Draft Genome Sequence of Pseudoalteromonas sp. Strain JC3

We report the draft genome sequence for Pseudoalteromonas sp. strain JC3, an isolate obtained from an aquaculture facility for whiteleg shrimp (Litopenaeus vannamei). The JC3 genome suggests multiple mechanisms for microbial interactions, including a type VI secretion system and potential for antibiotic production

General anesthesia does not have persistent effects on attention in rodents

Background: Studies in animals have shown that general anesthesia can cause persistent spatial memory impairment, but the influence of anesthetics on other cognitive functions is unclear. This study tested whether exposure to general anesthesia without surgery caused a persistent deficit in attention in rodents.Methods: To evaluate whether anesthesia has persistent effects on attention, rats were randomized to three groups. Group A was exposed for 2 h to isoflurane anesthesia, and tested the following seven days for attentional deficits. Group B was used as a control and received room air before attentional testing. Since there is some evidence that a subanesthetic dose of ketamine can improve cognition and reduce disorders of attention after surgery, rats in group C were exposed to isoflurane anesthesia in combination with a ketamine injection before cognitive assessment. Attention was measured in rats using the 5-Choice Serial Reaction Time Task, for which animals were trained to respond with a nose poke on a touchscreen to a brief, unpredictable visual stimulus in one of five possible grid locations to receive a food reward. Attention was analyzed as % accuracy, % omission, and premature responses.Results: Evaluating acute attention by comparing baseline values with data from the day after intervention did not reveal any differences in attentional measurements. No significant differences were seen in % accuracy, % omission, and premature responses for the three groups tested for 7 consecutive days.Conclusion: These data in healthy rodents suggest that general anesthesia without surgery has no persistent effect on attention and the addition of ketamine does not alter the outcome

The 2011 Eruption of the Recurrent Nova T Pyxidis; the Discovery, the Pre-eruption Rise, the Pre-eruption Orbital Period, and the Reason for the Long Delay

We report the discovery by M. Linnolt on JD 2455665.7931 (UT 2011 April 14.29) of the sixth eruption of the recurrent nova T Pyxidis. This discovery was made just as the initial fast rise was starting, so with fast notification and response by observers worldwide, the entire initial rise was covered (the first for any nova), and with high time resolution in three filters. The speed of the rise peaked at 9 mag/day, while the light curve is well fit over only the first two days by a model with a uniformly expanding sphere. We also report the discovery by R. Stubbings of a pre-eruption rise starting 18 days before the eruption, peaking 1.1 mag brighter than its long-time average, and then fading back towards quiescence 4 days before the eruption. This unique and mysterious behavior is only the fourth known anticipatory rise closely spaced before a nova eruption. We present 19 timings of photometric minima from 1986 to February 2011, where the orbital period is fast increasing with P/dot{P}=313,000 yrs. From 2008-2011, T Pyx had a small change in this rate of increase, so that the orbital period at the time of eruption was 0.07622950+-0.00000008 days. This strong and steady increase of the orbital period can only come from mass transfer, for which we calculate a rate of 1.7-3.5x10^-7 Mo/yr. We report 6116 magnitudes between 1890 and 2011, for an average B=15.59+-0.01 from 1967-2011, which allows for an eruption in 2011 if the blue flux is nearly proportional to the accretion rate. The ultraviolet-optical-infrared spectral energy distribution is well fit by a power law with flux proportional to nu^1.0, although the narrow ultraviolet region has a tilt with a fit of \nu^{1/3}. We prove that most of the T Pyx light is not coming from a disk, or any superposition of blackbodies, but rather is coming from some nonthermal source.Comment: ApJ submitted, 62 pages, 8 figures; much added data, updated analysi

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

Epigenetic control of gene transcription is critical for normal human development and cellular differentiation. While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human diseases, interindividual epigenetic variations in normal tissues due to aging, environmental factors, or innate susceptibility are poorly characterized. The plasticity, tissue-specific nature, and variability of gene expression are related to epigenomic states that vary across individuals. Thus, population-based investigations are needed to further our understanding of the fundamental dynamics of normal individual epigenomes. We analyzed 217 non-pathologic human tissues from 10 anatomic sites at 1,413 autosomal CpG loci associated with 773 genes to investigate tissue-specific differences in DNA methylation and to discern how aging and exposures contribute to normal variation in methylation. Methylation profile classes derived from unsupervised modeling were significantly associated with age (P,0.0001) and were significant predictors of tissue origin (P,0.0001). In solid tissues (n = 119) we found striking, highly significant CpG island–dependent correlations between age and methylation; loci in CpG islands gained methylation with age, loci not in CpG islands lost methylation with age (P,0.001), and this pattern was consistent across tissues and in an analysis of blood-derived DNA. Our data clearly demonstrate age- and exposure-related differences in tissue-specific methylation and significant age-associated methylation patterns which are CpG island context-dependent. This work provides novel insight into the role of aging and the environment in susceptibility to diseases such as cancer and critically informs the field of epigenomics by providing evidence of epigenetic dysregulation by age-related methylation alterations. Collectively we reveal key issues to consider both in the construction of reference and disease-related epigenomes and in the interpretation of potentially pathologically important alterations

Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (\u3cem\u3eCastanea mollissima\u3c/em\u3e) and plant reference genomes

Background Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. Results The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. Conclusions On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research

Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake

Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage I-IV) women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured 1,413 autosomal CpG loci associated with 773 cancer-related genes and validated select CpG loci with Sequenom EpiTYPER. Tumor grade, size, estrogen and progesterone receptor status, and triple negative status were significantly (Q-values \u3c0.05) associated with altered methylation of 209, 74, 183, 69, and 130 loci, respectively. Unsupervised clustering, using a recursively partitioned mixture model (RPMM), of all autosomal CpG loci revealed eight distinct methylation classes. Methylation class membership was significantly associated with patient race (P\u3c0.02) and tumor size (P\u3c0.001) in univariate tests. Using multinomial logistic regression to adjust for potential confounders, patient age and tumor size, as well as known disease risk factors of alcohol intake and total dietary folate, were all significantly (P\u3c0.0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns

A Pilot Study of the Effects of Mycoplasma ovipneumoniae Exposure on Domestic Lamb Growth and Performance

Mycoplasma ovipneumoniae is a globally distributed pathogen that has been associated with pneumonia in both domestic and wild Caprinae. It is closely related to M. hyopneumoniae, a respiratory pathogen of swine that is associated with decreased growth rates of pigs as well as clinical respiratory disease. In order to assess the effects of M. ovipneumoniae on lamb performance, we generated a cohort of lambs free of M. ovipneumoniae by segregation of test negative ewes after lambing, then compared the growth and carcass quality traits of M. ovipneumoniae-free and -colonized lambs from weaning to harvest. Some signs of respiratory disease were observed during the feeding trial in both lamb groups, but the M. ovipneumoniae-exposed group included more affected lambs and higher average disease scores. At harvest, lungs of lambs in both groups showed few grossly visible lesions, although the M. ovipneumoniae-exposed group did exhibit increased microscopic lung lesions (P\u3c0.05). In addition, M. ovipneumoniae exposed lambs produced lower average daily gains (P\u3c0.05), and lower yield grade carcasses (P\u3c0.05) compared to those of non-exposed lambs. The results demonstrated the feasibility of test and segregation for elimination of M. ovipneumoniae from groups of sheep and suggested that this pathogen may impair lamb growth and productivity even in the absence of overt respiratory disease

The Story Behind a Letter in Support of Professor Derrick Bell

Professor Derrick A. Bell, Jr. had a long and proud history of disturbing authority. He is widely noted as one of the founders of Critical Race Theory. His scholarship on race was not only a direct challenge to the traditionally conservative legal academy, but also to the more liberal bastions within the academy, such as the Critical Legal Studies movement. His writings about the role of race in American law have made him one of the most prominent legal scholars of a generation. However, Professor Bell did not merely write about racial injustices. He was willing to take risks to promote racial equality and ideological balance in the legal academy. In 1980, he resigned his deanship at the University of Oregon School of Law after the faculty refused to honor his recommendation that an Asian-American woman, Pat K. Chew, be hired. In 1987, after returning to Harvard, Professor Bell staged a sit-in to protest the Law School’s failure to grant tenure to two white professors, Claire Dalton and David Trubek, whose work was aligned with the Critical Legal Studies movement

Incidence and Outcomes Associated With Clostridium difficile Infections: A Systematic Review and Meta-analysis

Importance: An understanding of the incidence and outcomes of Clostridium difficile infection (CDI) in the United States can inform investments in prevention and treatment interventions. Objective: To quantify the incidence of CDI and its associated hospital length of stay (LOS) in the United States using a systematic literature review and meta-analysis. Data Sources: MEDLINE via Ovid, Cochrane Library Databases via Wiley, Cumulative Index of Nursing and Allied Health Complete via EBSCO Information Services, Scopus, and Web of Science were searched for studies published in the United States between 2000 and 2019 that evaluated CDI and its associated LOS. Study Selection: Incidence data were collected only from multicenter studies that had at least 5 sites. The LOS studies were included only if they assessed postinfection LOS or used methods accounting for time to infection using a multistate model or compared propensity score-matched patients with CDI with control patients without CDI. Long-term-care facility studies were excluded. Of the 119 full-text articles, 86 studies (72.3%) met the selection criteria. Data Extraction and Synthesis: Two independent reviewers performed the data abstraction and quality assessment. Incidence data were pooled only when the denominators used the same units (eg, patient-days). These data were pooled by summing the number of hospital-onset CDI incident cases and the denominators across studies. Random-effects models were used to obtain pooled mean differences. Heterogeneity was assessed using the I2 value. Data analysis was performed in February 2019. Main Outcomes and Measures: Incidence of CDI and CDI-associated hospital LOS in the United States. Results: When the 13 studies that evaluated incidence data in patient-days due to hospital-onset CDI were pooled, the CDI incidence rate was 8.3 cases per 10 000 patient-days. Among propensity score-matched studies (16 of 20 studies), the CDI-associated mean difference in LOS (in days) between patients with and without CDI varied from 3.0 days (95% CI, 1.44-4.63 days) to 21.6 days (95% CI, 19.29-23.90 days). Conclusions and Relevance: Pooled estimates from currently available literature suggest that CDI is associated with a large burden on the health care system. However, these estimates should be interpreted with caution because higher-quality studies should be completed to guide future evaluations of CDI prevention and treatment interventions