bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Conditioning Produces Merged Long-term Memory inDrosophila
Authors: Zhao Bohan , Sun Jiameng , Li Qian , Zhong Yi 
Published: January 2021

AbstractMultiple spaced trials of aversive differential conditioning can produce two independent long-term memories (LTMs) of opposite valence. One is an aversive memory for avoiding the conditioned stimulus (CS+), and the other is a safety memory for approaching the non-conditioned stimulus (CS–). Here, we show that a single trial of aversive differential conditioning yields one merged LTM (mLTM) for avoiding both CS+ and CS–. Such mLTM can be detected after sequential exposures to the shock-paired CS+ and unpaired CS–, and be retrieved by either CS+ or CS–. The formation of mLTM relies on triggering aversive-reinforcing dopaminergic neurons and subsequent new protein synthesis. Expressing mLTM involves αβ Kenyon cells and corresponding approach-directing mushroom body output neurons (MBONs), in which similar-amplitude long-term depression of responses to CS+ and CS– seems to signal the mLTM. Our results suggest that animals can develop distinct strategies for occasional and repeated threatening experiences.
Functional and multiscale 3D structural investigation of brain tissue through correlativein vivophysiology, synchrotron micro-tomography and volume electron microscopy
Authors: Bosch Carles , Ackels Tobias , Pacureanu Alexandra , Zhang Yuxin , Peddie Christopher J , Berning Manuel , Rzepka Norman , Zdora Marie-Christine , Whiteley Isabell , Storm Malte , Bonnin Anne , Rau Christoph , Margrie Troy , Collinson Lucy , Schaefer Andreas T 
Published: January 2021

AbstractAttributingin vivoneurophysiology to the brains’ ultrastructure requires a large field of view containing contextual anatomy. Electron microscopy (EM) is the gold standard technique to identify ultrastructure, yet acquiring volumes containing full mammalian neural circuits is challenging and time consuming using EM. Here, we show that synchrotron X-ray computed tomography (SXRT) provides rapid imaging of EM-prepared tissue volumes of several cubic millimetres. Resolution was sufficient for distinguishing cell bodies as well as for tracing apical dendrites in olfactory bulb and hippocampus, for up to 350 μm. Correlating EM with SXRT allowed us to associate dendritic spines on pyramidal cell apical dendrites in the stratum radiatum to their corresponding soma locations. Superficial pyramidal neurons had larger spine apparatus density compared to deeper ones, implying differential synaptic plasticity for superficial and deeper cells. Finally, we show that X-ray tomography and volume EM can be reliably correlated to priorin vivoimaging. Thus, combining functional measurements with multiscale X-ray microscopy and volume EM establishes a correlative workflow that enables functional and structural investigation of subcellular features in the context of cellular morphologies, tissues and ultimately whole organs.
Activity and stress during a critical period regulate olfactory sensory neuron differentiation
Authors: Jafari Shadi , Henriksson Johan , Yan Hua , Alenius Mattias 
Published: January 2021

AbstractHere, we reveal that the regulation ofDrosophilaodorant receptor (OR) expression during the pupal stage is permissive and imprecise. We found that olfactory sensory neuron activity directly after hatching both directs and refines OR expression. We demonstrate that, as in mice,dLsd1andSu(var)3-9balance heterochromatin formation to direct OR expression. Neuronal activity induces dLsd1andSu(var)3-9expression, linking neuronal activity to OR expression. OR expression refinement shows a restricted duration, suggesting a gene regulatory critical period brings olfactory sensory neuron differentiation to an end. Consistent with a change in differentiation, stress during the critical period repressesdLsd1andSu(var)3-9expression and makes the early permissive OR expression permanent. This induced permissive gene regulatory state makes OR expression resilient to stress later in life. Hence, during a critical period, OR activity feedback similar to in mouse OR selection, defines adult OR expression inDrosophila.
Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent
Authors: Waschke Leonhard , Donoghue Thomas , Fiedler Lorenz , Smith Sydney , Garrett Douglas D. , Voytek Bradley , Obleser Jonas 
Published: January 2021

AbstractA hallmark of electrophysiological brain activity is its 1/f-like spectrum – power decreases with increasing frequency. The steepness of this “roll-off” is approximated by the spectral exponent, which in invasively recorded neural populations reflects the balance of excitatory to inhibitory neural activity (E:I balance). Here, we first establish that the spectral exponent of non-invasive electroencephalography (EEG) recordings is highly sensitive to general (i.e., anaesthesia-driven) changes in E:I balance. Building on the EEG spectral exponent as a viable marker of E:I, we then demonstrate its sensitivity to the focus of selective attention in an EEG experiment during which participants detected targets in simultaneous audio-visual noise. In addition to these endogenous changes in E:I balance, EEG spectral exponents over auditory and visual sensory cortices also tracked auditory and visual stimulus spectral exponents, respectively. Individuals’ degree of this selective stimulus–brain coupling in spectral exponents predicted behavioural performance. Our results highlight the rich information contained in 1/f-like neural activity, providing a window into diverse neural processes previously thought to be inaccessible in non-invasive human recordings.
Simple and Rapid High-Throughput Assay to Identify HSV-1 ICP0 Transactivation Inhibitors
Authors: Ly Cindy Y. , Yu Chunmiao , McDonald Peter , Roy Anuradha , Johnson David , Davido David J. 
Published: January 2021

AbstractHerpes simplex virus 1 (HSV-1) is a ubiquitous virus that results in lifelong infections due to it’s ability to cycle between lytic replication and latency. As an obligate intracellular pathogen, HSV-1 exploits host cellular factors to replicate and aid in its life cycle. HSV-1 expresses infected cell protein 0 (ICP0), an immediate-early regulator, to stimulate the transcription of all classes of viral genes via its E3 ubiquitin ligase activity. Mechanisms by which ICP0 activates viral gene expression and the cellular factors involved are largely unknown. Here we report an automated, inexpensive, and rapid high-throughput approach to examine the effects of small molecule compounds on ICP0 transactivator function in cells. Two HSV-1 reporter viruses, KOS6β (wt) anddlx3.1-6β (ICP0-null mutant), were used to monitor ICP0 transactivation activity through the HSV-1 ICP6 promoter::laczexpression cassette. A ≥10-fold difference in β-galactosidase activity was observed in cells infected with KOS6β compared todlx3.1-6β, demonstrating that ICP0 potently transactivates the ICP6 promoter. We established the robustness and reproducibility with a Z′- factor score of ≥0.69, an important criterium for high-throughput analyses. Approximately 19,000 structurally diverse compounds were screened and 76 potential inhibitors of the HSV-1 transactivator ICP0 were identified. We expect this assay will aid in the discovery of novel inhibitors and tools against HSV-1 ICP0. Using well-annotated compounds could identify potential novel factors and pathways that interact with ICP0 to promote HSV-1 gene expression.
Effects of arsenic on the topology and solubility of promyelocytic leukemia (PML)-nuclear bodies
Authors: Hirano Seishiro , Udagawa Osamu 
Published: January 2021

AbstractPromyelocytic leukemia (PML) proteins are involved in the pathogenesis of acute promyelocytic leukemia (APL). Trivalent arsenic (As3+) is known to cure APL by binding to cysteine residues of PML and enhance the degradation of PML-retinoic acid receptor α (RARα), a t(15;17) gene translocation product in APL cells, and restore PML-nuclear bodies (NBs). The size, number, and shape of PML-NBs vary among cell types and during cell division. However, topological changes of PML-NBs in As3+-exposed cells have not been well-documented. We report that As3+-induced solubility shift underlies rapid SUMOylation of PML and late aggregation of PML-NBs. Most PML-NBs were toroidal and irregular-shaped inGFPPML-transduced CHO-K1 and HEK293 cells, respectively. The annular PML-NBs appeared unstable and dissipated into small PML-NBs in HEK cells. Exposure to As3+and antimony (Sb3+) greatly reduced the solubility of PML and enhanced SUMOylation within 2 h, and prolonged exposure resulted in PML-NB agglomeration. Exposure to bismuth (Bi3+), another Group 15 element, did not induce any of these changes. ML792, a SUMO activation inhibitor, reduced the number of PML-NBs and increased the size of the NBs, but had little effect on the As3+-induced solubility change of PML. The results show that SUMOylation regulates the dynamics of PML-NBs but does not contribute to the As3+-induced solubility change of PML.
Distinct lung-homing receptor expression and activation profiles on NK cell and T cell subsets in COVID-19 and influenza
Authors: Brownlie Demi , Rødahl Inga , Varnaite Renata , Asgeirsson Hilmir , Glans Hedvig , Falck-Jones Sara , Vangeti Sindhu , Buggert Marcus , Ljunggren Hans-Gustaf , Michaëlsson Jakob , Gredmark-Russ Sara , Smed-Sörensen Anna , Marquardt Nicole 
Published: January 2021

AbstractRespiratory viral infections with SARS-CoV-2 or influenza viruses commonly induce a strong infiltration of immune cells into the lung, with potential detrimental effects on the integrity of the lung tissue. Despite comprising the largest fractions of circulating lymphocytes in the lung, little is known about how blood natural killer (NK) cells and T cell subsets are equipped for lung-homing in COVID-19 and influenza. Using 28-colour flow cytometry and re-analysis of published RNA-seq datasets, we provide a detailed comparative analysis of NK cells and T cells in peripheral blood from moderately sick COVID-19 and influenza patients, focusing on the expression of chemokine receptors known to be involved in leukocyte recruitment to the lung. The results reveal a predominant role for CXCR3, CXCR6, and CCR5 in COVID-19 and influenza patients, mirrored by scRNA-seq signatures in peripheral blood and bronchoalveolar lavage from publicly available datasets. NK cells and T cells expressing lung-homing receptors displayed stronger phenotypic signs of activation as compared to cells lacking lung-homing receptors, and activation was overall stronger in influenza as compared to COVID-19. Together, our results indicate migration of functionally competent CXCR3+, CXCR6+, and/or CCR5+NK cells and T cells to the lungs in moderate COVID-19 and influenza patients, identifying potential common targets for future therapeutic interventions in respiratory viral infections.Author summaryThe composition of in particular CXCR3+and/or CXCR6+NK cells and T cells is altered in peripheral blood upon infection with SARS-CoV-2 or influenza virus in patients with moderate disease. Lung-homing receptor-expression is biased towards phenotypically activated NK cells and T cells, suggesting a functional role for these cells co-expressing in particular CXCR3 and/or CXCR6 upon homing towards the lung.
An advanced lentil backcross population developed from a cross betweenLens culinaris×L. ervoidesfor future disease resistance and genomic studies
Authors: Gela Tadesse S , Adobor Stanley , Khazaei Hamid , Vandenberg Albert 
Published: January 2021

AbstractGenetically accessible variation to some of the abiotic and biotic stresses are limited in the cultivated lentil (Lens culinarisMedik.) germplasm. Introgression of novel alleles from its wild relative species might be required for enhancing the genetic improvement of the crop.L. ervoides, one of the wild relatives of lentil, is a proven source of disease resistance for the crop. Here we introduce a lentil advanced backcross population (LABC-01) developed in cultivar CDC Redberry background, based onL. ervoidesalleles derived from an interspecific recombinant inbred population, LR-59-81. Two-hundred and seventeen individuals of the LABC-01 population at BC2F3:4generation were screened for the race 0 of anthracnose (Colletotrichum lentis) and stemphylium blight (Stemphylium botryosum) under controlled conditions. The population showed significant variations for both diseases and transfer of resistance alleles into the elite cultivar was evident. It also segregated for other traits such as days to flowering, seed coat colour, seed coat pattern and flower colour. Overall, we showed that LABC-01 population can be used in breeding programs worldwide to improve disease resistance and will be available as a valuable genetic resource for future genetic analysis of desired loci introgressed fromL. ervoides.
Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones
Authors: Yakubu Unekwu M. , Morano Kevin A. 
Published: January 2021

AbstractMolecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is related to the canonical Hsp70 class of protein folding molecular chaperones and interacts with Hsp70 as a nucleotide exchange factor (NEF), promoting rapid cycling of ADP for ATP. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles remain undefined. Previous work inDrosophila melanogasterhas shown that loss of the sole Hsp110 gene (Hsc70cb) accelerates the aggregation of polyglutamine (polyQ)-expanded human Huntingtin, while its overexpression protects against polyQ-mediated neuronal cell death. We hypothesize that in addition to its role as an Hsp70 NEF,DrosophilaHsp110 may function in the fly as a protective protein “holdase”, preventing the aggregation of unfolded polypeptides via the SBD-β subdomain. Using anin vitroprotein aggregation assay we demonstrate for the first time thatDrosophilaHsp110 effectively prevents aggregation of the model substrate citrate synthase. We also report the discovery of a redundant and heretofore unknown potent holdase capacity in a 138 amino-acid region of Hsp110 carboxyl-terminal to both SBD-β and SBD-α (henceforth called the C-terminal extension). This sequence is highly conserved in metazoan Hsp110 genes, completely absent from fungal representatives, includingSaccharomyces cerevisiae SSE1, and is computationally predicted to contain an intrinsically disordered region (IDR). We demonstrate that this IDR sequence within the human Hsp110s, Apg-1 and Hsp105α, inhibits the formation of amyloid Aβ-42 and α-synuclein fibrilsin vitrobut cannot mediate fibril disassembly. Together these findings demonstrate the existence of a second independent, passive holdase property of metazoan Hsp110 chaperones capable of suppressing both general protein aggregation and amyloidogenesis and raise the possibility of exploitation of this IDR for therapeutic benefit in combating neurodegenerative disease.
Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Authors: Trotter Valentine V. , Shatsky Maxim , Price Morgan N. , Juba Thomas R. , Zane Grant M. , De León Kara B. , Majumder Erica L. , Gui Qin , Ali Rida , Wetmore Kelly M. , Kuehl Jennifer V. , Arkin Adam P. , Wall Judy D. , Deutschbauer Adam M. , Chandonia John-Marc , Butland Gareth P. 
Published: January 2021

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRBDesulfovibrio vulgarisHildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein
Authors: Hodge Curtis D. , Rosenberg Daniel J. , Wilamowski Mateusz , Joachimiak Andrzej , Hura Greg L. , Hammel Michal 
Published: January 2021

AbstractMonoclonal antibodies (mAbs) are the basis of treatments and diagnostics for pathogens and other biological phenomena. We conducted a structural characterization of mAbs against the N-terminal domain of nucleocapsid protein (NPNTD) from SARS-CoV-2 using small angle X-ray scattering (SAXS). Our solution-based results distinguished the mAbs’ flexibility and how this flexibility impacts the assembly of multiple mAbs on an antigen. By pairing two mAbs that bind different epitopes on the NPNTD, we show that flexible mAbs form a closed sandwich-like complex. With rigid mAbs, a juxtaposition of the Fabs is prevented, enforcing a linear arrangement of the mAb pair, which facilitates further mAb polymerization. In a modified sandwich ELISA, we show the rigid mAb-pairings with linear polymerization led to increased NPNTDdetection sensitivity. These enhancements can expedite the development of more sensitive and selective antigen-detecting point-of-care lateral flow devices (LFA), key for early diagnosis and epidemiological studies of SARS-CoV-2 and other pathogens.
A fragment-based protein interface design algorithm for symmetric assemblies
Authors: Laniado Joshua , Meador Kyle , Yeates Todd O. 
Published: January 2021

ABSTRACTTheoretical and experimental advances in protein engineering have led to the creation of precisely defined, novel protein assemblies of great size and complexity, with diverse applications. One powerful approach involves designing a new attachment or binding interface between two simpler symmetric oligomeric protein components. The required methods of design, which present both similarities and key differences compared to problems in protein docking, remain challenging, and are not yet routine. With the aim of more fully enabling this emerging area of protein material engineering, we developed a computer program, Nanohedra, to introduce two key advances. First, we encoded in the program the construction rules (i.e. the search space parameters) that underlie all possible symmetric material constructions. Second, we developed algorithms for rapidly identifying favorable docking/interface arrangements based on tabulations of empirical patterns of known protein fragment-pair associations. As a result, the candidate poses that Nanohedra generates for subsequent amino acid interface design appear highly native-like (at the protein backbone level), while simultaneously conforming to the exacting requirements for symmetry-based assembly. A retrospective computational analysis of successful vs failed experimental studies supports the expectation that this should improve the success rate for this challenging area of protein engineering.
Essential Role of Placenta Derived Interferon Stimulated Gene 20 Against ZIKA Virus Infection
Authors: Ding Jiahui , Aldo Paulomi , Roberts Cai M. , Stabach Paul , Liu Hong , You Yuan , Qiu Xuemin , Jeong Jiwon , Maxwell Anthony , Lindenbach Brett , Braddock Demetrios , Liao Aihua , Mor Gil 
Published: January 2021

AbstractZika virus is a positive-sense single-stranded RNA virus, which can be transmitted across the placenta and leads to adverse effects on fetal development during pregnancy. The severity of these complications highlights the importance of prevention and treatment. However, no vaccines or drugs are currently available. In this study, we characterized the IFNβ-mediated antiviral response in trophoblast cells in order to identify critical components that are necessary for the successful control of viral replication; and determined whether we could use the components of the IFN-induced response as a replacement therapy for ZIKA viral infection during pregnancy. We identified and characterized interferon stimulated gene 20 (ISG20), playing a central role in controlling Zika infection in trophoblast cells, and successfully established a recombinant ISG20-Fc protein that effectively decrease viral titers in vitro and in vivo by maintaining its exonuclease activity and displaying immune modulatory functions. Therefore, rISG20-Fc is a promising anti-viral/immune modulatory approach for the control and prevention of RNA viral infections such as ZIKA virus.
CwlQ is required for swarming motility but not flagellar assembly inBacillus subtilis
Authors: Sanchez Sandra , Dunn Caroline M , Kearns Daniel B. 
Published: January 2021

ABSTRACTHydrolytic enzymes play an essential role in the remodeling of bacterial peptidoglycan (PG), an extracellular mesh-like structure that retains the membrane in the context of high internal osmotic pressure. Peptidoglycan (PG) integrity must be unfailingly stable to preserve cell integrity but must also be dynamically remodeled for the cell grow, divide and insert macromolecular machines. The flagellum is one such macromolecular machine that transits the PG and the insertion of which is aided by localized activity of a dedicated PG hydrolase in Gram-negative bacteria. To date, there is no known dedicated hydrolase in Gram-positive bacteria for insertion of flagella and here we take a reverse-genetic candidate-gene approach to find that cells mutated for the lytic transglycosylase CwlQ exhibited a severe defect in flagellar dependent swarming motility. We show that CwlQ required its active site to promote swarming, was expressed by the motility sigma factor SigD, and was secreted by the type III secretion system housed inside the flagellum. Nonetheless, cells mutated for CwlQ remained proficient for flagellar biosynthesis even when mutated in combination with four other hydrolases related to motility (LytC, LytD, LytF, and CwlO). The PG hydrolase essential for flagellar synthesis inB. subtilis, if any, remains unknown.