Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

A Survey of New Temperature-Sensitive, Embryonic-Lethal Mutations in C. elegans: 24 Alleles of Thirteen Genes

To study essential maternal gene requirements in the early C. elegans embryo, we have screened for temperature-sensitive, embryonic lethal mutations in an effort to bypass essential zygotic requirements for such genes during larval and adult germline development. With conditional alleles, multiple essential requirements can be examined by shifting at different times from the permissive temperature of 15°C to the restrictive temperature of 26°C. Here we describe 24 conditional mutations that affect 13 different loci and report the identity of the gene mutations responsible for the conditional lethality in 22 of the mutants. All but four are mis-sense mutations, with two mutations affecting splice sites, another creating an in-frame deletion, and one creating a premature stop codon. Almost all of the mis-sense mutations affect residues conserved in orthologs, and thus may be useful for engineering conditional mutations in other organisms. We find that 62% of the mutants display additional phenotypes when shifted to the restrictive temperature as L1 larvae, in addition to causing embryonic lethality after L4 upshifts. Remarkably, we also found that 13 out of the 24 mutations appear to be fast-acting, making them particularly useful for careful dissection of multiple essential requirements. Our findings highlight the value of C. elegans for identifying useful temperature-sensitive mutations in essential genes, and provide new insights into the requirements for some of the affected loci

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

β-Endorphin and sex differentially modulate the response to EtOH in a sitespecific manner

The effects of alcohol are multifaceted, involving brain circuits regulating reward, motivation, and stress, frequently via the endogenous opioid, beta-endorphin (β-E). It is currently unknown how alcohol affects neural circuit activation in females and how β-E affects ethanol\u27s ability to induce neuronal activation. Therefore, we investigated the impact of acute alcohol treatment on neuronal activation in reward-and stress-related brain circuitry in a sex-and β-E dependent manner. In this study, male and female control (C57BL/6J; β-E+/+) and β-E null (−/−) mice were injected intraperitoneally with 2 g/kg ethanol (EtOH) or saline. Post-injection, animals were sacrificed using ketamine/xylazine and perfused with saline followed by 4% paraformaldehyde. Brain sections (35 μm) were immunohistochemically processed for tyrosine hydroxylase (TH), dopamine\u27s ratelimiting enzyme, and c-fos, a neuronal activation marker. The number of c-fos immunoreactive cell nuclei, THimmunoreactivity, and TH/c-fos-ir cells were quantified in the nucleus accumbens (NAc), ventral tegmental area (VTA), paraventricular nucleus (PVN), central nucleus of the amygdala (CeA), paraventricular thalamic nucleus (PVA) and Edinger-Westphal nucleus (EW). In females, EtOH increased c-fos expression in the CeA, PVN, EW and NAc shell, while c-fos expression in the VTA, and TH expression in the VTA and NAc, depended on a genotype and treatment interaction. In males, EtOH increased c-fos in the CeA and PVN. EtOH also increased the number of double-labeled cells in the Arc, but only in females. These results suggest that the neurons in females are inherently more sensitive to EtOH, emphasizing the importance of studying the relationship between sex and alcohol addiction

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio)

We used microarray and quantitative real-time PCR (qRT-PCR) analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in the liver and brain. The transcriptome of whole zebrafish brain showed little response to 21 days of starvation. Only agouti-related protein 1 (agrp1) significantly responded, with increased expression in brains of starved fish. In contrast, a 21-day period of starvation significantly downregulated 466 and upregulated 108 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis, proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the unfolded protein response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss) and less similar to mouse, while the response of common carp (Cyprinus carpio) differed considerably from the other three species

Words matter: how ecologists discuss managed and non-managed bees and birds

Abstract: Effectively promoting the stability and quality of ecosystem services involves the successful management of domesticated species and the control of introduced species. In the pollinator literature, interest and concern regarding pollinator species and pollinator health dramatically increased in recent years. Concurrently, the use of loaded terms when discussing domesticated and non-native species may have increased. As a result, pollinator ecology has inherited both the confusion associated with invasion biology’s lack of a standardized terminology to describe native, managed, or introduced species as well as loaded terms with very strong positive or negative connotations. The recent explosion of research on native bees and alternative pollinators, coupled with the use of loaded language, has led to a perceived divide between native bee and managed bee researchers. In comparison, the bird literature discusses the study of managed (poultry) and non-managed (all other birds) species without an apparent conflict with regard to the use of terms with strong connotations or sentiment. Here, we analyze word usage when discussing non-managed and managed bee and bird species in 3614 ecological and evolutionary biology papers published between 1990 and 2019. Using time series analyses, we demonstrate how the use of specific descriptor terms (such as wild, introduced, and exotic) changed over time. We then conducted co-citation network analyses to determine whether papers that share references have similar terminology and sentiment. We predicted a negative language bias towards introduced species and positive language bias towards native species. We found an association between the term invasive and bumble bees and we observed significant increases in the usage of more ambiguous terms to describe non-managed species, such as wild. We detected a negative sentiment associated with the research area of pathogen spillover in bumble bees, which corroborates the subjectivity that language carries. We recommend using terms that acknowledge the role of human activities on pathogen spillover and biological invasions. Avoiding the usage of loaded terms when discussing managed and non-managed species will advance our understanding and promote effective and productive communication across scientists, general public, policy makers and other stake holders in our society

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish ( Danio rerio)

In this study, we tested for the presence of sexual dimorphism in the hepatic transcriptome of the adult zebrafish and examined the effect of long term manipulation of dietary carbohydrate on gene expression in both sexes. Zebrafish were fed diets comprised of 0%, 15%, 25%, or 35% carbohydrate from the larval stage through sexual maturity, then sampled for hepatic tissue, growth, proximate body composition, and retention efficiencies. Using Affymetrix microarrays and qRT-PCR, we observed substantial sexual dimorphism in the hepatic transcriptome. Males up-regulated genes associated with oxidative metabolism, carbohydrate metabolism, energy production, and amelioration of oxidative stress, while females had higher expression levels of genes associated with translation. Restriction of dietary carbohydrate (0% diet) significantly affected hepatic gene expression, growth performance, retention efficiencies of protein and energy, and percentages of moisture, lipid, and ash. The response of some genes to dietary manipulation varied by sex; with increased dietary carbohydrate, males up-regulated genes associated with oxidative metabolism (e.g.hadhβ) while females up-regulated genes associated with glucose phosphorylation (e.g. glucokinase). Our data support the use of the zebrafish model for the study of fish nutritional genomics, but highlight the importance of accounting for sexual dimorphism in these studies

<i>PIK3CA</i> missense mutations promote glioblastoma pathogenesis, but do not enhance targeted PI3K inhibition

<div><p>Background</p><p>Glioblastoma (GBM) is the most common adult primary brain tumor. Multimodal treatment is empiric and prognosis remains poor. Recurrent <i>PIK3CA</i> missense mutations (<i>PIK3CA</i>^<i>mut</i>) in GBM are restricted to three functional domains: adaptor binding (ABD), helical, and kinase. Defining how these mutations influence gliomagenesis and response to kinase inhibitors may aid in the clinical development of novel targeted therapies in biomarker-stratified patients.</p><p>Methods</p><p>We used normal human astrocytes immortalized via expression of hTERT, E6, and E7 (NHA). We selected two <i>PIK3CA</i>^<i>mut</i> from each of 3 mutated domains and induced their expression in NHA with (NHA^RAS) and without mutant <i>RAS</i> using lentiviral vectors. We then examined the role of <i>PIK3CA</i>^<i>mut</i> in gliomagenesis <i>in vitro</i> and in mice, as well as response to targeted PI3K (PI3Ki) and MEK (MEKi) inhibitors <i>in vitro</i>.</p><p>Results</p><p><i>PIK3CA</i>^<i>mut</i>, particularly helical and kinase domain mutations, potentiated proximal PI3K signaling and migration of NHA and NHA^RAS<i>in vitro</i>. Only kinase domain mutations promoted NHA colony formation, but both helical and kinase domain mutations promoted NHA^RAS tumorigenesis <i>in vivo</i>. <i>PIK3CA</i>^<i>mut</i> status had minimal effects on PI3Ki and MEKi efficacy. However, PI3Ki/MEKi synergism was pronounced in NHA and NHA^RAS harboring ABD or helical mutations.</p><p>Conclusion</p><p><i>PIK3CA</i>^<i>mut</i> promoted differential gliomagenesis based on the mutated domain. While <i>PIK3CA</i>^<i>mut</i> did not influence sensitivity to single agent PI3Ki, they did alter PI3Ki/MEKi synergism. Taken together, our results demonstrate that a subset of <i>PIK3CA</i>^<i>mut</i> promote tumorigenesis and suggest that patients with helical domain mutations may be most sensitive to dual PI3Ki/MEKi treatment.</p></div

Connecting breast cancer survivors for exercise: protocol for a two-arm randomized controlled trial

Abstract Background Peer-based exercise interventions that cultivate new opportunities for support with a fellow cancer survivor may result in increased exercise volume. It is not clear whether adding qualified exercise professional (QEP) support to peer-based interventions improves health outcomes. Therefore, the purpose of this study is to determine whether breast cancer survivor (BCS) dyads who receive 10 weekly sessions of virtually delivered QEP support have improved outcomes compared to BCS dyads who do not receive QEP support. Methods Participants Adult BCS with medical clearance for exercise, who have an internet-connected device, and currently engage in < 150 min of moderate-intensity exercise per week. Intervention BCS will be matched using evidence-based criteria. The intervention group will receive dyadic exercise information sessions and a program tailored by a QEP for 10 weeks (intervention period) and have access to the QEP for an additional 4 weeks (tapering period). The control will not receive any QEP support. Outcomes The primary outcome is post-intervention self-reported exercise volume. Secondary outcomes include device-assessed exercise volume (i.e., Fitbit), social support, and health-related quality of life. Randomization 108 participants, matched in dyads, will be randomized 1:1 to the MatchQEP or Match groups using a web-based scheme. Statistical analysis Outcomes will be measured at baseline, post-intervention, post-tapering, and at 12 weeks post-intervention follow-up. Discussion The findings from this RCT will determine if matched BCS dyads who receive 10 weeks of virtually delivered QEP support have higher levels of self-report and device-measured exercise, social support, and health related quality of life compared to matched dyads without QEP-delivered exercise guidance. To our knowledge this will be the first study to assess the combined effect of peer- and QEP support on exercise volume. Project findings will inform and optimize intervention methods aimed to increase exercise among BCS through accessible exercise supports. Trial Registration: The study is registered on ClinicalTrials.gov (study identifier: NCT04771975, protocol Version Number: 2, date: July 22, 2021)