PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo‐devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web‐based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de     

Response of transgenic tobacco overexpressing the CchGLP gene to cadmium and aluminium: phenotypic and microRNAs expression changes

Physiology and Molecular Biology of Plants - Transgenic tobacco (N. tabacum cv. Xanthi nc) expressing Capsicum chinense CchGLP gene that encodes an Mn-SOD, constitutively produces hydrogen...     

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site‐associated DNA sequencing (RAD‐Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F_ST 0.008; range 0.00–0.018) were concordant with previous microsatellite‐based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age‐1 and age‐2 families of full and half‐siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non‐native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.     

Filter feeding,deviations from bilateral symmetry,developmental noise,and heterochrony of hemichordate and cephalochordate gills

We measured gill slit fluctuating asymmetry (FA), a measure of developmental noise, in adults of three invertebrate deuterostomes with different feeding modes: the cephalochordate Branchiostoma floridae (an obligate filter feeder), the enteropneusts Protoglossus graveolens (a facultative filter feeder/deposit feeder) and Saccoglossus bromophenolosus (a deposit feeder). FA was substantially and significantly low in B. floridae and P. graveolens and high in S. bromophenolosus. Our results suggest that the gills of species that have experienced a relaxation of the filter feeding trait exhibit elevated FA. We found that the timing of development of the secondary collagenous gill bars, compared to the primary gill bars, was highly variable in P. graveolens but not the other two species, demonstrating an independence of gill FA from gill bar heterochrony. We also discovered the occasional ectopic expression of a second set of paired gills posterior to the first set of gills in the enteropneusts and that these were more common in S. bromophenolosus. Moreover, our finding that gill slits in enteropneusts exhibit bilateral symmetry suggests that the left‐sidedness of larval cephalochordate gills, and the directional asymmetry of Cambrian stylophoran echinoderm fossil gills, evolved independently from a bilaterally symmetrical ancestor.     

Focus: Preventive Medicine: Undiagnosed Hypertension and Undiagnosed Type 2 Diabetes among Overweight and Obese Marshallese Participants in a Diabetes Prevention Program

Hypertension and type 2 diabetes (T2D) are major public health issues that disproportionately affect minority communities, including Native Hawaiians and Pacific Islanders (NHPI). Minority communities are also more likely to have undiagnosed hypertension and T2D. Marshallese Pacific Islanders have been shown to have high proportions of diagnosed and undiagnosed hypertension and T2D. Using survey and biometric data collected from 378 overweight/obese Marshallese Pacific Islander adults, this study documents the prevalence of hypertension and T2D, as well as the prevalence of undiagnosed hypertension and T2D. The study also examines associations between undiagnosed hypertension and undiagnosed T2D and age group, sex, health care access (defined by foregone care due to cost and health insurance status), and body mass index (BMI). Among participants with blood pressure readings indicative of hypertension, 68.4% were undiagnosed, and among participants with HbA1c indicative of T2D, 31.6% were undiagnosed. A quarter of participants (24.5%) had blood pressure and HbA1c measures indicative of both undiagnosed hypertension and undiagnosed T2D. Undiagnosed hypertension was significantly associated with age group (p’s<0.0001) and sex (p=0.028). Undiagnosed T2D was significantly associated with age group (p’s<0.05), forgone care due to cost (p=0.018), health insurance status (p=0.035), and BMI (p=0.001). Participants in this study had high proportions of undiagnosed hypertension and undiagnosed T2D. These findings will be immediately useful for those working to address hypertension and T2D disparities among Marshallese and other NHPI populations.