated checkpoints and allowed cells to progress through cell cycle in the presence of DSBs. Such compromised intra-S phase checkpoints promoted gene amplification independently from mutant p53. Finally, cells adapted to endogenous replication stress by globally suppressing genes for DNA replication and cell cycle progression. Our results indicate that the MRN complex suppresses gene amplification by stabilizing replication forks and by securing DNA damage response to replication-associated DSBs.

Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery 1–3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome 4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.

Widespread antibiotic use in clinical medicine and the livestock industry has contributed to the global spread of multidrug-resistant (MDR) bacterial pathogens, includingAcinetobacter baumannii. We report on a method used to produce a personalized bacteriophage-based therapeutic treatment for a 68-year-old diabetic patient with necrotizing pancreatitis complicated by an MDRA. baumanniiinfection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a 4-month period. In the absence of effective antibiotics, two laboratories identified nine different bacteriophages with lytic activity for anA. baumanniiisolate from the patient. Administration of these bacteriophages intravenously and percutaneously into the abscess cavities was associated with reversal of the patient's downward clinical trajectory, clearance of theA. baumanniiinfection, and a return to health. The outcome of this case suggests that the methods described here for the production of bacteriophage therapeutics could be applied to similar cases and that more concerted efforts to investigate the use of therapeutic bacteriophages for MDR bacterial infections are warranted.

Objectives To assess the consumption of ultra-processed foods among inmates in a women’s prison in the State of São Paulo, Brazil. Methods We conducted a cross-sectional study in 2012/2013 with 1,013 female inmates. A structured interview questionnaire was used to collect socio-demographic, self-reported morbidity and healthy lifestyles and health-related behaviors data. The inmates’ usual diet was assessed with a food frequency questionnaire. Foods were classified as either natural or minimally processed, processed or ultra-processed. Results Inmates age ranged from 18 to 65 years, 51.7% were black, 80.3% had children, 69.5% smoked, 47% were overweight/obese and half of them had high blood triglycerides. The prevalence of daily consumption of natural or minimally processed foods (rice, beans and cassava flour) was 87.7%. The prevalence of daily consumption of green leafy and other vegetables was 63.7%. Almost two-thirds reported consuming milk and fried chicken frequently. A high prevalence of daily consumption of ultra-processed foods was observed in this study. Hot dog bread and sweet bread with margarine were consumed by 86.5% of the interviewees on a daily basis; sugar sweetened beverages by 68.4%, and biscuits as well as candies by 77.1%. Conclusions The women’s diet in the prison is of low quality, and may lead to metabolic alterations, obesity and other comorbidities. It is recommended that the prison’s Food Evaluation Committee considers improvements to the quality of the prisoners’ diets.

Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen-lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic-lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic-lysogenic decision in viral communities and to test models of the host density-dependent viral lytic-lysogenic switch.

Temperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the host’s genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts’ translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution.

Despite significant advances in multimodal imaging techniques and analysis approaches, unimodal studies are still the predominant way to investigate brain changes or group differences, including structural magnetic resonance imaging (sMRI), functional MRI (fMRI), diffusion tensor imaging (DTI) and electroencephalography (EEG). Multimodal brain studies can be used to understand the complex interplay of anatomical, functional and physiological brain alterations or development, and to better comprehend the biological significance of multiple imaging measures. To examine the function-structure associations of the brain in a more comprehensive and integrated manner, we reviewed a number of multimodal studies that combined two or more functional (fMRI and/or EEG) and structural (sMRI and/or DTI) modalities. In this review paper, we specifically focused onmultimodal neuroimaging studies on cognition, aging, disease and behavior. We also compared multiple analysis approaches, including univariate and multivariate methods. The possible strengths and limitations of each method are highlighted, which can guide readers when selecting a method based on a given research question. In particular, we believe that multimodal fusion approaches will shed further light on the neuronalmechanisms underlying the major structural and functional pathophysiological features of both the healthy brain (e.g. development) or the diseased brain (e. g. mental illness) and, in the latter case, may provide a more sensitive measure than unimodal imaging for disease classification, e. g. multimodal biomarkers, which potentially can be used to support clinical diagnosis based on neuroimaging techniques. (C) 2013 Elsevier Inc. All rights reserved.

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.