bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequences of Arthrobacter spp. that use a modified sulfoglycolytic Embden-Meyerhof-Parnas pathway
Authors: Kaur Arashdeep , van der Peet Phillip L. , Mui Janice W.-Y. , Herisse Marion , Pidot Sacha , Williams Spencer J. 
Published: November 2021

AbstractBackgroundSulfoglycolysis pathways enable the breakdown of the sulfosugar sulfoquinovose and environmental recycling of its carbon and sulfur content. Several pathways exist for the breakdown of sulfoquinovose that usually lead to production of C3-sulfonates (sulfolactate and 2,3-dihydroxypropanesulfonate) that are excreted and sustain secondary bacterial communities. The prototypical sulfoglycolytic pathway is a variant of the classical Embden-Meyerhof-Parnas pathway that has been described in gram-negative Escherichia coli and results in production of 2,3-dihydroxypropanesulfonate.ResultsWe used enrichment cultures to discover new sulfoglycolytic bacteria from Australian soil samples. Two gram-positive Arthrobacter spp. were isolated that produced sulfolactate as the metabolic end-product. Genome sequences identified a modified sulfoglycolytic Embden-Meyerhof-Parnas (sulfo-EMP) gene cluster that retained the core sulfoglycolysis genes encoding metabolic enzymes, but featuring the replacement of the gene encoding sulfolactaldehyde (SLA) reductase with SLA dehydrogenase, and the absence of sulfoquinovosidase and sulfoquinovose mutarotase genes. The gene clusters were broadly conserved across a range of other sequenced Actinobacteria.ConclusionsWe report the first gram-positive soil bacteria that utilize sulfo-EMP pathways to metabolize SQ. Excretion of sulfolactate is consistent with an aerobic saprophytic lifestyle. This work broadens our knowledge of the sulfo-EMP pathway to include soil bacteria.
Prediction of molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p-value and robust rank aggregation
Authors: Umesh Anushri , Guttula Praveen Kumar , Gupta Mukesh Kumar 
Published: November 2021

AbstractBovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. E.coli and S.aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E.coli is an opportunistic environmental pathogen, and S.aureus is a contagious pathogen. This study was designed to predict molecular markers of bovine mastitis by meta-analysis of differentially expressed genes (DEG) in E.coli or S.aureus infected mammary epithelial cells (MECs) using p-value combination and robust rank aggregation (RRA) methods. High throughput transcriptome of bovine (MECs, infected with E.coli or S.aureus, were analyzed, and correlation of z-scores were computed for the expression datasets to identify the lineage profile and functional ontology of DEGs. Key pathways enriched in infected MECs were deciphered by Gene Set Enrichment Analysis (GSEA), following which combined p-value and RRA were used to perform DEG meta-analysis to limit type I error in the analysis. The miRNA-Gene networks were then built to uncover potential molecular markers of mastitis. Lineage profiling of MECs showed that the gene expression levels were associated with mammary tissue lineage. The up-regulated genes were enriched in immune-related pathways whereas down-regulated genes influenced the cellular processes. GSEA analysis of DEGs deciphered the involvement of Toll-like receptor (TLR), and NF- Kappa B signalling pathway during infection. Comparison after meta-analysis yielded with genes ZC3H12A, RND1 and MAP3K8 having significant expression levels in both E.coli and S.aureus dataset and on evaluating miRNA-Gene network 7 pairs were common to both sets identifying them as potential molecular markers.
A Unified Genomic Mechanism of Cell-Fate Change
Authors: Tsuchiya Masa , Giuliani Alessandro , Zimatore Giovanna , Erenpreisa Jekaterina , Yoshikawa Kenichi 
Published: November 2021

AbstractThe purpose of our studies is to elucidate the nature of massive control of whole genome expression with a particular emphasis on cell-fate change. Whole genome expression is coordinated by the emergence of a critical point (CP: a peculiar set of bi-phasic genes) through the genome-engine. In response to stimuli, the genome expression self-organizes three critical states, each exhibiting distinct collective behaviors with its center of mass acting as a local attractor, coexisting with whole genome attractor (GA). Genome-engine mechanism accounts for local attractors interaction in phase space. The CP acts as the organizing center of cell-fate change, and its activation makes local perturbation spread over the genome affecting GA. The activation of CP is in turn elicited by ‘hot-spots’, genes with elevated temporal variance, normally in charge to keep genome expression at pace with microenvironment fluctuations. When hot-spots oscillation exceeds a given threshold, the CP synchronizes with the GA driving genome expression state transition. The expression synchronization wave invading the entire genome depends on the power law fusion-bursting dynamics of silencing pericentromere-associated heterochromatin domains and the consequent folding-unfolding status of transcribing euchromatin domains. The proposed mechanism is a unified step toward a time-evolutional transition theory of biological regulation.
Long-term culture system for deep-sea mussels Gigantidas childressi
Authors: Hiebenthal Claas , Gehlert Finn-Ole , Schmidt Mark , Reusch Thorsten B. H. , Melzner Frank 
Published: November 2021

AbstractThe simulation of deep-sea conditions in laboratories is technically challenging but necessary for experiments that aim at a deeper understanding of physiological mechanisms or host-symbiont interactions of deep-sea organisms. In a proof-of-concept study, we designed a recirculating system for long-term culture (>2 years) of deep-sea mussels Gigantidas childressi (previously Bathymodiolus childressi). Mussels were automatically (and safely) supplied with a maximum stable level of ~60 µM methane in seawater using a novel methane-air mixing system. Experimental animals also received daily doses of live microalgae. Condition indices of cultured G. childressi remained high over years, and low shell thickness growth could be detected, which is indicative of positive energy budgets. Using stable isotope data, we demonstrate that G. childressi in our culture system gained energy, both, from digestion of methane oxidizing endosymbionts and from digesting particulate food (microalgae). Limitations of the system, as well as opportunities for future experimental approaches involving deep-sea mussels are discussed.
Emerging Accessibility Patterns in Long Telomeric Overhangs
Authors: Shiekh Sajad , Mustafa Golam , Kodikara Sineth G. , Hoque Mohammed Enamul , Yokie Eric , Portman John J. , Balci Hamza 
Published: November 2021

AbstractWe present single molecule experimental and computational modeling studies investigating the accessibility of human telomeric overhangs of physiologically relevant lengths. We studied 25 different overhangs that contain 4-28 repeats of GGGTTA (G-Tract) sequence and accommodate 1-7 tandem G-quadruplex (GQ) structures. Using FRET-PAINT method, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to available sites. We report accessibility patterns that periodically change with overhang length and interpret these patterns in terms of the underlying folding landscape and folding frustration. Overhangs that have [4n]G-Tracts, (12, 16, 20…), demonstrate the broadest accessibility patterns where the PNA probe accesses G-Tracts throughout the overhang. On the other hand, constructs with [4n+2]G-Tracts, (14, 18, 22…), have narrower patterns where the neighborhood of the junction between single and double stranded telomere is most accessible. We interpret these results as the folding frustration being higher in [4n]G-Tract constructs compared to [4n+2]G-Tract constructs. We also developed a computational model that tests the consistency of different folding stabilities and cooperativities between neighboring GQs with the observed accessibility patterns. Our experimental and computational studies suggest the neighborhood of the junction between single and double stranded telomere is least stable and most accessible, which is significant as this is a potential site where the connection between POT1/TPP1 (bound to single stranded telomere) and other shelterin proteins (localized on double stranded telomere) is established.Significance StatementThe ends of eukaryotic linear chromosomes are capped by telomeres which terminate with a single-stranded overhang. Telomeric overhangs fold into compact structures, called G-quadruplex, that inhibit access to these critical genomic sites. We report single molecule measurements and computational modeling studies probing the accessibility of a set of human telomeric overhangs that covers a significant portion of the physiologically relevant length scale. We observe novel accessibility patterns which have a well-defined periodicity and show that certain regions are significantly more accessible than others. These accessibility patterns also suggest the underlying folding frustration of G-quadruplexes depends on telomere length. These patterns have significant implications for regulating the access of DNA processing enzymes and DNA binding proteins that can target telomeric overhangs.
Particle-associated and free-living microbial assemblages are distinct in a permanently redox-stratified freshwater lake
Authors: Cohen Ashley B. , Klepac-Ceraj Vanja , Butler Kristen , Weber Felix , Garber Arkadiy I. , Christensen Lisa N. , Cram Jacob A. , McCormick Michael L. , Taylor Gordon T. 
Published: November 2021

AbstractMicrobial assemblages associated with biogenic particles are phylogenetically distinct from free-living counterparts, yet biogeochemically coupled. Compositions may vary with organic carbon and inorganic substrate availability and with redox conditions, which determine reductant and oxidant availability. To explore microbial assemblage compositional responses to steep oxygen and redox gradients and seasonal variability in particle and substrate availability, we analyzed taxonomic compositions of particle-associated (PA) and free-living (FL) bacteria and archaea in permanently redox-stratified Fayetteville Green Lake. PA and FL assemblages (> 2.7 µm and 0.2 – 2.7 µm) were surveyed at the peak (July) and end (October) of concurrent cyanobacteria, purple and green sulfur bacteria blooms that result in substantial vertical fluxes of particulate organic carbon. Assemblage compositions varied significantly among redox conditions and size fractions (PA or FL). Temporal differences were only apparent among samples from the mixolimnion and oxycline, coinciding with seasonal hydrographic changes. PA assemblages of the mixolimnion and oxycline shifted from aerobic heterotrophs in July to fermenters, iron-reducers, and denitrifiers in October, likely reflecting seasonal variability in photoautotroph biomass and inorganic nitrogen. Within a light-scattering layer spanning the lower oxycline and upper monimolimnion, photoautotrophs were more abundant in July than in October, when Desulfocapsa, a sulfate-reducing and sulfur-disproportionating bacterium, and Chlorophyte chloroplasts were abundant in PA assemblages. In this layer, microbial activity and cell concentrations were also highest. Below, the most abundant resident taxa were sulfate-reducing bacteria and anaerobic respirers. Results suggest PA and FL assemblage niche partitioning interconnects multiple elemental cycles that involve particulate and dissolved phases.
Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma
Authors: Resztak Justyna , Choe Jane , Nirmalan Shreya , Wei Julong , Bruinsma Julian , Houpt Russell , Alazizi Adnan , Mair-Meijers Henriette E. , Wen Xiaoquan , Slatcher Richard B. , Zilioli Samuele , Pique-Regi Roger , Luca Francesca 
Published: November 2021

AbstractPuberty is an important developmental period marked by hormonal, metabolic and immune changes. Puberty also marks a shift in sex differences in susceptibility to asthma. Yet, little is known about the gene expression changes in immune cells that occur during pubertal development. Here we assess pubertal development and leukocyte gene expression in a longitudinal cohort of 251 children with asthma. We identify substantial gene expression changes associated with age and pubertal development. Gene expression changes between pre- and post-menarcheal females suggest a shift from predominantly innate to adaptive immunity. We show that genetic effects on gene expression change dynamically during pubertal development. Gene expression changes during puberty are correlated with gene expression changes associated with asthma and may explain sex differences in prevalence. Our results show that molecular data used to study the genetics of early onset diseases should consider pubertal development as an important factor that modifies the transcriptome.
Variation in gene expression patterns across a conifer hybrid zone highlights the architecture of adaptive evolution under novel selective pressures
Authors: Menon Mitra , Swenson Jared , Moler Ehren , Whipple Amy V. , Waring Kristen M. , Eckert Andrew J. 
Published: November 2021

SummaryVariation in gene expression among natural populations are key contributors to adaptive evolution. Understanding the architecture underlying adaptive trait evolution provides insights into the adaptive potential of populations exposed to novel selective pressures.We investigated patterns and processes driving trait differentiation under novel climatic conditions by combining common garden experiments with transcriptome-wide datasets obtained from Pinus strobiformis - Pinus flexilis hybrid zone populations.We found strong signals of genotype-environment interactions at the individual transcript and the co-expression module level, a marked influence of drought related variables on adaptive evolution and an environment dependent influence of P. flexilis ancestry on survival. Using co-expression network connectivity as a proxy for pleiotropy we highlight that adaptive transcripts were pleiotropic across both gardens and modules with strong population differentiation exhibited lower preservation across gardens.Our work highlights the utility of integrating transcriptomics with space-for-time substitution studies to evaluate the adaptive potential of long-lived species. We conclude by suggesting that the combination of pleiotropic trait architectures and substantial genetic variation may enable long-lived forest tree species to respond to rapid shift in climatic conditions.
Highly efficient Runx1 enhancer eR1-mediated genetic engineering for fetal, child and adult hematopoietic stem cells
Authors: Koh Cai Ping , Bahirvani Avinash Govind , Wang Chelsia Qiuxia , Yokomizo Tomomasa , Ng Cherry Ee Lin , Du Linsen , Tergaonkar Vinay , Voon Dominic Chih-Cheng , Hosoi Hiroki , Sonoki Takashi , Michelle Mok Meng Huang , Niibori-Nambu Akiko , Zhang Yi , Perkins Archibald S. , Hossain Zakir , Tenen Daniel G. , Ito Yoshiaki , Venkatesh Byrappa , Osato Motomi 
Published: November 2021

SummaryA cis-regulatory genetic element which targets gene expression to stem cells, termed stem cell enhancer, serves as a molecular handle for stem cell-specific genetic engineering. Here we show the generation and characterization of a tamoxifen-inducible CreERT2 transgenic (Tg) mouse employing previously identified hematopoietic stem cell (HSC) enhancer for Runx1, eR1 (+24m). Kinetic analysis of labeled cells after tamoxifen injection and transplantation assays revealed that eR1-driven CreERT2 activity marks dormant adult HSCs which slowly but steadily contribute to unperturbed hematopoiesis. Fetal and child HSCs which are uniformly or intermediately active were also efficiently targeted. Notably, a gene ablation at distinct developmental stages, enabled by this system, resulted in different phenotypes. Similarly, an oncogenic Kras induction at distinct ages caused different spectrums of malignant diseases. These results demonstrate that the eR1-CreERT2 Tg mouse serves as a powerful resource for the analyses of both normal and malignant HSCs at all developmental stages.
Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution
Authors: Palivec Vladimír , Johannessen Christian , Kaminský Jakub , Martinez-Seara Hector 
Published: November 2021

AbstractSugars are crucial components in biosystems and industrial applications. In aqueous environments, the natural state of short saccharides or charged glycosaminoglycans is floating and wiggling in solution. Therefore, tools to characterize their structure in a native aqueous environment are crucial but not always available. Here, we show that a combination of Raman/ROA and, on occasions, NMR experiments with Molecular Dynamics (MD) and Quantum Mechanics (QM) is a viable method to gain insights into structural features of sugars in solutions. Combining these methods provides information about accessible ring puckering conformers and their proportions. It also provides information about the conformation of the linkage between the sugar monomers, i.e., glycosidic bonds, allowing for identifying significantly accessible conformers and their relative abundance. For mixtures of sugar moieties, this method enables the deconvolution of the Raman/ROA spectra to find the actual amounts of its molecular constituents, serving as an effective analytical technique. For example, it allows calculating anomeric ratios for reducing sugars and analyzing more complex sugar mixtures to elucidate their real content. Altogether, we show that combining Raman/ROA spectroscopies with simulations is a versatile method applicable to saccharides. It allows for accessing many features with precision comparable to other methods routinely used for this task, making it a viable alternative. Furthermore, we prove that the proposed technique can scale up by studying the complicated Raffinose trisaccharide, and therefore, we expect its wide adoption to characterize sugar structural features in solution.
Heat-induced transposition increases drought tolerance in Arabidopsis
Authors: Thieme Michael , Brêchet Arthur , Keller Bettina , Bucher Etienne , Roulin Anne C. 
Published: November 2021

AbstractEukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognized as a source of genetic diversity and powerful drivers of evolution. Yet, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scare. Here, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in Arabidopsis thaliana. We exposed high-copy TE lines (hcLines) with up to ∼8 fold increased copy numbers of the heat-responsive ONSEN TE (AtCOPIA78) to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis and water consumption. This is one of the rare empirical examples substantiating the adaptive potential of mobilized stress-responsive TEs in eukaryotes. Our work sheds light on the relationship between TEs and their hosts and demonstrates the importance of TE-mediated loss-of-function mutations in stress adaptation, particularly in the face of global warming.
Brain monoaminergic activity during predator inspection in the Trinidadian guppy (Poecilia reticulata)
Authors: Dimitriadou S. , Winberg S. , Thörnqvist P.-O. , Croft DP. , Darden SK. 
Published: November 2021

AbstractTo understand the processes underpinning social decision-making, we need to determine how internal states respond to information gathered from the social environment. Brain monoamine neurotransmitters are key in the appraisal of the social environment and can reflect the internal state underlying behavioural responses to social stimuli. Here we determined the effects of conspecific partner cooperativeness during predator inspection on brain monoamine metabolic activity in Trinidadian guppies (Poecilia reticulata). We quantified the concentration of dopamine, serotonin and their metabolites across brain sections sampled immediately after ostensibly experiencing cooperation or defection from social partners whilst inspecting a predator model. Our results indicate dopaminergic and serotonergic activity differs with the cooperativeness experienced; these different neurotransmission profiles are likely to affect the expression and regulation of downstream behaviours that ultimately contribute to the patterning of cooperative interactions among individuals in the population.List of abbreviations used
SRSF3 is a key regulator of epicardial formation
Authors: Lupu Irina-Elena , Bruche Susann , Chakrabarti Anob M. , McCracken Ian R. , Carsana Tamara , Redpath Andia N. , Smart Nicola 
Published: November 2021

AbstractThe epicardium is a fundamental regulator of cardiac development and regeneration, functioning to secrete essential growth factors and to produce epicardium-derived cells (EPDCs) that contribute most coronary mural cells and cardiac fibroblasts. The molecular mechanisms controlling epicardial formation have not been fully elucidated. In this study, we found that the RNA-binding protein SRSF3 is highly expressed in the embryonic proepicardium and epicardial layer. Deletion ofSrsf3from the murine proepicardium led to proliferative arrest, which prevented proper epicardial formation. Induction ofSrsf3deletion after the proepicardial stage resulted in impaired epicardial proliferation and EPDC formation by E13.5. Single-cell RNA-sequencing showed SRSF3-depleted epicardial cells were eliminated, however, the surviving non-recombined cells became hyperproliferative and, remarkably, compensated for the early deficit, via a mechanism that involvedSrsf3up-regulation This unexpected finding attests the importance of SRSF3 in controlling epicardial proliferation, and highlights the significant confounding effect of mosaic recombination on embryonic phenotyping. Mapping the SRSF3–RNA interaction network by endogenous irCLIP identified binding to major cell cycle regulators, such asCcnd1andMap4k4, with both splicing and non-splicing roles. This research defines SRSF3 as a key regulator of epicardial cell proliferation.