Easyfig: a genome comparison visualizer SULLIVAN, Mitchell J; PETTY, Nicola K; BEATSON, Scott A
Bioinformatics,
04/2011, Letnik:
27, Številka:
7
Journal Article
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Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ...ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.
Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/.
is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we ...describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety "Finola." The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (
), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (
) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis.
and
(which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug- and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.
Glycogen, a hyperbranched complex glucose polymer, is an intracellular glucose store that provides energy for cellular functions, with liver glycogen involved in blood-glucose regulation. Liver ...glycogen comprises complex α particles made up of smaller β particles. The recent discovery that these α particles are smaller and fewer in diabetic, compared with healthy, mice highlights the need to elucidate the nature of α-particle formation; this paper tests various possibilities for binding within α particles. Acid hydrolysis effects, examined using dynamic light scattering and size exclusion chromatography, showed that the binding is not simple α-(1→4) or α-(1→6) glycosidic linkages. There was no significant change in α particle size after the addition of various reagents, which disrupt disulfide, protein, and hydrogen bonds and hydrophobic interactions. The results are consistent with proteinaceous binding between β particles in α particles, with the inability of protease to break apart particles being attributed to steric hindrance.
The pathogen Staphylococcus aureus colonizes and infects a variety of different sites within the human body. To adapt to these different environments, S. aureus relies on a complex and finely tuned ...regulatory network. While some of these networks have been well-elucidated, the functions of more than 50% of the transcriptional regulators in S. aureus remain unexplored. Here, we assess the contribution of the LacI family of metabolic regulators to staphylococcal virulence. We found that inactivating the purine biosynthesis regulator purR resulted in a strain that was acutely virulent in bloodstream infection models in mice and in ex vivo models using primary human neutrophils. Remarkably, these enhanced pathogenic traits are independent of purine biosynthesis, as the purR mutant was still highly virulent in the presence of mutations that disrupt PurR’s canonical role. Through the use of transcriptomics coupled with proteomics, we revealed that a number of virulence factors are differentially regulated in the absence of purR. Indeed, we demonstrate that PurR directly binds to the promoters of genes encoding virulence factors and to master regulators of virulence. These results guided us into further ex vivo and in vivo studies, where we discovered that S. aureus toxins drive the death of human phagocytes and mice, whereas the surface adhesin FnbA contributes to the increased bacterial burden observed in the purR mutant. Thus, S. aureus repurposes a metabolic regulator to directly control the expression of virulence factors, and by doing so, tempers its pathogenesis.
Induced pluripotent stem cells (iPSCs) hold great promise for modeling human hematopoietic diseases. However, intrinsic variability in the capacities of different iPSC lines for hematopoietic ...development complicates comparative studies and is currently unexplained. We created and analyzed 3 separate iPSC clones from fibroblasts of 3 different normal individuals using a standardized approach that included excision of integrated reprogramming genes by Cre-Lox mediated recombination. Gene expression profiling and hematopoietic differentiation assays showed that independent lines from the same individual were generally more similar to one another than those from different individuals. However, one iPSC line (WT2.1) exhibited a distinctly different gene expression, proliferation rate, and hematopoietic developmental potential relative to all other iPSC lines. This “outlier” clone also acquired extensive copy number variations (CNVs) during reprogramming, which may be responsible for its divergent properties. Our data indicate how inherent and acquired genetic differences can influence iPSC properties, including hematopoietic potential.
•Normal induced pluripotent stem cells exhibit donor-specific gene expression signatures and the capacity for hematopoietic development.•CNVs acquired during reprogramming or selection of rare CNVs present in the starting cell population may alter iPSC developmental potential.
Staphylococcus aureus is a successful pathogen that produces a wide range of virulence factors that it uses to subvert and suppress the immune system. These include the bicomponent pore-forming ...leukocidins. How the expression of these toxins is regulated is not completely understood. Here, we describe a screen to identify transcription factors involved in the regulation of leukocidins. The most prominent discovery from this screen is that SarS, a known transcription factor which had previously been described as a repressor of alpha-toxin expression, was found to be a potent repressor of leukocidins LukED and LukSF-PV. We found that inactivating
resulted in increased virulence both in an
model using primary human neutrophils and in an
infection model in mice. Further experimentation revealed that SarS represses leukocidins by serving as an activator of Rot, a critical repressor of toxins, as well as by directly binding and repressing the leukocidin promoters. By studying contemporary clinical isolates, we identified naturally occurring mutations in the
promoter that resulted in overexpression of
and increased repression of leukocidins in USA300 bloodstream clinical isolates. Overall, these data establish SarS as an important repressor of leukocidins and expand our understanding of how these virulence factors are being regulated
and
by S. aureus.
Diamond Blackfan anemia (DBA) is a congenital disorder with erythroid (Ery) hypoplasia and tissue morphogenic abnormalities. Most DBA cases are caused by heterozygous null mutations in genes encoding ...ribosomal proteins. Understanding how haploinsufficiency of these ubiquitous proteins causes DBA is hampered by limited availability of tissues from affected patients. We generated induced pluripotent stem cells (iPSCs) from fibroblasts of DBA patients carrying mutations in RPS19 and RPL5. Compared with controls, DBA fibroblasts formed iPSCs inefficiently, although we obtained 1 stable clone from each fibroblast line. RPS19-mutated iPSCs exhibited defects in 40S (small) ribosomal subunit assembly and production of 18S ribosomal RNA (rRNA). Upon induced differentiation, the mutant clone exhibited globally impaired hematopoiesis, with the Ery lineage affected most profoundly. RPL5-mutated iPSCs exhibited defective 60S (large) ribosomal subunit assembly, accumulation of 12S pre-rRNA, and impaired erythropoiesis. In both mutant iPSC lines, genetic correction of ribosomal protein deficiency via complementary DNA transfer into the “safe harbor” AAVS1 locus alleviated abnormalities in ribosome biogenesis and hematopoiesis. Our studies show that pathological features of DBA are recapitulated by iPSCs, provide a renewable source of cells to model various tissue defects, and demonstrate proof of principle for genetic correction strategies in patient stem cells.
•Ribosome biogenesis and hematopoiesis are impaired in iPSCs from DBA patients.•The abnormalities of DBA iPSCs are ameliorated by genetic restoration of the defective ribosomal protein genes.
•Offspring amygdala microglia count were associated with maternal diet and adiposity.•Microglia number in the offspring were not associated with maternal inflammation.•Offspring cytokines were ...positively associated with maternal chemokines.•Offspring chemokines were negatively associated with maternal chemokines.•Maternal diet and adiposity exert unique effect on offspring inflammatory outcomes.
The obesity epidemic affects 40% of adults in the US, with approximately one-third of pregnant women classified as obese. Previous research suggests that children born to obese mothers are at increased risk for a number of health conditions. The mechanisms behind this increased risk are poorly understood. Increased exposure to in-utero inflammation induced by maternal obesity is proposed as an underlying mechanism for neurodevelopmental alterations in offspring. Utilizing a non-human primate model of maternal obesity, we hypothesized that maternal consumption of an obesogenic diet will predict offspring peripheral (e.g., cytokines and chemokines) and central (microglia number) inflammatory outcomes via the diet’s effects on maternal adiposity and maternal inflammatory state during the third trimester. We used structural equation modeling to simultaneously examine the complex associations among maternal diet, metabolic state, adiposity, inflammation, and offspring central and peripheral inflammation. Four latent variables were created to capture maternal chemokines and pro-inflammatory cytokines, and offspring cytokine and chemokines. Model results showed that offspring microglia counts in the basolateral amygdala were associated with maternal diet (β = −0.622, p < 0.01), adiposity (β = 0.593, p < 0.01), and length of gestation (β = 0.164, p < 0.05) but not with maternal chemokines (β = 0.135, p = 0.528) or maternal pro-inflammatory cytokines (β = 0.083, p = 0.683). Additionally, we found that juvenile offspring peripheral cytokines (β = −0.389, p < 0.01) and chemokines (β = −0.298, p < 0.05) were associated with a maternal adiposity-induced decrease in maternal circulating chemokines during the third trimester (β = −0.426, p < 0.01). In summary, these data suggest that maternal diet and adiposity appear to directly predict offspring amygdala microglial counts while maternal adiposity influences offspring peripheral inflammatory outcomes via maternal inflammatory state.
Poor metabolic health during pregnancy is associated with health concerns for pregnant individuals and their offspring. Lower socioeconomic status (SES) is one risk factor for poor metabolic health, ...and may be related to limited access to healthful and affordable foods (e.g., living in a food desert). This study evaluates the respective contributions of SES and food desert severity on metabolic health during pregnancy. The food desert severity of 302 pregnant individuals was determined using the United States Department of Agriculture Food Access Research Atlas. SES was measured using total household income adjusted for household size, years of education, and amount of reserve savings. Information about participants' glucose concentrations one hour following an oral glucose tolerance test during the second trimester was extracted from medical records and percent adiposity during the second trimester was assessed using air displacement plethysmography. Information about participants' nutritional intake during the second trimester was obtained by trained nutritionists via three unannounced 24-h dietary recalls. Structural equation models showed that lower SES predicted higher food desert severity (β = - 0.20, p = 0.008) and higher adiposity (β = - 0.27, p = 0.016) and consumption of a more pro-inflammatory diet (β = - 0.25, p = 0.003) during the second trimester of pregnancy. Higher food desert severity also predicted higher percent adiposity during the second trimester (β = 0.17, p = 0.013). Food desert severity significantly mediated the relationship between lower SES and higher percent adiposity during the second trimester (β
= - 0.03, 95% CI - 0.079, - 0.004). These findings indicate that access to healthful and affordable foods is a mechanism by which SES contributes to adiposity during pregnancy and may inform interventions intended to improve metabolic health during pregnancy.
Abstract
Numerous reports document the spread of SARS-CoV-2, but there is limited information on its introduction before the identification of a local case. This may lead to incorrect assumptions ...when modeling viral origins and transmission. Here, we utilize a sample pooling strategy to screen for previously undetected SARS-CoV-2 in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across the Mount Sinai Health System in New York. The patients had been previously evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We identify SARS-CoV-2 RNA from specimens collected as early as 25 January 2020, and complete SARS-CoV-2 genome sequences from multiple pools of samples collected between late February and early March, documenting an increase prior to the later surge. Our results provide evidence of sporadic SARS-CoV-2 infections a full month before both the first officially documented case and emergence of New York as a COVID-19 epicenter in March 2020.
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