bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems
Authors: McGonigle Julia M. , Lang Susan Q. , Brazelton William J. 
Published: November 2019

ABSTRACTThe Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by low-abundance Chloroflexi species. Additionally, we present evidence that metabolically diverse, formate-utilizing Sulfurovum species are living in the transition zone between the interior and exterior of the chimneys.IMPORTANCEPrimitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also extraterrestrial ecosystems that might support life. The microscopic life covering towering chimney structures at the Lost City has been well characterized, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.
High throughput, error corrected Nanopore single cell transcriptome sequencing
Authors: Lebrigand Kevin , Magnone Virginie , Barbry Pascal , Waldmann Rainer 
Published: November 2019

ABSTRACTDroplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. We introduce an approach that combines Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length sequence information with the 10×Genomics single cell isolation system. This allows to examine differential RNA splicing and RNA editing at a single cell level.
The human α-defensin-derived peptide HD5(1-9) inhibits cellular attachment and entry of human cytomegalovirus
Authors: Böffert Rebecca , Businger Ramona , Preiß Hannes , Ehmann Dirk , Truffault Vincent , Simon Claudia , Ruetalo Natalia , Hamprecht Klaus , Müller Patrick , Wehkamp Jan , Schindler Michael 
Published: November 2019

ABSTRACTHuman cytomegalovirus (HCMV) infection causes severe illness in newborns and immunocompromised patients. Since treatment options are limited there is an unmet need for new therapeutic approaches. Defensins are cationic peptides, produced by various human tissues, which serve as antimicrobial effectors of the immune system. Furthermore, some defensins are proteolytically cleaved, resulting in the generation of smaller fragments with increased activity. Together, this led us to hypothesize that defensin-derived peptides are natural human inhibitors of virus infection with low toxicity. We screened several human defensin HNP4- and HD5-derived peptides and found HD5(1-9) to be antiviral without toxicity at high concentrations. HD5(1-9) inhibited HCMV cellular attachment and thereby entry and was active against primary as well as a multiresistant HCMV isolate. Moreover, cysteine and arginine residues were identified to mediate the antiviral activity of HD5(1-9). Altogether, defensin-derived peptides, in particular HD5(1-9), qualify as promising candidates for further development as a novel class of HCMV entry inhibitors.AUTHOR SUMMARYDefensins are peptides produced by various human organs which take part in the natural defense against pathogens. Recently, it has been shown that defensins are further cleaved to smaller peptides that have high intrinsic anti-microbial activity. We here challenged the hypothesis that these peptides might have antiviral activity, and due to their presumably natural occurrence, low toxicity. Indeed, we found one peptide fragment that turned out to block the attachment of the human cytomegalovirus (HCMV) to cells. Furthermore, this peptide did not show toxicity in various cellular assays or impede the embryonic development of zebrafish at the concentrations used to block HCMV. This is important, since HCMV is one of the most important viral congenital infections. Altogether, our results hold promise for the development of a new class of antivirals against HCMV.
Immunoglobulin J chain as a non-invasive indicator of pregnancy in the cheetah (Acinonyx jubatus)
Authors: Byron Michael J. , Koester Diana C. , Edwards Katie L. , Mozdziak Paul E. , Farin Charlotte E. , Crosier Adrienne E. 
Published: November 2019

AbstractThe North American cheetah population serves as a reservoir for the species, and acts as a research population to help understand the unique biology of the species. Little is known about the intrauterine physiology of the cheetah, including embryo differentiation, implantation, and the development of the placenta. After mating, cheetah females frequently experience (30-65% of matings) a non-pregnant luteal phase where progestogen metabolite levels match those found in pregnant females for the first ~55 days of gestation, but parturition does not occur. Immunoglobulin J chain (IgJ) is a molecule that is involved in the activation of the secretory immune response and has been found to be indicative of pregnancy in the cheetah using fecal monitoring. In this study, western blotting was employed to track IgJ abundance in pooled weekly fecal samples following natural breeding or exogenous stimulation to ovulate, and IgJ levels were compared between individuals undergoing a pregnant (n = 12) and non-pregnant (n = 19) luteal phase. It was revealed that IgJ abundance was increased in pregnant females compared to non-pregnant females at week 4 and week 8 post-breeding, indicating the potential modulation of maternal immunity in response to sensitive events such as implantation and the increased secretory activity of the placenta. IgJ levels also tended to be higher early after breeding in females that were bred naturally with intact males compared to exogenously stimulated females with no exposure to seminal plasma, indicating the promotion of maternal tolerance to seminal antigens present upon embryonic implantation. Monitoring fecal IgJ may be a potential method to determine gestational status in the cheetah and will aid future conservation efforts of the species.
Function of ex vivo stimulated Natural killer T cells from patients with chronic HIV-1 infection
Authors: Thapa Prakash , Nehete Pramod , He Hong , Nehete Bharti , Buchl Stephanie J. , Bull Lara M. , Lu Hongzhou , Arduino Roberto C. , Sastry K. Jagannadha , Zhou Dapeng 
Published: November 2019

AbstractNatural killer T (NKT) cells are innate immune cells that are responsible for the first line of antiviral defense, through crosstalk with downstream antigen-presenting cells, natural killer cells, and adaptive immune cells. Previous studies have indicated that NKT cell function is severely impaired in patients with chronic HIV-1 infection. It was reported that alpha-galactosylceramide, a potent agonist antigen for NKT cells, failed to trigger the expansion of NKT cells, or the production of anti-viral cytokines by NKT cells from HIV-1 infected patients in an in vitro assay, in which peripheral blood mononuclear cells (PBMCs) were cultured in the presence of alpha-galactosylceramide. In this study, we stimulated banked peripheral blood mononuclear cells from HIV-1-infected patients with dendritic cells (DC) generated ex vivo and loaded with alpha-galactosylceramide. The results showed that NKT cells were expanded in HIV infected subjects except in patients with advanced AIDS. Expanded NKT cells were capable of producing antiviral cytokines. Our results indicate that NKT cells in HIV infected individuals are potential targets for therapeutic intervention.
Genomic landscape of reproductive isolation inLucaniakillifish: The role of sex chromosomes and salinity
Authors: Berdan Emma L. , Fuller Rebecca C. , Kozak Genevieve M. 
Published: November 2019

ABSTRACTUnderstanding how speciation occurs and how reproductive barriers contribute to population structure at a genomic scale requires elucidating the genetic architecture of reproductive isolating barriers. In particular, it is crucial to determine if loci underlying reproductive isolation are genetically linked or if they are located on sex chromosomes, which have unique inheritance and population genetic properties. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are closely related species that have diverged across a salinity gradient and are reproductively isolated by assortative mating, hybrid male infertility, viability of hybrid offspring at high salinities, as well as reduced overall fitness of F2 offspring and backcrosses toL. goodei. We conducted QTL mapping in backcrosses betweenL. parvaandL. goodeito determine the genetic architecture of sex determination, mate attractiveness, fertility, and salinity tolerance. We find that the sex locus appears to be male determining and located on a chromosome that has undergone a Robertsonian fusion inL. parvarelative toL. goodei. We find that the sex locus on the fused chromosome is involved in several genomic incompatibilities, which affect the survival of backcrossed offspring. Among the backcrossed offspring that survived to adulthood, we find that one QTL for male attractiveness toL. goodeifemales is closely linked to this sex locus on chromosome 1. Males homozygous forL. goodeialleles at the sex locus laid more eggs withL. goodeifemales. QTL associated with salinity tolerance were spread across the genome but did not tend to co-localize with reproductive isolation. Thus, speciation in this system appears to be driven by reinforcement and indirect selection against hybrids rather than direct natural selection for salinity tolerance. Our work adds to growing evidence that sex chromosome evolution may contribute to speciation.
EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen
Authors: Marković Vedrana , Cvrčková Fatima , Potocký Martin , Pejchar Přemysl , Kollárová Eva , Kulich Ivan , Synek Lukáš , Žárský Viktor 
Published: November 2019

ABSTRACTPollen development, pollen grain germination and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Pollen grains undergo two major developmental switches: dehydration characterized by metabolic quiescent state, and rehydration upon pollination that leads to extraordinary metabolic and membrane trafficking activity, resulting in germination and rapid tip growth of pollen tubes. To sustain these processes, many plant housekeeping genes evolved their pollen-specific paralogs. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicles to the plasma membrane. Here, we describe that EXO70A2 (At5g52340) is the main exocyst EXO70 isoform in Arabidopsis pollen, which governs the conventional secretory function of the exocyst, analogically to EXO70A1 (At5g03540) in the sporophyte. Our analysis of a CRISPR-generated exo70a2 mutant revealed that EXO70A2 is essential for efficient pollen maturation, pollen grain germination and pollen tube growth. GFP:EXO70A2 was localized similarly to other exocyst subunits to the apical domain in growing pollen tube tips characterized by intensive exocytosis. Moreover, EXO70A2 could substitute for the EXO70A1 function in the sporophyte, indicating functional redundancy of these two closely related isoforms. Phylogenetic analysis revealed that the ancient duplication of EXO70A to two (or more) paralogs, one of which is highly expressed in pollen, occurred independently in monocots and dicots. In summary, EXO70A2 is a crucial component of the exocyst complex in the Arabidopsis pollen required for efficient plant sexual reproduction.
Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
Authors: Shanmuganandam Somasundhari , Hu Yiheng , Strive Tanja , Schwessinger Benjamin , Hall Robyn N. 
Published: November 2019

AbstractEuropean brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of the gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. We analysed the faecal microbiome of wild hares and rabbits from a sympatric environment, additionally comparing Illumina and Nanopore sequencing platforms. The faecal microbiomes varied significantly between hares and rabbits, despite both species occupying a similar habitat. Moreover, we identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria, and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the faecal microbiota between hares and rabbits in Australia may be associated with differences in diet, and potentially behaviour, of the host species in their non-native range, which may influence the environmental impacts that these species have in Australia.
The role of hippocampus during observational learning
Authors: Fuentealba Yerko , Valdés José L 
Published: November 2019

ABSTRACTObservational learning is a fundamental cognitive ability present in several species, where a naïve animal imitates a goal-directed behavior from the observation of a congener which acts as a demonstrator. Recent evidence in bat and rats suggests that hippocampal place cells of an observer may generate a spatial representation of the locations visited by a demonstrator, during spatial navigation. However, it is still unclear whether this hippocampal neural activity is critical for the process of observational learning or if the patterns of activity during observation differ from those emerging from the execution of a spatial memory task previously observed. To test this idea, we assess the role of the hippocampus by pharmacological reversible inactivation during the observation of a spatial learning task, demonstrating a critical role for this structure in observational learning. Then we recorded the neuronal activity of principal pyramidal cells of the same animal when it was observing or solving the memory task, and two different representation of the space emerged after observation or navigation. This evidences demonstrated that the hippocampus is necessary for observational learning and indicated that the observed and executed hippocampal representation are different, confirming the idea that the hippocampus could represent the position of others in the space, and use this information to improve his behavioral performance.
Neuronal Proteostasis is mediated by the switch-like expression of Heme-regulated Kinase 1, acting as both a sensor and effector
Authors: Alvarez-Castelao Beatriz , tom Dieck Susanne , Fusco Claudia M. , Donlin-Asp Paul G. , Perez Julio D. , Schuman Erin M. 
Published: November 2019

AbstractAll cells, including neurons, have regulatory feedback mechanisms that couple protein synthesis and degradation to maintain and optimize protein concentrations in the face of intra- and extracellular perturbations. We examined the feedback between the major protein degradation pathway, the ubiquitin-proteasome system (UPS), and protein synthesis in neurons. When protein degradation by the UPS was inhibited we observed a coordinate dramatic reduction in nascent protein synthesis in both neuronal cell bodies and dendrites. The mechanism for translation inhibition involved the phosphorylation of eIF2a, surprisingly mediated by eIF2a kinase 1, or heme-regulated kinase inhibitor (HRI), known for its sensitivity to heme levels in erythrocyte precursors (Han et al., 2001). Under basal conditions, neuronal expression of HRI is barely detectable. Following proteasome inhibition, HRI protein levels increase owing to stabilization of the short-lived HRI protein and enhanced translation via the increased availability of tRNAs for rare codons. Once expressed, HRI is constitutively active in neurons because endogenous heme levels are so low; HRI activity results in eIF2a phosphorylation and the resulting inhibition of translation. These data demonstrate a novel role for HRI in neurons, acting as an “immediate early protein” that senses and responds to compromised function of the proteasome to restore proteostasis.One sentence summaryProteasome inhibition leads to a compensatory reduction in neuronal protein synthesis via the stabilization and enhanced translation of short-lived HRI kinase, which is constitutively active upon expression owing to low neuronal heme levels.
Structure of the cell-binding component of theClostridium difficilebinary toxin reveals a novel macromolecular assembly
Authors: Xu Xingjian , Godoy-Ruiz Raquel , Adipietro Kaylin A. , Peralta Christopher , Ben-Hail Danya , Varney Kristen M. , Cook Mary E. , Roth Braden M. , Wilder Paul T. , Cleveland Thomas , Grishaev Alexander , Neu Heather M. , Michel Sarah , Yu Wenbo , Beckett Dorothy , Rustandi Richard R. , Lancaster Catherine , Loughney John W. , Kristopeit Adam , Christanti Sianny , Olson Jessica W. , MacKerell Alex D. , Georges Amedee des , Pozharski Edwin , Weber David J. 
Published: November 2019

AbstractTargetingClostridium difficileinfection (CDI) is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent CDI often has a binary toxin termed theC. difficiletoxin (CDT), in addition to the enterotoxins TsdA and TsdB. CDT has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single particle cryoEM, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, two novel di-heptamer structures foractivated CDTb (aCDTb; 1.0 MDa) were solved at atomic resolution including a symmetric (SymCDTb; 3.14 Å) and an asymmetric form (AsymCDTb; 2.84 Å). Roles played by two receptor-binding domains of aCDTb were of particular interest since RBD1 lacks sequence homology to any other known toxin, and the RBD2 domain is completely absent in other well-studied heptameric toxins (i.e. anthrax). ForAsymCDTb, a novel Ca2+binding site was discovered in RBD1 that is important for its stability, and RBD2 was found to be critical for host cell toxicity and the novel di-heptamer fold for both forms of aCDTb. Together, these studies represent a starting point for structure-based drug-discovery strategies to targeting CDT in the most severe strains of CDI.SIGNIFICANCE STATEMENTThere is a high burden fromC. difficileinfection (CDI) throughout the world, and the Center for Disease Control (CDC) reports more than 500,000 cases annually in the United States, resulting in an estimated 15,000 deaths. In addition to the large clostridial toxins, TcdA/TcdB, a thirdC. difficilebinary toxin (CDT) is associated with the most serious outbreaks of drug resistant CDI in the 21stcentury. Here, structural biology and biophysical approaches were used to characterize the cell binding component of CDT, termed CDTb, at atomic resolution. Surprisingly, two novel structures were solved from a single sample that help to explain the molecular underpinnings ofC. difficiletoxicity. These structures will also be important for targeting this human pathogen via structure-based therapeutic design methods.
Transcriptional changes are regulated by metabolic pathway dynamics but decoupled from protein levels
Authors: Feltham Jack E. , Xi Shidong , Murray Struan C. , Wouters Meredith , Urdiain-Arraiza Julian , Heilig Raphael , George Charlotte , Townley Anna F. , Roberts Emile , Kessler Benedikt M. , Liberatori Sabrina , Charles Philip D. , Angel Andrew , Fischer Roman , Mellor Jane 
Published: November 2019

AbstractTranscription is necessary for the synthesis of new proteins, often leading to the assumption that changes in transcript levels lead to changes in protein levels which directly impact a cell’s phenotype. Using a synchronized biological rhythm, we show that despite genome-wide partitioning of transcription, transcripts and translation levels into two phase-shifted expression clusters related to metabolism, detectable protein levels remain constant over time. This disconnect between cycling translation and constant protein levels can be explained by slow protein turnover rates, with overall protein levels maintained by low level pulses of new protein synthesis. Instead, rhythmic post-translational regulation of the activities of different proteins, influenced by the metabolic state of the cells, appears to be key to coordinating the physiology of the biological rhythm with cycling transcription. Thus, transcriptional and translational cycling reflects, rather than drives, metabolic and biosynthetic changes during biological rhythms. We propose that transcriptional changes are often the consequence, rather than the cause, of changes in cellular physiology and that caution is needed when inferring the activity of biological processes from transcript data.
Changes in protein levels do not explain the changing states of a biological rhythmSlow protein turnover rates decouple proteins levels from a rhythmic transcriptomeMetabolites determine protein activity via rhythmic post-translational modificationsCycling protein activity explains rhythmic transcription and ribosome biogenesisA cycling transcriptome is a consequence, not a cause, of physiological changes