Allopolyploids of the Genus Elymus (Triticeae, Poaceae): a Phylogenetic Perspective

The wheat tribe, Triticeae, includes many genomically distinct polyploid taxa. Elymus is an entirely allopolyploid genus, with all species containing the St genome of Pseudoroegneria. The St genome may be combined with one or more distinct genomes representing multiple, diverse diploid donors from throughout the tribe. This study includes a simultaneous phylogenetic analysis of new and previously published data from several distinct Elymus groups, including North American and Eurasian StStHH tetraploids, in which the H genome is derived from Hordeum, Eurasian StStYY tetraploids, in which the Y genome is derived from an unknown donor, and a putative StStStStHH hexaploid. Elymus species were analyzed with a broad sample of diploid genera from within the tribe using a combination of molecular data from the chloroplast and the nuclear genomes. The data confirm the genomic constitution of the StStHH and StStYY tetraploids, but do not provide additional information on the identity of the Y-genome donor. The genomic diversity in the hexaploid is greater than expected, inconsistent with the hypothesis of an StStStStHH genome complement

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective

<p>Abstract</p> <p>Background</p> <p><it>Stowaway </it>elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs). The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing <it>Stowaway </it>activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss.</p> <p>Results</p> <p>A <it>Stowaway</it>-like element resides within the fourth intron of a β-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the β-amylase gene tree topology, and in light of sequence comparisons of the β-amylase elements to Triticeae <it>Stowaway </it>elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages) and two flanking deletions. The sequences that do contain elements are polyphyletic on the β-amylase tree, and their elements are divergent at the sequence level. The β-amylase elements do not form a monophyletic group relative to other <it>Stowaway </it>elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another.</p> <p>Conclusion</p> <p>Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a <it>Stowaway</it>-like element has undergone multiple deletions from and insertions into the same site in β-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of <it>Stowaway </it>polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide insights into the dynamics of element evolution over an extended time scale. The historical perspective provided by a phylogenetic approach is complementary to the few studies in which ongoing MITE activity has been documented.</p

Circuit architecture explains functional similarity of bacterial heat shock responses

Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TF). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator sigma32 in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical model of the two systems focusing on the negative feedbacks, where free chaperons suppress sigma32 activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constrains on chaperone-TF binding affinities: the binding constant of free sigma32 to chaperon DnaK, known to be in 100 nM range, set the lower limit of amount of free chaperon that the system can sense the change at the heat shock, while the binding affinity of HrcA to chaperon GroE set the upper limit and have to be rather large extending into the micromolar range.Comment: 17 pages, 5 figure

Coinage Metal Bis(amidinate) Complexes as Building Blocks for Self‐Assembled One‐Dimensional Coordination Polymers

The pyridyl functionalized amidinate [{PyC≡CC(NDipp)$_{2}$}Li(thf)$_{2}$]n was used to synthesize a series of bis-amidinate complexes [{PyC≡CC(NDipp)$_{2}$}$_{2}$M$_{2}$] (M=Cu, Ag, Au) with fully supported metallophilic interactions. These metalloligands were then used as building blocks for the synthesis of one-dimensional heterobimetallic coordination polymers using Zn(hfac)$_{2}$ (hfac=hexaflouroacetylacetonate) for self-assembly. Interestingly, the three coordination polymers [{PyC≡CC(NDipp)$_{2}$}$_{2}$M$_{2}$][Zn(hfac)$_{2}$] (M=Cu, Ag, Au), exhibit a zig zag shape in the solid state. To achieve linear coordination geometry other connectors such as M’(acac) (M’=Ni, Co) (acac=acetylacetonate) were investigated. The thus obtained compounds [{PyC≡CC(NDipp)$_{2}$}$_{2}$Cu$_{2}$][M’(acac)$_{2}$] (M’=Ni, Co) are indeed linear heterobimetallic coordination polymers featuring a metalloligand backbone with fully supported metallophilic interactions

Stress-Induced Transcriptomic Changes in Females with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reveal Disrupted Immune Signatures

Conceptualization, L.N.; methodology, D.J.V.B. and L.N.; validation, E.O. and L.N.; formal analysis, D.J.V.B., J.G., M.P. (Melanie Perez), O.Z., M.P. (Meha Pandya), and L.N.; investigation, J.G., A.J., M.P. (Melanie Perez), O.Z., F.C. and E.O.; resources, N.K. and L.N.; data curation, D.J.V.B., J.G., A.J., M.P. (Melanie Perez), O.Z., M.P. (Meha Pandya) and E.O.; writing— original draft preparation, J.G.; writing—review and editing, J.G., E.O. and L.N.; supervision, L.N.; project administration, L.N.; funding acquisition, N.K. and L.N. All authors have read and agreed to the published version of the manuscript.Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic, complex multi-organ illness characterized by unexplained debilitating fatigue and post-exertional malaise (PEM), which is defined as a worsening of symptoms following even minor physical or mental exertion. Our study aimed to evaluate transcriptomic changes in ME/CFS female patients undergoing an exercise challenge intended to precipitate PEM. Our time points (baseline before exercise challenge, the point of maximal exertion, and after an exercise challenge) allowed for the exploration of the transcriptomic response to exercise and recovery in female patients with ME/CFS, as compared to healthy controls (HCs). Under maximal exertion, ME/CFS patients did not show significant changes in gene expression, while HCs demonstrated altered functional gene networks related to signaling and integral functions of their immune cells. During the recovery period (commonly during onset of PEM), female ME/CFS patients showed dysregulated immune signaling pathways and dysfunctional cellular responses to stress. The unique functional pathways identified provide a foundation for future research efforts into the disease, as well as for potential targeted treatment options.This study was supported by NIH award 1R15NS087604-01A1 and Presidential Faculty Research and Development Grant (PFRDG17) from Nova Southeastern University (all awarded to LN). We are grateful to all the participants who took part in the studies. The study used PBMC samples collected under NIH awards 5R01NS090200-02 (co-PI: NK) and 5R01AR057853-04 (PI: NK). The sponsors had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Opinions, interpretations, conclusions, and recommendations are those of the author and are not necessarily endorsed by the National Institute of Health.Medicin

A Longitudinal Study

Adverse experiences interact with individual vulnerability in the etiology of mental disorders, but due to the paucity of longitudinal studies, their precise interplay remains unclear. Here, we investigated how individual differences in threat responsiveness modulated adjustments in negative affect during the COVID-19 pandemic. Participants (N = 441) underwent a fear conditioning and generalization experiment between 2013 and 2020 and were reassessed regarding anxiety and depression symptoms after the pandemic outbreak. Participants showed increased levels of negative affect following pandemic onset, which were partly modulated by laboratory measures of threat responsiveness. Decreased differentiation of threat and safety signals in participants with higher prepandemic depression and anxiety scores in the laboratory assessment were most predictive of increased symptom levels after the onset of the pandemic. However, effects were small and should be replicated in independent samples to further characterize how individual differences in threat processing interact with adverse experiences in the development of psychopathology.Peer Reviewe

Inorganic Fillers and Their Effects on the Properties of Flax/PLA Composites after UV Degradation

Data Availability Statement: The data that support the findings of this study are available on request from the corresponding author.Copyright © 2023 by the authors. The present investigation seeks to assess the impact of fillers on the mechanical characteristics of entirely biodegradable composites, introducing an advanced solution to fulfil long-term durability demands within point-of-purchase (POP) industries. The inclusion of calcium carbonate (CaCO3) fillers on the various properties of the flax fibre-reinforced composites, after accelerated irradiation in an ultraviolet (UV) radiation exposure has been investigated in the present study. Different types of flax fibre-reinforced poly lactic acid (PLA) biocomposites (with and without filler) were fabricated. The mechanical (tensile and flexural), and physical properties of the specimens were assessed after 500 h of exposure to accelerated UV irradiation of 0.48 W/m2 at 50 °C and were compared with those of the unexposed specimens. The results indicate that the presence of the inorganic filler significantly improved the performance of the biocomposites compared to the unfilled biocomposites after UV exposure. After adding 20% of fillers, the tensile strength was increased by 2% after UV degradation, whereas the biocomposite without filler lost 18% of its strength after UV exposure. This can be attributed to the change in the photo-degradation of the PLA due to the presence of the CaCO3 filler, which acts as a safeguard against UV light penetration by creating a protective barrier. The scanning electron microscopy (SEM) images of the degraded specimen surface show substantial difference in the surface topography of the composites with and without fillers.INTERREG VA Program, FLOWER project, grant number 23