Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mohl, J. E., Fetcher, N., Stunz, E., Tang, J., & Moody, M. L. Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event. Scientific Reports, 10(1), (2020): 8990, doi:10.1038/s41598-020-65693-8.Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.We thank Thomas Parker for providing crucial logistical support at Toolik Field station and Darrel Dech, Stephen Turner, and Mayra Melendez for assistance in field sampling. Funding for this research was provided through the National Science Foundation (NSF/PLR 1418010 to NF, NSF/PLR 1417645 to MLM, NSF/PLR 1417763 to JT) and JEM received funding in part from NIH Grant #5G12RR007592 from the National Center for Research Resources (NCRR)/NIH to UTEP’s Border Biomedical Research Center. Significant logistic support came from Toolik Field Station and the Arctic LTER (NSF/PLR 1637459)

Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum0

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM

Human macrophage polarization in the response to

Infection with Mycobacterium leprae, the causative organism of leprosy, is still endemic in numerous parts of the world including the southwestern United States. The broad variation of symptoms in the leprosy disease spectrum range from the milder tuberculoid leprosy (paucibacillary) to the more severe and disfiguring lepromatous leprosy (multibacillary). The established thinking in the health community is that host response, rather than M. leprae strain variation, is the reason for the range of disease severity. More recent discoveries suggest that macrophage polarization also plays a significant role in the spectrum of leprosy disease but to what degree it contributes is not fully established. In this study, we aimed to analyze if different strains of M. leprae elicit different transcription responses in human macrophages, and to examine the role of macrophage polarization in these responses. Genomic DNA from three different strains of M. leprae DNA (Strains NHDP, Br4923, and Thai-53) were used to stimulate human macrophages under three polarization conditions (M1, M1-activated, and M2). Transcriptome analysis revealed a large number of differentially expressed (DE) genes upon stimulation with DNA from M. leprae strain Thai-53 compared to strains NHDP and Br4923, independent of the macrophage polarization condition. We also found that macrophage polarization affects the responses to M. leprae DNA, with up-regulation of numerous interferon stimulated genes. These findings provide a deeper understanding of the role of macrophage polarization in the recognition of M. leprae DNA, with the potential to improve leprosy treatment strategies

Identification of novel point mutations in c-kit gene from Leukemia cases: a study from Lucknow, Uttar Pradesh, India

The c-kit gene is a receptor tyrosine kinase (RTK) class III that is expressed in early hematopoietic progenitor cells. Aberrantly activated RTK and related downstream signaling partners have been reported as key elements in the molecular pathogenesis of several malignancies. Within the c-kit gene exon-11 is the most frequent site for mutations in different kinds of tumours. Mutations in c-kit gene may enhance or interfere with the ability of c-kit receptor to initiate the intracellular pathways resulting in cell proliferation. Therefore, we aimed to screen the mutations in c-kit gene at exon-8 and -11 in malignant Leukemias. Ninety Leukemia cases were studied and analyzed by mutation- specific PCR-SSCP followed by DNA sequencing. Twenty point mutations were detected in eight AML (acute myeloid Leukemia) cases within exon-11 which includes Tyr568Ser, Ile571Thr, Thr574Pro, Gln575His, Tyr578Pro, Asp579His, His580Gln, Arg586Thr, Asn587Asp and Arg588Met. The substitutions Lys550Asn, Ile571Leu and Trp582Ser were observed in two independent cases and four novel point mutations at codons Ile563Lys, Val569Leu, Tyr570Ser, and Pro577Ser. Further, six point mutations were detected at exon-8 in six cases (four AML and two CML cases), comprising three novel mutations Asn423Asp, Gln448Thr, and Gln448His. The point mutations Thr417Asp, Tyr418Phe, and Leu421His were observed, but were detected only in three cases. These observations suggest that mutations in c-kit gene might represent a useful molecular genetic marker in Leukemia and incidence of mutation at exon- 8 and -11 is high and might be involve in pathogenesis of AML. Resumen El gen c-kit, que codifica para un receptor tirosina quinasa (RTK) de clase III, se expresa en las primeras células progenitoras hematopoyéticas. La activación de este RTK y su vía de señalización se encuentran involucradas en la patogénesis molecular de varias enfermedades. La mutación del gen c-kit en el exón 11 es una de las mutaciones más frecuentemente reportadas en diferente tipos de tumores. Mutaciones en c-kit podrían incrementar o interferir con la habilidad del receptor c-kit para iniciar la activación de cascadas de señalización intracelulares responsables en la proliferación celular. Por estas razones, estudiamos las mutaciones del gen c-kit en el exon 8 y 11 en casos con Leucemias. Noventa casos de Leucemia en la India fueron estudiados mediante PCR SSCP, seguida por secuenciación de DNA. Veinte mutaciones puntuales fueron detectadas en el exon 11 en tan solo ocho de los casos con AML (leucemia mieloide aguda), entre las que encontraron las mutaciones Tyr568Ser, Ile571Thr, Thr574Pro, Gln575His, Tyr578Pro, Asp579His, His580Gln, Arg586Thr, Asn587Asp y Arg588Met. Las sustituciones Lys550Asn, Ile571Leu y Trp582Ser fueron observadas en tan solo dos casos. Además, cuatro nuevas mutaciones para los codones Ile563Lys, Val569Leu, Tyr570Ser, y Pro577Ser se observaron en este estudio. En el exon 8, seis mutaciones puntuales fueron observadas y en seis de los casos (cuatro en AML y dos en CML) encontramos tres nuevas mutaciones Asn423Asp, Gln448Thr y Gln448His. Sin embargo, las mutaciones puntuales Thr417Asp, Tyr418Phe y Leu421His fueron observadas en varias ocasiones, pero en tan solo tres de los casos estudiados. Estas observaciones sugieren que las mutaciones en c-kit podrían representar un marcador genético para Leucemia. La incidencia en la mutación del exon 8 y 11 es elevada y podría estar relacionada con la patogénesis de la AML. Palabras clave: c-kit, exones 8 y 11, Leucemia, mutación, SSCP PAGE

Prediction of O-Glycosylation in Proteins for Different Polypeptide Galnac-Transferases

Mucin-type O-Glycosylation is a posttranslational modification of proteins found on secreted and cell surface proteins in most animals which serves multiple important biological functions. In humans, mutations and changes in the expression levels of O-glycosylating polypeptide GalNac-transferases (GALNTs) have been linked to diabetes and multiple cancers. In most animals the GALNTs are compose a large family of isoforms with humans having 20 isoforms. Presently, the prediction of the sites that will be O-glycosylated is a difficult task due to each isoforms different substrate preference. In this work ISOGlyP, an isoform specific O-glycosylation prediction program, was redesigned and expanded to incorporate new programming features and to increase its overall accuracy. ISOGlyP was shown to perform as well as NetOglyc4.0, another commonly used O-glycosylation predicting program which lacks GALNT specificity. ISOGlyP was redesigned so that the core prediction program could be accommodate additional functionality, for example the inclusion of new data and the ability to perform further data analyses, in addition to providing online access at ISOGlyP.utep.edu via a web.py framework. This included the recognition of the effects of prior GalNAc glycosylation of the peptide and the differences between the glycosylation of threonine and serine residues. One novel feature that was developed the ability to generate a list of peptide sequences specific for one or more GALNTs with the exclusion of other GALNTs. To further increase the accuracy of the prediction additional features, such as protein structure, predicted protein disorder, coiled regions and relative solvent accessibility, were tested for incorporation into the predictive algorithm. Finally, an iterative approach to mimic the O-glycosylation of a protein with multiple glycosites was created. This approach will help us model how the presence of different sets of transferases could alter the overall glycosylation of a protein. It is anticipated that ISOGlyP, by linking GALNTs to the sites that they glycosylate, will be an invaluable tool for the prediction and interpretation of mucin type O-glycosylation, from which a better understand the biological roles of mucin type O-glycosylation can be obtained

HIV-1 Induced Bystander Apoptosis

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What Makes GPCRs from Different Families Bind to the Same Ligand?

G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs

RNA Post-transcriptional Modifications of an Early-Stage Large-Subunit Ribosomal Intermediate

Protein production by ribosomes is fundamental to life, and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all of the ribosome assembly intermediates and on each pathway. There are 26 RNA post-transcriptional modifications in 23S RNA of the mature Escherichia coli (E. coli) large ribosomal subunit. The levels of these modifications have been investigated extensively only for a small number of large subunit intermediates and under a limited number of cellular and environmental conditions. In this study, we determined the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine, 5-hydroxycytosine, and seven pseudouridines in an early-stage E. coli large-subunit assembly intermediate with a sedimentation coefficient of 27S. The 27S intermediate is one of three large subunit intermediates accumulated in E. coli cells lacking the DEAD-box RNA helicase DbpA and expressing the helicase inactive R331A DbpA construct. The majority of the investigated modifications are incorporated into the 27S large subunit intermediate to similar levels to those in the mature 50S large subunit, indicating that these early modifications or the enzymes that incorporate them play important roles in the initial events of large subunit ribosome assembly

Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks

Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens

The Genomic Landscape of a Restricted ALL Cohort from Patients Residing on the U.S./Mexico Border

Next-generation sequencing (NGS) has identified unique biomarkers yielding new strategies in precision medicine for the treatment of Acute lymphoblastic leukemia (ALL). Hispanics show marked health disparities in ALL, often absent in clinical trials or cancer research. Thus, it is unknown whether Hispanics would benefit equally from curated data currently guiding precision oncology. Using whole-exome sequencing, nine ALL patients were screened for mutations within genes known to possess diagnostic, prognostic and therapeutic value. Genes mutated in Hispanic ALL patients from the borderland were mined for potentially pathogenic variants within clinically relevant genes. KRAS G12A was detected in this unique cohort and its frequency in Hispanics from the TARGET-ALL Phase II database was three-fold greater than that of non-Hispanics. STAT5B N642H was also detected with low frequency in Hispanic and non-Hispanic individuals within TARGET. Its detection within this small cohort may reflect a common event in this demographic. Such variants occurring in the MAPK and JAK/STAT pathways may be contributing to Hispanic health disparities in ALL. Notable variants in ROS1, WT1, and NOTCH2 were observed in the ALL borderland cohort, with NOTCH2 C19W occurring most frequently. Further investigations on the pathogenicity of these variants are needed to assess their relevance in ALL