A comprehensive platform for highly multiplexed mammalian functional genetic screens

<p>Abstract</p> <p>Background</p> <p>Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens.</p> <p>Results</p> <p>Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens.</p> <p>Conclusion</p> <p>Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.</p

Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae) - A comparison with haploid males, queens and workers

In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males

A General Strategy to Endow Natural Fusion-protein-Derived Peptides with Potent Antiviral Activity

Fusion between the viral and target cell membranes is an obligatory step for the infectivity of all enveloped virus, and blocking this process is a clinically validated therapeutic strategy

Interventions outside the workplace for reducing sedentary behaviour in adults under 60 years of age

Background Adults spend a majority of their time outside the workplace being sedentary. Large amounts of sedentary behaviour increase the risk of type 2 diabetes, cardiovascular disease, and both all‐cause and cardiovascular disease mortality. Objectives Primary • To assess effects on sedentary time of non‐occupational interventions for reducing sedentary behaviour in adults under 60 years of age Secondary • To describe other health effects and adverse events or unintended consequences of these interventions • To determine whether specific components of interventions are associated with changes in sedentary behaviour • To identify if there are any differential effects of interventions based on health inequalities (e.g. age, sex, income, employment) Search methods We searched CENTRAL, MEDLINE, Embase, Cochrane Database of Systematic Reviews, CINAHL, PsycINFO, SportDiscus, and ClinicalTrials.gov on 14 April 2020. We checked references of included studies, conducted forward citation searching, and contacted authors in the field to identify additional studies. Selection criteria We included randomised controlled trials (RCTs) and cluster RCTs of interventions outside the workplace for community‐dwelling adults aged 18 to 59 years. We included studies only when the intervention had a specific aim or component to change sedentary behaviour. Data collection and analysis Two review authors independently screened titles/abstracts and full‐text articles for study eligibility. Two review authors independently extracted data and assessed risk of bias. We contacted trial authors for additional information or data when required. We examined the following primary outcomes: device‐measured sedentary time, self‐report sitting time, self‐report TV viewing time, and breaks in sedentary time. Main results We included 13 trials involving 1770 participants, all undertaken in high‐income countries. Ten were RCTs and three were cluster RCTs. The mean age of study participants ranged from 20 to 41 years. A majority of participants were female. All interventions were delivered at the individual level. Intervention components included personal monitoring devices, information or education, counselling, and prompts to reduce sedentary behaviour. We judged no study to be at low risk of bias across all domains. Seven studies were at high risk of bias for blinding of outcome assessment due to use of self‐report outcomes measures. Primary outcomes Interventions outside the workplace probably show little or no difference in device‐measured sedentary time in the short term (mean difference (MD) ‐8.36 min/d, 95% confidence interval (CI) ‐27.12 to 10.40; 4 studies; I² = 0%; moderate‐certainty evidence). We are uncertain whether interventions reduce device‐measured sedentary time in the medium term (MD ‐51.37 min/d, 95% CI ‐126.34 to 23.59; 3 studies; I² = 84%; very low‐certainty evidence) We are uncertain whether interventions outside the workplace reduce self‐report sitting time in the short term (MD ‐64.12 min/d, 95% CI ‐260.91 to 132.67; I² = 86%; very low‐certainty evidence). Interventions outside the workplace may show little or no difference in self‐report TV viewing time in the medium term (MD ‐12.45 min/d, 95% CI ‐50.40 to 25.49; 2 studies; I² = 86%; low‐certainty evidence) or in the long term (MD 0.30 min/d, 95% CI ‐0.63 to 1.23; 2 studies; I² = 0%; low‐certainty evidence). It was not possible to pool the five studies that reported breaks in sedentary time given the variation in definitions used. Secondary outcomes Interventions outside the workplace probably have little or no difference on body mass index in the medium term (MD ‐0.25 kg/m², 95% CI ‐0.48 to ‐0.01; 3 studies; I² = 0%; moderate‐certainty evidence). Interventions may have little or no difference in waist circumference in the medium term (MD ‐2.04 cm, 95% CI ‐9.06 to 4.98; 2 studies; I² = 65%; low‐certainty evidence). Interventions probably have little or no difference on glucose in the short term (MD ‐0.18 mmol/L, 95% CI ‐0.30 to ‐0.06; 2 studies; I² = 0%; moderate‐certainty evidence) and medium term (MD ‐0.08 mmol/L, 95% CI ‐0.21 to 0.05; 2 studies, I² = 0%; moderate‐certainty evidence) Interventions outside the workplace may have little or no difference in device‐measured MVPA in the short term (MD 1.99 min/d, 95% CI ‐4.27 to 8.25; 4 studies; I² = 23%; low‐certainty evidence). We are uncertain whether interventions improve device‐measured MVPA in the medium term (MD 6.59 min/d, 95% CI ‐7.35 to 20.53; 3 studies; I² = 70%; very low‐certainty evidence). We are uncertain whether interventions outside the workplace improve self‐reported light‐intensity PA in the short‐term (MD 156.32 min/d, 95% CI 34.34 to 278.31; 2 studies; I² = 79%; very low‐certainty evidence). Interventions may have little or no difference on step count in the short‐term (MD 226.90 steps/day, 95% CI ‐519.78 to 973.59; 3 studies; I² = 0%; low‐certainty evidence) No data on adverse events or symptoms were reported in the included studies. Authors' conclusions Interventions outside the workplace to reduce sedentary behaviour probably lead to little or no difference in device‐measured sedentary time in the short term, and we are uncertain if they reduce device‐measured sedentary time in the medium term. We are uncertain whether interventions outside the workplace reduce self‐reported sitting time in the short term. Interventions outside the workplace may result in little or no difference in self‐report TV viewing time in the medium or long term. The certainty of evidence is moderate to very low, mainly due to concerns about risk of bias, inconsistent findings, and imprecise results. Future studies should be of longer duration; should recruit participants from varying age, socioeconomic, or ethnic groups; and should gather quality of life, cost‐effectiveness, and adverse event data. We strongly recommend that standard methods of data preparation and analysis are adopted to allow comparison of the effects of interventions to reduce sedentary behaviour

Caste-specific gene expression in the stingless bee Melipona quadrifasciata - Are there common patterns in highly eusocial bees?

Caste polyphenism is a multifaceted phenomenon, most evident in the marked differences in reproductive capacity and longevity between queens and workers. The mechanisms underlying caste differentiation and division of labor are mainly addressed in the honey bee, and recently have been studied at the molecular level. Yet, generalizations drawn from studies on this model organism require validation by comparative studies. We choose Melipona quadrifasciata, a sister-group species to honey bees, to investigate differences in gene expression between newly emerged adult queens and workers. RNA extracts were subjected to a differential display protocol (DDRT-PCR). The putative differentially expressed genes, for which annotation was available, were validated by RT-PCR and hybridization. Differential expression was observed for myosin, projectin, kettin, cytochrome P450, Rab11 and Sas10. Except for kettin, all of these were overexpressed in the worker caste. Projectin and kettin could play roles in caste-specific flight muscle organization. The putative Rab11 and Sas10 homolog genes could be involved in fertility-related cell signaling and in longevity-related gene silencing, respectively. Cytochrome P450 overexpression in Melipona workers corroborates similar findings in the honey bee, thus indicating a common function in the social insect caste syndrome.51435235

Modified approaches on Lung Cancer Cell Extraction and Classification fromComputerized Tomography Images

Abstract: Lung Tumor Delineation is a critical aspect in radiotherapy treatment for cancer