bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spinning sugars in antigen biosynthesis: a direct study of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases
Authors: Cross Alice R. , Roy Sumita , Vega Mirella Vivoli , Rejzek Martin , Nepogodiev Sergey A. , Cliff Matthew , Salmon Debbie , Isupov Michail N. , Field Robert A. , Prior Joann L. , Harmer Nicholas J. 
Published: October 2021

AbstractThe sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii respectively. Streptose forms the central moiety of the antibiotic streptomycin, whilst DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalysed by the enzymes RmlA/RmlB/RmlC/RmlD. Streptose and DHHS biosynthesis unusually require a ring contraction step that might be performed by the orthologues of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii proposed the StrM and CBU1838 proteins respectively as RmlC orthologues. Here, we demonstrate through both coupled and direct observation studies that both enzymes can perform the RmlC 3’’,5’’ double epimerisation activity; and that this activity supports TDP-rhamnose biosynthesis in vivo. We demonstrate that proton exchange is faster at the 3’’ position than the 5’’ position, in contrast to a previously studied orthologue. We solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to previously characterised enzymes. These results further support the hypothesis that streptose and DHHS are biosynthesised using the TDP pathway and are consistent with the ring contraction step being performed on a double epimerised substrate, most likely by the RmlD paralogue. This work will support the determination of the full pathways for streptose and DHHS biosynthesis.
Deep neural networks and visuo-semantic models explain complementary components of human ventral-stream representational dynamics
Authors: Jozwik Kamila M , Kietzmann Tim C , Cichy Radoslaw M , Kriegeskorte Nikolaus , Mur Marieke 
Published: October 2021

ABSTRACTDeep neural networks (DNNs) are promising models of the cortical computations supporting human object recognition. However, despite their ability to explain a significant portion of variance in neural data, the agreement between models and brain representational dynamics is far from perfect. We address this issue by asking which representational features are currently unaccounted for in neural timeseries data, estimated for multiple areas of the ventral stream via source-reconstructed magnetoencephalography (MEG) data acquired in human participants (9 females, 6 males) during object viewing. We focus on the ability of visuo-semantic models, consisting of human-generated labels of object features and categories, to explain variance beyond the explanatory power of DNNs alone. We report a gradual reversal in the relative importance of DNN versus visuo-semantic features as ventral-stream object rep-resentations unfold over space and time. While lower-level visual areas are better explained by DNN features, especially during the early phase of the response (< 128 ms after stimulus onset), higher-level cortical dynamics are best accounted for by visuo-semantic features during a later time window (starting 146 ms after stimulus onset). Among the visuo-semantic features, object parts and basic categories drive the advantage over DNNs. These results show that a significant component of the variance unexplained by DNNs in higher-level cortical dynamics is structured, and can be explained by readily nameable aspects of the objects. We conclude that current DNNs fail to fully capture dynamic representations in higher-level human visual cortex and suggest a path toward more accurate models of ventral stream computations.SIGNIFICANCE STATEMENTWhen we view objects such as faces and cars in our visual environment, their neural representations dynamically unfold over time at a millisecond scale. These dynamics reflect the cortical computations that support fast and robust object recognition. Deep neural networks (DNNs) have emerged as a promising framework for modeling these computations but cannot yet fully account for the neural dynamics. Using magnetoencephalography data acquired in human observers during object viewing, we show that readily nameable aspects of objects, such as “eye”, “wheel”, and “face”, can account for variance in the neural dynamics over and above DNNs. These findings suggest that DNNs and humans may in part rely on different object features for visual recognition and provide guidelines for model improvement.
Autotaxin is a Potential Link between Genetic Risk Factors and Pathogenesis of Systematic Lupus Erythematosus in Plasmacytoid Dendritic Cells
Authors: Tsuchida Yumi , Shoda Hirofumi , Nakano Masahiro , Ota Mineto , Okamura Tomohisa , Yamamoto Kazuhiko , Kurano Makoto , Yatomi Yutaka , Fujio Keishi , Sawada Tetsuji 
Published: October 2021

AbstractBackgroundThe importance of autotaxin, an enzyme that catalyzes lysophospholipid production, has recently been recognized in various diseases, including cancer and autoimmune diseases. Herein, we examined the role of autotaxin in systemic lupus erythematosus (SLE), utilizing data from ImmuNexUT, a comprehensive database consisting of transcriptome data and expression quantitative trait locus (eQTL) data of immune cells from patients with immune-mediated disorders.MethodsSerum autotaxin concentrations in patients with SLE and healthy controls (HCs) were compared. The transcriptome data of patients with SLE and age-and sex-matched HCs were obtained from ImmuNexUT. The expression of ENPP2, the gene encoding autotaxin, was examined in peripheral blood immune cells. Next, weighted gene correlation network analysis (WGCNA) was performed to identify genes with expression patterns similar to ENPP2. The ImmuNexUT eQTL database and public epigenomic databases were used to infer the relationship between autotaxin and pathogenesis of SLE.ResultsAutotaxin levels were elevated in the serum of patients with SLE compared to HCs. Furthermore, the expression of ENPP2 was higher in plasmacytoid dendritic cells (pDCs) than in other immune cell subsets, and its expression was elevated in pDCs of patients with SLE compared to HCs. In WGCNA, ENPP2 belonged to a module that correlated with disease activity. This module was enriched in interferon-associated genes and included genes whose expression was influenced by single-nucleotide polymorphisms associated with SLE, suggesting that it is a key module connecting genetic risk factors of SLE with disease pathogenesis. Analysis utilizing the ImmuNexUT eQTL database and public epigenomic databases suggested that the increased expression of ENPP2 in pDCs from patients with SLE may be caused by increased expression of interferon-associated genes and increased binding of STAT3 complexes to the regulatory region of ENPP2.ConclusionsAutotaxin may play a critical role in connecting genetic risk factors of SLE to disease pathogenesis in pDCs.
Urinary bladder enlargement across nine rodent models of diabetes: correlations with glucose and insulin levels
Authors: Yesilyurt Zeynep E. , Matthes Jan , Hintermann Edith , Castañeda Tamara R. , Elvert Ralf , Beltran-Ornelas Jesus H. , Silva-Velasco Diana L. , Xia Ning , Kannt Aimo , Christen Urs , Centurion David , Li Huige , Pautz Andrea , Arioglu-Inan Ebru , Michel Martin C. 
Published: October 2021

AbstractThe urinary bladder is markedly enlarged in the type 1 diabetes mellitus model of streptozotocin (STZ)-injected rats, but much less data exist for models of type 2 diabetes (T2DM). Diabetic polyuria has been proposed to explain bladder enlargement. We have collected data on bladder weight and blood glucose from 16 studies representing 9 distinct rodent diabetes (7 T2DM) and obesity models; some included arms with diets and/or pharmacological treatments. Data were analyzed for bladder enlargement and for correlations between bladder weight on the one and glucose levels on the other hand. Our data confirm major bladder enlargements in STZ rats, minor if any enlargement in fructose-fed rats, db/db mice and mice on a high-fat diet. For the first time we report bladder weight data on 5 other models with presence and degree of bladder enlargement being heterogeneous across models. Bladder weight was correlated with plasma glucose in some but not other models, but correlations were moderate to weak except for RIP-LMCV mice. We conclude that the presence and extent of bladder enlargement varies markedly across diabetes models, particularly TD2M models; our data do not support the idea that bladder enlargement is primarily driven by glucose levels/glucosuria.
The Isl1/Shh/Wnt5a cascade controls the invasion of myoblasts by tuning the CXCL12/CXCR4 axis during tongue morphogenesis
Authors: Zhang Wei , Yu Jiaojiao , Fu Guoquan , Huang Ruiqi , Li Jianying , Huang Huarong , Liu Jing , Yu Dongliang , Gan Lin , Qiu Mengsheng , Zhang Zunyi , Li Feixue 
Published: October 2021

AbstractThe migration and invasion of myoblast cells derive from the occipital somites is critical for tongue morphogenesis. However, the molecular mechanisms underlying myoblast migration and invasion remain elusive. In this study, we report that transcription factor Isl1 is required for tongue development. Loss of Isl1 in the distal mandibular epithelium results in aglossia due to the defect of myoblast cells invasion. In the absence of Isl1 expression, myoblast cells in the first branchial arch fail to migrate into the presumptive tongue primordium. Down-regulation of Shh was detected in the distal mandibular epithelium after Isl1 deletion. As a downstream target gene of Shh, Wnt5a attracts the migration of mesenchymal cells expressing chemokine ligand 12 (CXCL12). CXCL12+ mesenchymal cells in the Isl1 mutant embryo fail to migrate to the distal region but accumulate in a relatively small proximal domain of the first branchial arch. CXCL12 serves as a bidirectional cue for myoblasts that express its receptor CXCR4, attracting CXCR4+ myoblasts invasion at low concentration but repelling at high concentration. The defect in the distal migration of CXCL12+ mesenchymal cells leads to a high local concentration of CXCL12, thereby preventing the invasion of CXCR4+ myoblasts. In addition, transgenic activation of Ihh alleviates the defect in tongue development and rescues the invasion of myoblasts, corroborating the functional involvement of Hedgehog signaling in tongue development. In summary, this study provides the first line of genetic evidence for the Isl1/Shh/Wnt5a cascade to regulate myoblasts invasion by tuning the CXCL12/CXCR4 axis.
Going Beyond the Point Neuron: Active Dendrites and Sparse Representations for Continual Learning
Authors: Grewal Karan , Forest Jeremy , Cohen Benjamin P. , Ahmad Subutai 
Published: October 2021

AbstractBiological neurons integrate their inputs on dendrites using a diverse range of non-linear functions. However the majority of artificial neural networks (ANNs) ignore biological neurons’ structural complexity and instead use simplified point neurons. Can dendritic properties add value to ANNs? In this paper we investigate this question in the context of continual learning, an area where ANNs suffer fromcatastrophic forgetting(i.e., ANNs are unable to learn new information without erasing what they previously learned). We propose that dendritic properties can help neurons learn context-specific patterns and invoke highly sparse context-specific subnetworks. Within a continual learning scenario, these task-specific subnetworks interfere minimally with each other and, as a result, the network remembers previous tasks significantly better than standard ANNs. We then show that by combining dendritic networks with Synaptic Intelligence (a biologically motivated method for complex weights) we can achieve significant resilience to catastrophic forgetting, more than either technique can achieve on its own. Our neuron model is directly inspired by the biophysics of sustained depolarization following dendritic NMDA spikes. Our research sheds light on how biological properties of neurons can be used to solve scenarios that are typically impossible for traditional ANNs to solve.
Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during algal blooms
Authors: Vincent Flora , Gralka Matti , Schleyer Guy , Schatz Daniella , Cabrera-Brufau Miguel , Kuhlisch Constanze , Sichert Andreas , Vidal-Melgosa Silvia , Mayers Kyle , Barak-Gavish Noa , Flores J.Michel , Masdeu-Navarro Marta , Egge Jorun Karin , Larsen Aud , Heheman Jan-Hendrik , Marrasé Celia , Simó Rafel , Cordero Otto X. , Vardi Assaf 
Published: October 2021

AbstractAlgal blooms are hotspots of marine primary production and play central roles in microbial ecology and global nutrient cycling. When blooms collapse, organic carbon is transferred to higher trophic levels, microbial respiration or sinking in proportions that depend on the dominant mortality agent. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains an open question. Here, we characterized the consequences of viral infection on the microbiome composition and biogeochemical landscape of marine ecosystems by conducting a large-scale mesocosm experiment. Moniroting of seven induced coccolithophore blooms, which showed different degrees of viral infection, revealed that only high levels of viral infection caused significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, viral infection favored the growth of eukaryotic heterotrophs (thraustochytrids) over bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection can increase per-cell rates of extracellular carbon release by 2-4.5 fold. This happened via production of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain
Authors: Jibiki Kazuya , Liu Mo-yan , Lei Chao-sen , Kodama Takashi S. , Kojima Chojiro , Fujiwara Toshimichi , Yasuhara Noriko 
Published: October 2021

AbstractImportin α has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non-nuclear transport functions. In both nuclear transport and non-nuclear transport, a functional domain called the IBB domain (importin β binding domain) plays a key role in regulating importin α behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin α function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin α IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across organisms and families, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex-forming ability between families and for functional switching.
AT-752, a double prodrug of a guanosine nucleotide analog, inhibits yellow fever virus in a hamster model
Authors: Lin Kai , Good Steven S. , Julander Justin G. , Weight Abbie , Moussa Adel , Sommadossi Jean-Pierre 
Published: October 2021

AbstractYellow fever virus (YFV) is a zoonotic pathogen re-emerging in parts of the world, causing a viral hemorrhagic fever associated with high mortality rates. While an effective vaccine is available, having an effective antiviral against YFV is critical against unexpected outbreaks, or when vaccination is not recommended. We have previously identified AT-281, the free base of AT-752, an orally available double prodrug of a guanosine nucleotide analog, as a potent inhibitor of YFV in vitro, with a 50% effective concentration (EC50) of 0.31 μM. In hamsters infected with YFV (Jimenez strain), viremia rose about 4 log10-fold and serum alanine aminotransferase (ALT) 2-fold compared to sham-infected animals. Treatment with 1000 mg/kg AT-752 for 7 days, initiated 4 h prior to viral challenge, reduced viremia to below the limit of detection by day 4 post infection (pi) and returned ALT to normal levels by day 6 pi. When treatment with AT-752 was initiated 2 days pi, the virus titer and ALT dropped >2 log10 and 53% by day 4 and 6 pi, respectively. In addition, at 21 days pi, 70 – 100% of the infected animals in the treatment groups survived compared to 0% of the untreated group (p<0.001). Moreover, in vivo formation of the active triphosphate metabolite AT-9010 was measured in the animal tissues, with the highest concentrations in liver and kidney, organs that are vulnerable to the virus. The demonstrated in vivo activity of AT-752 suggests that it is a promising compound for clinical development in the treatment of YFV infection.Author summaryYellow fever virus (YFV) is transmitted by mosquitoes, and its infection can lead to a lethal viral hemorrhagic fever associated with liver damage. While an effective vaccine is available, in places where the vaccination rate is low, in the event of an unexpected outbreak, or where vaccination is not recommended individually, having an effective antiviral treatment is critical. We previously reported that the nucleotide analog prodrug AT-752 potently inhibited the YFV in cultured cells. Here we showed that in hamsters infected with YFV, oral treatment with 1000 mg/kg AT-752 for 7 days reduced the production of infectious virus particles in the blood, and decreased serum alanine aminotransferase, a marker of liver damage, to levels measured in uninfected animals. In addition, at 21 days after infection, 70 – 100% of the infected animals in the treatment groups survived compared to 0% in the untreated group. Moreover, the amount of the active metabolite formed from AT-752 was highest in the livers and kidneys of the treated animals, organs that are targeted by the virus. These results suggest that AT-752 is a promising compound to develop for the treatment of YFV infection.
The pre-existing human antibody repertoire to computationally optimized influenza H1 hemagglutinin vaccines
Authors: Nagashima Kaito , Dzimianski John V. , Han Julianna , Abbadi Nada , Gingerich Aaron D. , Royer Fredejah , O’Rourke Sara , Sautto Giuseppe A. , Ross Ted M. , Ward Andrew B. , DuBois Rebecca M. , Mousa Jarrod J. 
Published: October 2021

AbstractThe computationally optimized broadly reactive antigen (COBRA) approach has previously been used to generate hemagglutinin (HA) immunogens for several influenza subtypes that expand vaccine-elicited antibody breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA antigens. Cross-reactivity between wild type HA and H1 COBRA HA proteins were observed at both the oligoclonal B cell level and for a subset of isolated monoclonal antibodies (mAbs). The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 head and stem domains, and the majority of the mAbs had HAI and neutralizing activity against pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had HAI and neutralizing activity against a pre-pandemic H1 strain. One mAb, P1-05, targets the stem region of H1 HA proteins, but does not compete with known stem-targeting H1 mAbs. We determined that mAb P1-05 recognizes a recently discovered membrane proximal epitope on HA, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by P1-05. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA- reactive B cells that target head, central stalk, and anchor epitopes, and demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.SignificanceInfluenza imposes significant human and economic costs every year. The current seasonal vaccine elicits primarily strain-specific antibodies, and year to year vaccine effectiveness is variable. The COBRA approach could provide longer protection and obviate the requirement for annual vaccination. Whereas COBRA HAs have previously been evaluated in animal models, the pre-existing COBRA HA-reactive human B cell population has yet to be elucidated, and is important to identify specific B cells that may be recalled by H1 HA COBRA vaccination. This work demonstrates that seasonally vaccinated individuals possess a functional B cell population targeting both head and stem domains that could be recalled with COBRA HA immunogens.
Intestinal Gluconeogenesis Regulates Brown and White Adipose Tissues Functions in mice
Authors: Vily-Petit Justine , Soty-Roca Maud , Silva Marine , Micoud Manon , Bron Clara , Raffin Margaux , Beiroa Daniel , Nogueiras Rubén , Roussel Damien , Gautier-Stein Amandine , Rajas Fabienne , Cota Daniela , Mithieux Gilles 
Published: October 2021

ABSTRACTObjectiveIntestinal gluconeogenesis, via the initiation of a gut-brain nervous circuit, accounts for the metabolic benefits linked to dietary proteins or fermentable fibre in rodents and has been positively correlated with the rapid amelioration of body weight after gastric bypass surgery in obese humans. In particular, the activation of intestinal gluconeogenesis moderates the development of hepatic steatosis accompanying obesity. In this study, we investigated the specific effects of intestinal gluconeogenesis on adipose tissue metabolism, independently of its induction by nutritional manipulation.MethodsWe used two transgenic mouse models of suppression or overexpression of G6PC, the catalytic subunit of glucose-6 phosphatase, the key enzyme of endogenous glucose production, specifically in the intestine.ResultsUnder a hypercaloric diet, mice with a genetic overexpression of intestinal gluconeogenesis showed a lower adiposity and higher thermogenic capacities than wild-type mice, featuring marked browning of white adipose tissue and prevention of the whitening of brown adipose tissue. Suppression of sympathetic nervous signalling in brown adipose tissue impairs the activation of thermogenesis. Conversely, mice with genetic suppression of intestinal gluconeogenesis exhibit an increase in adiposity under standard diet, associated with a decreased expression of markers of thermogenesis in both the brown and white adipose tissues.ConclusionIntestinal gluconeogenesis is sufficient in itself to activate the sympathetic nervous system and prevent the expansion and the metabolic alterations of brown and white adipose tissues metabolism under high calorie diet, thus preventing the development of obesity. These data increase knowledge of the mechanisms of weight reduction in gastric bypass surgery and pave the way of new approaches to prevent or cure obesity.