bluuebunny/crossref_metadata_2025 huggingface dataset:
Elevated SARS-CoV-2 Antibodies Distinguish Severe Disease in Early COVID-19 Infection
Authors: Haddad Natalie S. , Nguyen Doan C. , Kuruvilla Merin E. , Morrison-Porter Andrea , Anam Fabliha , Cashman Kevin S. , Ramonell Richard P. , Kyu Shuya , Saini Ankur Singh , Cabrera-Mora Monica , Derrico Andrew , Alter David , Roback John D. , Horwath Michael , O’Keefe James B. , Wu Henry M. , Ian Wong An-Kwok , Dretler Alexandra W. , Gripaldo Ria , Lane Andrea N. , Wu Hao , Lee Saeyun , Hernandez Mindy , Engineer Vanessa , Varghese John , Le Sang , Sanz Iñaki , Daiss John L. , Eun-Hyung Lee F.
Published: December 2020

Background

SARS-CoV-2 has caused over 36,000,000 cases and 1,000,000 deaths globally. Comprehensive assessment of the multifaceted anti-viral antibody response is critical for diagnosis, differentiation of severe disease, and characterization of long-term immunity. Initial observations suggest that severe disease is associated with higher antibody levels and greater B cell/plasmablast responses. A multi-antigen immunoassay to define the complex serological landscape and clinical associations is essential.

Methods

We developed a multiplex immunoassay and evaluated serum/plasma from adults with RT-PCR-confirmed SARS-CoV-2 infections during acute illness (N=52) and convalescence (N=69); and pre-pandemic (N=106) and post-pandemic (N=137) healthy adults. We measured IgA, IgG, and/or IgM against SARS-CoV-2 Nucleocapsid (N), Spike domain 1 (S1), receptor binding domain (S1-RBD) and S1-N-terminal domain (S1-NTD).

Results

To diagnose infection, the combined [IgA+IgG+IgM] or IgG for N, S1, and S1-RBD yielded AUC values −0.90 by ROC curves. From days 6-30 post-symptom onset, the levels of antigen-specific IgG, IgA or [IgA+IgG+IgM] were higher in patients with severe/critical compared to mild/moderate infections. Consistent with excessive concentrations of antibodies, a strong prozone effect was observed in sera from severe/critical patients. Notably, mild/moderate patients displayed a slower rise and lower peak in anti-N and anti-S1 IgG levels compared to severe/critical patients, but anti-RBD IgG and neutralization responses reached similar levels at 2-4 months.

Conclusion

This SARS-CoV-2 multiplex immunoassay measures the magnitude, complexity and kinetics of the antibody response against multiple viral antigens. The IgG and combined-isotype SARS-CoV-2 multiplex assay is highly diagnostic of acute and convalescent disease and may prognosticate severity early in illness.

One Sentence Summary

In contrast to patients with moderate infections, those with severe COVID-19 develop prominent, early antibody responses to S1 and N proteins.
Strawberry sweetness and consumer preference are enhanced by specific volatile compounds
Authors: Fan Zhen , Hasing Tomas , Johnson Timothy S. , Garner Drake M. , Barbey Christopher R. , Colquhoun Thomas A. , Sims Charles A. , Resende Marcio F. R. , Whitaker Vance M.
Published: December 2020

Breeding crops for improved flavor is challenging due to the high cost of sensory evaluation and the difficulty of connecting sensory experience to chemical composition. The main goal of this study was to identify the chemical drivers of sweetness and consumer liking for fresh strawberries (Fragaria ×ananassa). Fruit of 148 strawberry samples from cultivars and breeding selections were grown and harvested over seven years and were subjected to both sensory and chemical analyses. Each panel consisted of at least 100 consumers, resulting in more than 15,000 sensory data points per descriptor. Three sugars, two acids and 113 volatile compounds were quantified. Consumer liking was highly associated with sweetness intensity, texture liking, and flavor intensity, but not sourness intensity. Partial least square analyses revealed 20 volatile compounds that increased sweetness perception independently of sugars; 18 volatiles that increased liking independently of sugars; and 15 volatile compounds that had positive effects on both. Machine learning-based predictive models including sugars, acids, and volatiles explained at least 25% more variation in sweetness and liking than models accounting for sugars and acids only. Volatile compounds such as γ-dodecalactone; 5-hepten-2-one, 6-methyl; and multiple medium-chain fatty acid esters may serve as targets for breeding or quality control attributes for strawberry products. A genetic association study identified two loci controlling ester production, both on linkage group 6A. Co-segregating makers in these regions can be used for increasing multiple esters simultaneously. This study demonstrates a paradigm for improvement of fruit sweetness and flavor in which consumers drive the identification of the most important chemical targets, which in turn drives the discovery of genetic targets for marker-assisted breeding.
Chromosomal-scaleDe novoGenome Assemblies of Cynomolgus Macaque and Common Marmoset
Authors: Jayakumar Vasanthan , Nishimura Osamu , Kadota Mitsutaka , Hirose Naoki , Sano Hiromi , Murakawa Yasuhiro , Yamamoto Yumiko , Nakaya Masataka , Tsukiyama Tomoyuki , Seita Yasunari , Nakamura Shinichiro , Kawai Jun , Sasaki Erika , Ema Masatsugu , Kuraku Shigehiro , Kawaji Hideya , Sakakibara Yasubumi
Published: December 2020

Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Their genomes were sequenced and assembled initially using short-read sequences, with the advent of massively parallel sequencing. However, the resulting contig sequences tended to remain fragmentary, and long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performedde novogenome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. Firstly we assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data. The scaffolded sequences obtained were further refined based on assembly results of alternate de novo assemblies and Hi-C contact maps by resolving identified inconsistencies. The final assemblies achieved N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively, and the numbers of scaffolds longer than 10Mb are equal to their chromosome numbers. The high fidelity of our assembly is ascertained by concordance to the BAC-end read pairs observed for common marmoset, as well as a high resemblance of their karyotypic organization. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.
Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae
Authors: Kramer Netanel , Tamir Raz , Ben-Zvi Or , Jacques Steven L. , Loya Yossi , Wangpraseurt Daniel
Published: December 2020

The coral-algal photosymbiosis fuels global coral-reef primary productivity, extending from sea level to as deep as 150 m (i.e., mesophotic). Currently, it is largely unknown how such mesophotic reefs thrive despite extremely limited light conditions. Here, we show that corals exhibit a plastic response to mesophotic conditions that involves a spatially optimized regulation of the bio-optical properties by coral host and symbiont. In contrast to shallow corals, mesophotic corals absorbed up to three-fold more light, resulting in excellent photosynthetic response under light conditions of only ~3% of the incident surface irradiance. The enhanced light harvesting capacity of mesophotic corals is regulated by average refractive index fluctuations in the coral skeleton that give rise to optical scattering and facilitate light transport and absorption by densely pigmented host tissue. The results of this study provide fundamental insight into the energy efficiency and light-harvesting mechanisms underlying the productivity of mesophotic coral reef ecosystems, yet also raise concerns regarding their ability to withstand prolonged environmental disturbances.
Gut Microbe-Targeted Choline Trimethylamine Lyase Inhibition Improves Obesity Via Rewiring of Host Circadian Rhythms
Authors: Schugar Rebecca C. , Gliniak Christy M. , Helsley Robert N. , Brown Amanda L. , Burrows Amy , Finney Chelsea , Fung Kevin K. , Allen Frederick M. , Ferguson Daniel , Gromovsky Anthony D. , Neumann Chase , McMillan Amy , Buffa Jennifer A. , Anderson James T. , Mehrabian Margarete , Goudzari Maryam , Willard Belinda , Mak Tytus D. , Armstrong Andrew R. , Swanson Garth , Keshavarzian Ali , Garcia-Garcia Jose Carlos , Wang Zeneng , Lusis Aldons J. , Hazen Stanley L. , Brown J. Mark
Published: December 2020

Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (ob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake, but is instead associated with beneficial remodeling of the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism, and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have untapped potential as anti-obesity therapeutics.
Redefining the role of Ca2+-permeable channels in photoreceptor degeneration using diltiazem
Authors: Das Soumyaparna , Popp Valerie , Power Michael , Groeneveld Kathrin , Melle Christian , Rogerson Luke , Achury Marlly , Schwede Frank , Strasser Torsten , Euler Thomas , Paquet-Durand François , Nache Vasilica
Published: December 2020

Hereditary degeneration of photoreceptors has been linked to over-activation of Ca2+-permeable channels, excessive Ca2+-influx, and downstream activation of Ca2+-dependent calpain-type proteases. Unfortunately, after more than 20 years of pertinent research, unequivocal evidence proving significant and reproducible photoreceptor protection with Ca2+-channel blockers is still lacking. Here, we show that both D- and L-cis enantiomers of the anti-hypertensive drug diltiazem were very effective at blocking photoreceptor Ca2+-influx, most probably by blocking the pore of Ca2+-permeable channels. Yet, unexpectedly, this block neither reduced the activity of calpain-type proteases, nor did it result in photoreceptor protection. Remarkably, application of the L-cis enantiomer of diltiazem even led to a strong increase in photoreceptor cell death. These findings shed doubt on the previously proposed links between Ca2+and retinal degeneration and are highly relevant for future therapy development as they may serve to refocus research efforts towards alternative, Ca2+-independent degenerative mechanisms.
Diversity of developing peripheral glia revealed by single cell RNA sequencing
Authors: Tasdemir-Yilmaz OE , Druckenbrod NR , Olukoya OO , Yung AR , Bastille I , Pazyra-Murphy MF , Sitko A , Hale EB , Vigneau S , Gimelbrant AA , Kharchenko P , Goodrich LV , Segal RA
Published: December 2020

The peripheral nervous system responds to a wide variety of sensory stimuli, a process that requires great neuronal diversity. These diverse peripheral sensory neurons are closely associated with glial cells that originate from the neural crest (NC). However, the molecular nature and origins of diversity among peripheral glia is not understood. Here we used single cell RNA sequencing to profile and compare developing and mature glia from somatosensory lumbar dorsal root ganglia (DRG) and auditory spiral ganglia (SG). We found that the glial precursors (GPs) differ in their transcriptional profile and prevalence in these two systems. Despite their unique features, somatosensory and auditory GPs undergo convergent differentiation to generate myelinating and non-myelinating Schwann cells that are molecularly uniform. By contrast, although satellite glia surround the neuronal cell bodies in both ganglia, we found that those in the SG express multiple myelination-associated genes, while DRG satellite cells express components that suppress myelination. Lastly, we identified a set of glial signature genes that are also expressed by placode-derived supporting cells, providing new insights into commonalities among glia across the nervous system. This comprehensive survey of gene expression in peripheral glia constitutes a valuable resource for understanding how glia acquire specialized functions and how their roles differ across sensory modalities.
Granzyme B prevents aberrant IL-17 production and intestinal pathogenicity in CD4+T cells
Authors: Hoek Kristen L. , Greer Michael J. , McClanahan Kathleen G. , Nazmi Ali , Piazuelo M. Blanca , Singh Kshipra , Wilson Keith T. , Olivares-Villagómez Danyvid
Published: December 2020

CD4+T cell activation and differentiation are important events that set the stage for proper immune responses. Many factors are involved in the activation and differentiation of T cells, and these events are tightly controlled to prevent unwanted and/or exacerbated immune responses that may harm the host. It has been well documented that granzyme B, a potent serine protease involved in cell-mediated cytotoxicity, is readily expressed by certain CD4+T cells, such as regulatory T cells and CD4+CD8αα+intestinal intraepithelial lymphocytes, both of which display cytotoxicity associated with granzyme B. However, because not all CD4+T cells expressing granzyme B are cytotoxic, additional roles for this protease in CD4+T cell biology remain unknown. Here, using a combination ofin vivoandin vitroapproaches, we report that granzyme B-deficient CD4+T cells display increased IL-17 production. In the adoptive transfer model of intestinal inflammation, granzyme B-deficient CD4+T cells triggered a more rapid disease onset than their WT counterparts, and presented a differential transcription profile. Similar results were also observed in granzyme B-deficient mice infected withCitrobacter rodentium. Our results suggest that granzyme B modulates CD4+T cell differentiation, providing a new perspective into the biology of this enzyme.
Significant inactivation of SARS-CoV-2 by a green tea catechin, a catechin-derivative and galloylated theaflavinsin vitro
Authors: Ohgitani Eriko , Shin-Ya Masaharu , Ichitani Masaki , Kobayashi Makoto , Takihara Takanobu , Kawamoto Masaya , Kinugasa Hitoshi , Mazda Osam
Published: December 2020

Potential effects of teas and their constituents on SARS-CoV-2 infection were studiedin vitro. Infectivity of SARS-CoV-2 was significantly reduced by a treatment with green tea, roasted green tea or oolong tea. Most remarkably, exposure to black tea for 1 min decreased virus titer to an undetectable level (less than 1/1,000 of untreated control). An addition of (-) epigallocatechin gallate (EGCG) significantly inactivated SARS-CoV-2, while theasinensin A (TSA) and galloylated theaflavins including theaflavin 3, 3’-di-gallate (TFDG) had more remarkable anti-viral activities. Virus treated with TSA at 500 μM or TFDG at 100 μM showed less than 1/10,000 infectivity compared with untreated virus. TSA and TFDG significantly inhibited interaction between recombinant ACE2 and RGD of S protein. These results strongly suggest that EGCG, and more remarkably TSA and galloylated theaflavins, inactivate the novel coronavirus.
Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity
Authors: Giroux Nicholas S. , Ding Shengli , McClain Micah T. , Burke Thomas W. , Petzold Elizabeth , Chung Hong A. , Palomino Grecia R. , Wang Ergang , Xi Rui , Bose Shree , Rotstein Tomer , Nicholson Bradly P. , Chen Tianyi , Henao Ricardo , Sempowski Gregory D. , Denny Thomas N. , Ko Emily R. , Ginsburg Geoffrey S. , Kraft Bryan D. , Tsalik Ephraim L. , Woods Christopher W. , Shen Xiling
Published: December 2020

SARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide insight into COVID-19 physiology. We analyzed PBMCs from subjects with variable symptom severity at different stages of clinical illness before and after IgG seroconversion to SARS-CoV-2. Prior to seroconversion, PBMC transcriptomes did not distinguish symptom severity. In contrast, changes in chromatin accessibility were associated with symptom severity. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif occupancy for individual PBMC cell types. The most extensive remodeling occurred in CD14+ monocytes where sub-populations with distinct chromatin accessibility profiles were associated with disease severity. Our findings indicate that pre-seroconversion chromatin remodeling in certain innate immune populations is associated with divergence in symptom severity, and the identified transcription factors, regulatory elements, and downstream pathways provide potential prognostic markers for COVID-19 subjects.

One sentence summary

Chromatin accessibility in immune cells from COVID-19 subjects is remodeled prior to seroconversion to reflect disease severity.
Leptospira interrogans triosephosphate isomerase: exploring the structural determinants of stability, high reaction rate and specificity.
Authors: PAREEK VIDHI , Dhayabarn Vaigundan , Balaram Hemalatha , Krishnaswamy Patnam R
Published: December 2020

Leptospires are zoonotic pathogens that cause significant socio-economic burden in developing countries, world-wide. The pathogenic species Leptospira interrogans (Li) is an important and interesting target for investigating the enzymes essential to its metabolic needs and adaptations. We cloned and expressed triosephosphate isomerase (LiTIM), a central metabolic flux regulator of Li, in AA200, E. coli TIM null strain. LiTIM was obtained as an active dimer (D-GAP to DHAP, kcat = 1740 /s and Km (D-GAP) = 0.21 mM, at 25 C) with mid-transition concentrations, Cm, 0.8 mM and 2.6 mM, respectively, for guanidine hydrochloride and urea induced equilibrium unfolding. We report the high resolution X-ray structures of LiTIM in apo and substrate (DHAP) bound forms. Our analysis highlights key features of TIM that regulate the mode of substrate binding and transition state stabilization and thus play a decisive role in attainment of high proficiency for the isomerisation reaction while avoiding the elimination reaction. Unexpected differences in the effect of temperature on stability and activity were observed for the three mesophilic pathogenic TIMs viz. from Li, Plasmodium falciparum (Pf) and Trypanosoma brucei (Tb). LiTIM and TbTIM (Tm = 46.5 C) were more susceptible to unfolding and precipitation compared to PfTIM (Tm = 67 C). In contrast, the initial (or zero point) activity of PfTIM rises till 50 C and saturates unlike LiTIM and TbTIM which show a rise till 55 C and 60 C, respectively. These observations could be rationalized by sequence comparison and examination of the structures of the three TIMs.
The Genetic Architecture of Robustness for Flight Performance inDrosophila
Authors: Spierer Adam N. , Rand David M.
Published: December 2020

A central challenge of quantitative genetics is partitioning phenotypic variation into genetic and non-genetic components. These non-genetic components are usually interpreted as environmental effects; however, variation between genetically identical individuals in a common environment can still exhibit phenotypic variation. A trait’s resistance to variation is called robustness, though the genetics underlying it are poorly understood. Accordingly, we performed an association study on a previously studied, whole organism trait: flight performance. Using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, we surveyed variation at the level of single nucleotide polymorphisms and whole genes using additive, marginal, and epistatic analyses that associated with robustness for flight performance. Many genes had developmental and neurodevelopmental annotations, and many more were identified from associations that differed between sexes. Additionally, many genes were pleiotropic, with several annotated for fitness-associated traits (e.g. gametogenesis and courtship). Our results corroborate a previous study for genetic modifiers of micro-environmental variation, and have sizable overlap with studies for modifiers of wing morphology and courtship behavior. These results point to an important and shared role for genetic modifiers of robustness of flight performance affecting development, neurodevelopment, and behavior.
Reduced Liver-Specific PGC1a Increases Susceptibility for Short-Term Diet-induced Weight Gain in Male Mice
Authors: Morris E. Matthew , Noland Roberto D. , Ponte Michael E. , Montonye Michelle L. , Christianson Julie A. , Stanford John A. , Miles John M. , Hayes Matthew R. , Thyfault John P.
Published: December 2020

Central integration of peripheral neural signals is one mechanism by which systemic energy homeostasis is regulated. Previous work described increased acute food intake following chemical reduction of hepatic fatty acid oxidation and ATP levels, which was prevented by common hepatic branch vagotomy (HBV). However, possible offsite actions of the chemical compounds confound the precise role of liver energy metabolism. Herein, we used a liver-specific PGC1a heterozygous (LPGC1a) mouse model, with associated reductions in mitochondrial fatty acid oxidation and respiratory capacity, to assess the role of liver energy metabolism in systemic energy homeostasis. LPGC1a male mice have 70% greater high-fat/high-sucrose (HFHS) diet-induced weight gain and 35% greater positive energy balance compared to wildtype (WT) (p<0.05). The greater energy balance was associated with altered feeding behavior and lower activity energy expenditure during HFHS in LPGC1a males. Importantly, no differences in HFHS-induced weight gain or energy metabolism was observed between female WT and LPGC1a mice. WT and LPGC1a mice underwent sham or HBV to assess whether vagal signaling was involved in HFHS-induced weight gain of male LPGC1a mice. HBV increased HFHS-induced weight gain (85%, p<0.05) in male WT, but not LPGC1a mice. As above, sham LPGC1a males gain 70% more weight during short-term HFHS feeding than sham WT (p<0.05). These data demonstrate a sexspecific role of reduced liver energy metabolism in acute diet-induced weight gain, and the need of more nuanced assessment of the role of vagal signaling in short-term diet-induced weight gain.

Key Points Summary

Reduced liver PGC1a expression results in reduced mitochondrial fatty acid oxidation and respiratory capacity in male mice.

Male mice with reduced liver PGC1a expression (LPGC1a) demonstrate greater short-term high-fat/high-sucrose diet-induced weight gain compared to wildtype.

Greater positive energy balance during HFHS feeding in male LPGC1a mice is associated with altered food intake patterns and reduced activity energy expenditure.

Female LPGC1a mice do not have differences in short-term HFHS-induced body weight gain or energy metabolism compared to wildtype.

Disruption of vagal signaling through common hepatic branch vagotomy increases short-term HFHS-induced weight gain in male wildtype mice, but does not alter male LPGC1a weight gain.
Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
Authors: Sirén Jouni , Monlong Jean , Chang Xian , Novak Adam M. , Eizenga Jordan M. , Markello Charles , Sibbesen Jonas A. , Hickey Glenn , Chang Pi-Chuan , Carroll Andrew , Gupta Namrata , Gabriel Stacey , Blackwell Thomas W. , Ratan Aakrosh , Taylor Kent D. , Rich Stephen S. , Rotter Jerome I. , Haussler David , Garrison Erik , Paten Benedict
Published: December 2020

We introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg)1, maps reads to thousands of human genomes at around the same speed BWA-MEM2maps reads to a single reference genome, while maintaining comparable accuracy to VG-MAP, vg’s original mapper. We have developed efficient genotyping pipelines using Giraffe. We demonstrate improvements in genotyping for single-nucleotide variants (SNVs), small insertions and deletions (indels) and structural variations (SVs) genome-wide. We use Giraffe to genotype about 167 thousand structural variants ascertained from long read studies in 5,202 human genomes sequenced with short reads, including the complete 1000 Genomes Project dataset, at an average cost of $1.50 per sample. We determine the frequency of these variations in diverse human populations, characterize their complex allelic variations and identify thousands of expression quantitative trait loci (eQTLs) driven by these variations.
The aging whole blood transcriptome reveals a potential role of FASLG in COVID-19
Authors: de Almeida Chuffa Luiz Gustavo , Souza Jeferson dos Santos , de Mello Mariana Costa , de Oliveira Neto Mario , Carvalho Robson Francisco
Published: December 2020

The risk for severe illness from COVID-19 increases with age as older patients are at the highest risk. Although it is still unclear whether the virus is blood-transmitted, the viral RNA is detected in serum. Identifying how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interacts with specific blood components during aging is expected to guide proper therapies. Considering that all human coronavirus require host cellular molecules to promote infection, we investigated the aging whole blood transcriptome from the Genotype-Tissue Expression (GTEx) database to explore differentially expressed genes (DEGs) translated into proteins potentially interacting with viral proteins. From a total of 22 DEGs in aged blood, five genes (FASLG, CTSW, CTSE, VCAM1, andBAG3) changed expression during aging. These age-related genes are involved in immune response, inflammation, cell component and cell adhesion, and platelet activation/aggregation. Both males and females older than 50 overexpressFASLGcompared with younger adults (20-30 years old), possibly inducing a hyper-inflammatory cascade that activates specific immune cells. Furthermore, the expression of cathepsins (CTSWandCTSE) and the anti-apoptotic co-chaperone moleculeBAG3was significantly increased throughout aging in both gender. By exploring publicly available Single-Cell RNA-Sequencing (scRNA-Seq) data on peripheral blood of SARS-CoV-2-infected patients, we foundFASLGandCTSWexpressed mainly in natural killer (NK) cells and CD8+ (cytotoxic) T lymphocytes whereasBAG3was expressed in CD4+ T cells, naive T cells, and CD14+ monocytes. The increased expression ofFASLGin blood during aging may explain why older patients are more prone to severe acute viral infection complications. These results indicateFASLGas a prognostic candidate and potential therapeutic target for more aggressive clinical manifestation of COVID-19.
The ascending arousal system promotes optimal performance through meso-scale network integration in a visuospatial attentional task
Authors: Wainstein Gabriel , Rojas-Libano Daniel , Medel Vicente , Alnæs Dag , Kolskår Knut K. , Endestad Tor , Laeng Bruno , Ossandon Tomas , Crossley Nicolás , Matar Elie , Shine James M.
Published: December 2020

Previous research has shown that the autonomic nervous system provides essential constraints over ongoing cognitive function. However, there is currently a relative lack of direct empirical evidence for how this interaction manifests in the brain at the macro-scale level. Here, we examine the role of ascending arousal and attentional load on large-scale network dynamics by combining pupillometry, functional MRI and graph theoretical analysis to analyze data from a visual motion-tracking task with a parametric load manipulation. We found that attentional load effects were observable in measures of pupil diameter and in a set of brain regions that parametrically modulated their BOLD activity and meso-scale network-level integration. In addition, the regional patterns of network reconfiguration were correlated with the spatial distribution of theα2a adrenergic receptor. Our results further solidify the relationship between ascending noradrenergic activity, large-scale network integration, and cognitive task performance.

Author Summary

In our daily lives, it is usual to encounter highly demanding cognitive tasks. They have been traditionally regarded as challenges that are solved mainly through cerebral activity, specifically via information-processing steps carried by neurons in the cerebral cortex. Activity in cortical networks thus constitutes a key factor for improving our understanding cognitive processes. However, recent evidence has shown that evolutionary older players in the central nervous system, such as brainstem’s ascending modulatory systems, might play an equally important role in diverse cognitive mechanisms. Our article examines the role of the ascending arousal system on large-scale network dynamics by combining pupillometry, functional MRI and graph theoretical analysis.
Deletion of PI3-Kinase Promotes Myelodysplasia Through Dysregulation of Autophagy in Hematopoietic Stem Cells
Authors: Ames Kristina , Kaur Imit , Shi Yang , Tong Meng , Sinclair Taneisha , Hemmati Shayda , Glushakow-Smith Shira G. , Tein Ellen , Gurska Lindsay , Dubin Robert , Shan Jidong , Pradhan Kith , Verma Amit , Montagna Cristina , Gritsman Kira
Published: December 2020

Hematopoietic stem cells (HSCs) maintain the blood system through a delicate equilibrium between self-renewal and differentiation. Most hematopoietic growth factors and cytokines signal through phosphoinositide 3-kinase (PI3K) via three Class IA catalytic PI3K isoforms (P110α, β, and δ), encoded byPik3ca, Pik3cb, andPik3cd, respectively. The PI3K/AKT pathway is commonly activated in acute myeloid leukemia (AML), and PI3K is a common therapeutic target in cancer. However, it is not known whether PI3K is required for HSC differentiation or self-renewal. We previously demonstrated that individual PI3K isoforms are dispensable in HSCs1,2. To determine the redundant roles of PI3K isoforms in HSCs, we generated a triple knockout (TKO) mouse model with deletion of all three Class IA PI3K isoforms in the hematopoietic system. Surprisingly, we observed significant expansion of TKO HSCs after transplantation, with decreased differentiation capacity and impaired multilineage repopulation. Additionally, the bone marrow of TKO mice exhibited myelodysplastic features with chromosomal abnormalities. Interestingly, we found that macroautophagy (thereafter autophagy) is impaired in TKO HSCs, and that pharmacologic induction of autophagy improves their differentiation. Therefore, we have uncovered important roles for PI3K in autophagy regulation in HSCs to maintain the balance between self-renewal and differentiation.
Strain specific persistence in the murine lung ofAspergillus fumigatusconidia causes an Allergic Broncho-Pulmonary Aspergillosis-like disease phenotype
Authors: Jones Jane T. , Liu Ko-Wei , Wang Xi , Kowalski Caitlin H. , Ross Brandon S. , Mills Kathleen A. M. , Kerkaert Joshua D. , Hohl Tobias M. , Lofgren Lotus A. , Stajich Jason E. , Obar Joshua J. , Cramer Robert A.
Published: December 2020

Aspergillus fumigatusis a filamentous fungus which can cause multiple diseases in humans. Allergic Broncho-pulmonary Aspergillosis (ABPA) is a disease diagnosed primarily in Cystic Fibrosis patients caused by a severe allergic response often to long-termA. fumigatuscolonization in the lungs. Mice develop an allergic response to repeated inhalation ofA. fumigatusspores; however, no strains have been identified that can survive long-term in the mouse lung and cause ABPA-like disease. We characterizedA. fumigatusstrain W72310 by whole genome sequencing andin vitroandin vivoviability assays in comparison to a common reference strain, CEA10. W72310 was resistant to leukocyte-mediated killing and persisted in the mouse lung longer than CEA10, a phenotype that correlated with greater resistance to oxidative stressors, hydrogen peroxide and menadione,in vitro. In animals both sensitized and challenged with W72310, conidia, but not hyphae, were viable in the lungs for up to 21 days in association with eosinophilic airway inflammation, airway leakage, serum IgE, and mucus production. W72310-sensitized mice that were recall-challenged with conidia had increased inflammation, Th1 and Th2 cytokines, and airway leakage compared to controls. Collectively, our studies demonstrate that a unique strain ofA. fumigatusresistant to leukocyte killing can persist in the mouse lung in conidial form and elicit features of ABPA-like disease.

IMPORTANCE

Allergic Broncho-pulmonary Aspergillosis (ABPA) patients often present with long-term colonization ofAspergillus fumigatus. Current understanding of ABPA pathogenesis has been complicated by a lack of long-termin vivofungal persistence models. We have identified a clinical isolate ofA. fumigatus, W72310, which persists in the murine lung and causes an ABPA-like disease phenotype. Surprisingly, while viable, W72310 showed little to no growth beyond the conidial stage in the lung. This indicates that it is possible thatA. fumigatuscan cause allergic disease in the lung without any significant hyphal growth. The identification of this strain ofA. fumigatuscan not only be used to better understand disease pathogenesis of ABPA and potential anti-fungal treatments, but also to identify features of fungal strains that drive long-term fungal persistence in the lung. Consequently, these observations are a step toward helping resolve the long-standing question when to utilize antifungal therapies in patients with ABPA and fungal allergic type diseases.
Host-age prediction from fecal microbiome composition in laboratory mice
Authors: Low Adrian , Soh Melissa , Miyake Sou , Seedorf Henning
Published: December 2020

The life-long relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Changes in microbiome composition throughout the lifespan of a host remain, however, largely understudied. In this study, the fecal microbiome of conventionally raised C57BL/6J mice was analyzed throughout almost the entire expected lifespan, from ‘maturing’ (9 weeks) until ‘very old’ age (112 weeks). Analysis of alpha and beta diversity suggests that gradual microbiome changes occur throughout the entire murine life but appear to be more pronounced in ‘maturing’ to ‘middle-aged’ phases. Phylum-level analysis indicates a shift in the Firmicutes/Bacteroidetes ratio in favor of the Firmicutes in the second year of adulthood. Varying successional patterns throughout life were observed for many Firmicutes OTUs, while relative abundances of Bacteroidetes OTUs varied primarily in the early life phases. Microbiome configurations at given time points were used as training sets in a Bayesian model, which in turn effectively enabled the prediction of host age. The fecal microbiome composition may therefore serve as an accurate biomarker for aging. This study further suggests that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies.

Importance

The life-long relationship between microorganisms and hosts has a profound impact on the overall physiology of the holobiont. Understanding the extent of gut microbiome compositional changes over the expected mouse lifespan may allow to better understand the interplay of microbiome and the host at the different life stages. In this study, we performed a two-year longitudinal study of murine fecal microbiome. Using fine-scale microbiome profiling we were able to predict the host age from the fecal microbiome composition. Moreover, we observed that the rate of compositional change appears to slow with age. The description of the compositional changes in commonly used C57BL/6J mice can be used to optimize selection of age-associated mouse models and highlights the use of microbiome-profiling as biomarker for aging.
NGLY1 knockdown or pharmacological inhibition induces cellular autophagy
Authors: Needs Sarah H , Bootman Martin D , Grotzke Jeff E , Kramer Holger B , Allman Sarah A
Published: December 2020

Pan-caspase inhibitor Z-VAD-fmk acts as an inhibitor of peptide:N-glycanase (NGLY1); an endoglycosidase which cleavesN-linked glycans from glycoproteins exported from the endoplasmic reticulum during ER-associated degradation (ERAD). PharmacologicalN-glycanase inhibition by Z-VAD-fmk or siRNA knockdown (KD) induces GFP-LC3 positive puncta in HEK 293 cells. Activation of ER stress markers or reactive oxygen species (ROS) induction are not observed. In NGLY1 inhibition or KD, upregulation of autophagosome formation without impairment of autophagic flux are observed. Enrichment and proteomics analysis of autophagosomes after Z-VAD-fmk treatment or NGLY1 KD reveals comparable autophagosomal protein content. Upregulation of autophagy represents a cellular adaptation to NGLY1 inhibition or KD, and ATG13-deficient mouse embryonic fibroblasts (MEFs) show reduced viability under these conditions. In contrast, treatment with pan-caspase inhibitor, Q-VD-OPh does not induce cellular autophagy. Therefore, experiments with Z-VAD-fmk are complicated by the effects of NGLY1 inhibition and Q-VD-OPh represents an alternative caspase inhibitor free from this limitation.
ProbingE. coliSSB Protein-DNA topology by reversing DNA backbone polarity
Authors: Kozlov Alexander G. , Lohman Timothy M.
Published: December 2020

E. colisingle strand (ss) DNA binding protein (SSB) is an essential protein that binds ssDNA intermediates formed during genome maintenance. SSB homo-tetramers bind ssDNA in two major modes differing in occluded site size and cooperativity. The (SSB)35mode in which ssDNA wraps on average around two subunits is favored at low [NaCl] and high SSB to DNA ratios and displays high “unlimited”, nearest-neighbor cooperativity forming long protein clusters. The (SSB)65mode, in which ssDNA wraps completely around four subunits of the tetramer, is favored at higher [NaCl] (> 200 mM) and displays “limited” low cooperativity. Crystal structures ofE. coliSSB andP. falciparumSSB show ssDNA bound to the SSB subunits (OB-folds) with opposite polarities of the sugar phosphate backbones. To investigate whether SSB subunits show a polarity preference for binding ssDNA, we examinedEcSSB andPfSSB binding to a series of (dT)70constructs in which the backbone polarity was switched in the middle of the DNA by incorporating a reverse polarity (RP) phosphodiester linkage, either 3’-3’ or 5’-5’. We find only minor effects on the DNA binding properties for these RP constructs, although (dT)70with a 3’-3’ polarity switch shows decreased affinity forEcSSB in the (SSB)65mode and lower cooperativity in the (SSB)35mode. However, (dT)70in which every phosphodiester linkage is reversed, does not form a completely wrapped (SSB)65mode, but rather bindsEcSSB in the (SSB)35mode, with little cooperativity. In contrast,PfSSB, which binds ssDNA only in an (SSB)65mode and with opposite backbone polarity and different topology, shows little effect of backbone polarity on its DNA binding properties. We present structural models suggesting that strict backbone polarity can be maintained for ssDNA binding to the individual OB-folds if there is a change in ssDNA wrapping topology of the RP ssDNA.

Statement of Significance

Single stranded (ss) DNA binding (SSB) proteins are essential for genome maintenance. Usually homo-tetrameric, bacterial SSBs bind ssDNA in multiple modes, one of which involves wrapping 65 nucleotides of ssDNA around all four subunits. Crystal structures ofE. coliandP. falciparumSSB-ssDNA complexes show ssDNA bound with different backbone polarity orientations raising the question of whether these SSBs maintain strict backbone polarity in binding ssDNA. We show that bothE. coliandP. falciparumSSBs can still form high affinity fully wrapped complexes with non-natural DNA containing internal reversals of the backbone polarity. These results suggest that both proteins maintain a strict backbone polarity preference, but adopt an alternate ssDNA wrapping topology.
Structural basis of FANCD2 deubiquitination by USP1-UAF1
Authors: Rennie Martin L. , Arkinson Connor , Chaugule Viduth K. , Toth Rachel , Walden Helen
Published: December 2020

Ubiquitin-Specific Protease 1 (USP1), together with the cofactor UAF1, acts during DNA repair processes to specifically to remove mono-ubiquitin signals. The mono-ubiquitinated FANCI-FANCD2 heterodimer is one such substrate and is involved in the repair of DNA interstrand crosslinks via the Fanconi Anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin, and bound to mono-ubiquitinated FANCI-FANCD2 substrate. Crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1. A cryoEM reconstruction of USP1-UAF1 in complex mono-ubiquitinated FANCI-FANCD2, highlights a highly orchestrated deubiquitination process with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for their requirement despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.
Distinct temporal expression of GW182 in neurons regulates dendritic arborization
Authors: Nawalpuri Bharti , Muddashetty Ravi
Published: December 2020

Precise development of the dendritic architecture is a critical determinant of mature neuronal circuitry. MicroRNA-mediated regulation of protein synthesis plays a crucial role in dendritic morphogenesis but the role of miRISC protein components in this process is less studied. Here, we show an important role of a key miRISC protein GW182 in the regulation of dendritic growth. We have identified a distinct brain region specific Spatio-temporal expression pattern of GW182 during rat postnatal development. We found that the window of peak GW182 expression coincides with the period of extensive dendritic growth, both in the hippocampus and cerebellum. Perturbation of GW182 function during a specific temporal window resulted in reduced dendritic growth of cultured hippocampal neurons. Mechanistically, we show that GW182 modulates dendritic growth by regulating global somato-dendritic translation, and actin cytoskeletal dynamics of developing neurons. Furthermore, we found that GW182 affects dendritic architecture by regulating the expression of actin modulator LIMK1. Taken together, our data reveal a previously undescribed neurodevelopmental expression pattern of GW182 and its role in dendritic morphogenesis, through both translational control and actin cytoskeletal rearrangement.

GW182 is a key component of miRNA induced silencing complex (miRISC). Nawalpuri et al. show that GW182 has a unique temporal expression profile during neuronal development. The developmentally controlled expression of GW182 influences dendritic morphology by regulating the expression of actin modulator LIMK1.
Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor
Authors: Uberoi Aayushi , Bartow-McKenney Casey , Zheng Qi , Flowers Laurice , Campbell Amy , Knight Simon A.B. , Chan Neal , Wei Monica , Lovins Victoria , Bugayev Julia , Horwinski Joseph , Bradley Charles , Meyer Jason , Crumrine Debra , Sutter Carrie Hayes , Elias Peter , Mauldin Elizabeth , Sutter Thomas R. , Grice Elizabeth A.
Published: December 2020

The epidermis forms a barrier that defends the body from desiccation and entry of harmful substances, while sensing and integrating environmental signals. The tightly orchestrated cellular changes required for the proper formation and maintenance of this epidermal barrier occur in the context of the skin microbiome. Using germ free mice, we demonstrate the microbiota is necessary for proper differentiation and repair of the epidermal barrier. These effects were mediated by the aryl hydrocarbon receptor (AHR) in keratinocytes, a xenobiotic receptor also implicated in epidermal differentiation. Murine skin lacking keratinocyte AHR was more susceptible to barrier damage and infection, during steady state and epicutaneous sensitization. Colonization with a defined consortium of human skin isolates restored barrier competence in an AHR-dependent manner. We reveal a fundamental mechanism whereby the microbiota regulates skin barrier formation and repair, with far-reaching implications for the numerous skin disorders characterized by epidermal barrier dysfunction.
Structural basis of the regulation of normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2
Authors: Sato Ko , Kumar Amarjeet , Hamada Keisuke , Okada Chikako , Oguni Asako , Machiyama Ayumi , Sakuraba Shun , Nishizawa Tomohiro , Nureki Osamu , Kono Hidetoshi , Ogata Kazuhiro , Sengoku Toru
Published: December 2020

Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression by antagonizing the repressive effect of polycomb-group proteins. Aberrant upregulation of H3K36me2, either by overexpression or point mutations of NSD2/MMSET, an H3K36 dimethyltransferase, is found in various cancers, including multiple myeloma. To understand the mechanism underlying its regulation, here we report the cryo-electron microscopy structure of the catalytic fragment of NSD2 bound to the nucleosome at 2.8 Å resolution. The nucleosomal DNA is partially unwrapped at superhelix location +5.5, facilitating the access of NSD2 to H3K36. NSD2 interacts with DNA and H2A along with H3. The autoinhibitory loop of NSD2 changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed two oncogenic mutations, E1099K and T1150A, to aberrantly activate NSD2 by increasing its catalytic turnover but not the nucleosome affinity. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing the catalytic turnover. Our analyses would guide the development of specific inhibitors of NSD2 for the treatment of various cancers.
Universal grey number theory for the uncertainty presence of wiper structural system
Authors: Liang Zhiqiang , Liu Xintian , Yansong Wang , Wang Xiaolan
Published: December 2020

Purpose

This study aims to accurately evaluate the influence of various error intervals on the performance of the wiper.

Design/methodology/approach

The wiper structural system is decomposed into classical four-link planar for kinematics analysis, and it was modeled respectively by using interval method, universal grey number theory and enumeration approach depending on the nature of uncertainty.

Findings

The universal grey number theory is a viable methodology for the accurate analysis of uncertain structural system.

Originality/value

(1) The model of uncertain wiper structural system is established. (2) Universal grey number theory and new parameters are adopted to analyze the presence of uncertain wiper structural system. (3) Comparative analysis of response quantities is obtained by interval method, universal grey number theory and enumeration method.