The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an ...environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.
Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a ...characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants.Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs.This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.
Climatic adaptation is an example of a genotype-by-environment interaction (GxE) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; ...however, surprisingly few studies have examined how genome-wide patterns of gene expression GxE are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C sub(4) grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive GxE. While less well-represented, we observe 1294 genes (7.8%) with trans effects. Trans-by-environment interactions are weaker and much less common than cis GxE, occurring in only 0.7% of trans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant GxE. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among GxE genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting GxE and trans regulation, indicating that expression GxE and heterosis may result from the evolution of transcription factors or their binding sites. P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
The purpose of this journal-ready dissertation study was to examine the extent to which differences were present in college readiness in reading, mathematics, and in both subjects for Texas high ...school students by their demographic characteristics. In the first investigation, the degree to which ethnic/racial (i.e., Black and White) differences were present in college readiness in reading, in mathematics, and in both subjects was determined. Concerning the second investigation, the extent to which differences existed in college readiness in reading, in mathematics, and in both subjects between Hispanic and White students was addressed. Regarding the third investigation, the degree to which gender differences was present exist in college readiness in reading, in mathematics, and in both subjects was ascertained. In each of these three investigations, data for five school years (i.e., 2012-2013, 2013-2014, 2013-2015, 2015-2016, and 2016-2017) were analyzed. A non-experimental, causal comparative research design was used in this study in which Texas archival data were analyzed for the 2012-2013 through the 2016-2017 school years. Inferential statistical procedures were calculated to determine the differences in college readiness in reading, in mathematics, and in both subjects by ethnicity/race (i.e., Black and White students in study one and Hispanic and White students in study two) and gender in study three. In the first investigation, White students were statistically significantly more college ready in reading, in mathematics, and in both subjects than were Black students in each of the five school years. In the second study, White students were statistically significantly more college ready in reading, in mathematics, and in both subjects than were Hispanic students in all five school years. In the third investigation, results were mixed as girls were statistically significantly more college ready in reading in three school years; boys were more college ready in mathematics in four school years; and girls were more college ready in both subjects in three school years. Effect sizes for the first two studies were moderate to large, whereas the effect sizes for the gender differences study were small.
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; ...however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
... another interpretation of these results is possible. Because group environment was measured using self-report measures, it is possible that patients with personality characteristics that are ...likely to produce good outcomes in CBT (such as task orientation or internal locus of control) perceive the group in a more independence-fostering way than do other group members; other articles examining CBT group treatments for MDD have found that perceived mastery over events and perceptions of selfcontrol lead to better outcomes (Hoberman et al., 1988; Rehm, 1983).
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