bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of SYCP3-related XLR3 disrupts the initiation of meiotic sex chromosome inactivation in mouse spermatogenesis
Authors: Naveh Natali Sobel , Foley Robert J. , DeNegre Katelyn R. , Evans Tristan C. , Czechanski Anne , Reinholdt Laura G. , O’Neill Michael J. 
Published: March 2021

AbstractIn mammals, the X and Y chromosomes share only small regions of homology called pseudo-autosomal regions (PAR) where pairing and recombination in spermatocytes can occur. Consequently, the sex chromosomes remain largely unsynapsed during meiosis I and are sequestered in a nuclear compartment known as the XY body where they are transcriptionally silenced in a process called meiotic sex chromosome inactivation (MSCI). MSCI mirrors meiotic silencing of unpaired chromatin (MSUC), the sequestration and transcriptional repression of unpaired DNA observed widely in eukaryotes. MSCI is initiated by the assembly of the axial elements of the synaptonemal complex (SC) comprising the structural proteins SYCP2 and SYCP3 followed by the ordered recruitment of DNA Damage Response (DDR) factors to effect gene silencing. However, the precise mechanism of how unsynapsed chromatin is detected in meiocytes is poorly understood. The sex chromosomes in eutherian mammals harbor multiple clusters ofSYCP3-like amplicons comprising theXlrgene family, only a handful of which have been functionally studied. We used a shRNA-transgenic mouse model to create a deficiency in the testis-expressed multicopyXlr3genes to investigate their role in spermatogenesis. Here we show that knockdown ofXlr3in mice leads to spermatogenic defects and a skewed sex ratio that can be traced to MSCI breakdown. Spermatocytes deficient in XLR3 form the XY body and the SC axial elements therein, but are compromised in their ability to recruit DDR components to the XY body.Author SummaryA key event in the production of sperm is the pairing and synapsis of homologous chromosome pairs to facilitate genetic recombination during the first meiotic division. Chromosomal abnormalities that undermine pairing and synapsis in spermatocytes trigger a checkpoint that leads to removal of the abnormal cells via programmed cell death. In mammals, the sex chromosomes, X and Y, lack homology through most of their length and remain largely unpaired. To avoid triggering the checkpoint the X and Y are sequestered in a specialized nuclear compartment called the XY body. DNA damage response (DDR) proteins are recruited to the XY body in a highly ordered progression leading to repression of all gene transcription from the sex chromosomes. We show that knocking down expression of the X-linkedSYCR3-like gene,Xlr3,disrupts sex chromosome gene silencing by interfering with recruitment of DDR factors, leading to compromised sperm production.
Structural insights into the activation of human calcium-sensing receptor
Authors: Chen Xiaochen , Wang Lu , Ding Zhanyu , Cui Qianqian , Han Li , Kou Yongjun , Zhang Wenqing , Wang Haonan , Jia Xiaomin , Dai Mei , Shi Zhenzhong , Li Yuying , Li Xiyang , Geng Yong 
Published: March 2021

AbstractHuman calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that maintains Ca2+homeostasis in serum. Here, we present the cryo-electron microscopy structures of the CaSR in the inactive and active states. Complemented with previously reported crystal structures of CaSR extracellular domains, it suggests that there are three distinct conformations: inactive, intermediate and active state during the activation. We used a negative allosteric nanobody to stabilize the CaSR in the fully inactive state and found a new binding site for Ca2+ion that acts as a composite agonist with L-amino acid to stabilize the closure of active Venus flytraps. Our data shows that the agonist binding leads to the compaction of the dimer, the proximity of the cysteine-rich domains, the large-scale transitions of 7-transmembrane domains, and the inter-and intrasubunit conformational changes of 7-transmembrane domains to accommodate the downstream transducers. Our results reveal the structural basis for activation mechanisms of the CaSR.
Acclimation ofChlamydomonas reinhardtiito Nitric Oxide Stress Related to Respiratory Burst Oxidase-Like 2
Authors: Kuo Eva YuHua , Lee Tse-Min 
Published: March 2021

AbstractThe acclimation mechanism ofChlamydomonas reinhardtiito nitric oxide (NO) was studied by exposure toS-nitroso-N-acetylpenicillamine (SNAP), a NO donor. Treatment with 0.1 or 0.3 mM SNAP transiently inhibited photosynthesis within 1 h, followed by a recovery without growth impairment, while 1.0 mM SNAP treatment caused irreversible photosynthesis inhibition and mortality. The SNAP effects are avoided in the presence of the NO scavenger, 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-l-oxyl-3-oxide (cPTIO). RNA-seq, qPCR, and biochemical analyses were conducted to decode the metabolic shifts under sub-lethal NO stress by exposure to 0.3 mM SNAP in the presence or absence of 0.4 mM cPTIO. These findings revealed that the acclimation to NO stress comprises a temporally orchestrated implementation of metabolic processes: 1. trigger of NO scavenging elements to reduce NO level; 2. prevention of photo-oxidative risk through photosynthesis inhibition and antioxidant defense system induction; 3. acclimation to nitrogen and sulfur shortage; 4. degradation of damaged proteins through protein trafficking machinery (ubiquitin, SNARE, and autophagy) and molecular chaperone system for dynamic regulation of protein homeostasis. NO increased NADPH oxidase activity and respiratory burst oxidase-like 2 (RBOL2) transcript abundance, which were not observed in therbol2insertion mutant. Changes in gene expression in therbol2mutant and increased mortality under NO stress demonstrate that NADPH oxidase (RBOL2) is involved in the modulation of some acclimation processes (NO scavenging, antioxidant defense system, autophagy, and heat shock proteins) forChlamydomonasto cope with NO stress. Our findings provide insight into the molecular events underlying acclimation mechanisms inChlamydomonasto sub-lethal NO stress.One-sentence SummaryAcclimation machinery is triggered inChlamydomonas reinhardtiicells against sub-lethal nitric oxide stress.
Supramolecular cylinders target bulge structures in the 5’ UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication
Authors: Melidis Lazaros , Hill Harriet J. , Coltman Nicholas J. , Davies Scott P. , Winczura Kinga , Chauhan Tasha , Craig James S. , Garai Aditya , Hooper Catherine A..J. , Egan Ross T. , McKeating Jane A. , Hodges Nikolas J. , Stamataki Zania , Grzechnik Pawel , Hannon Michael J. 
Published: March 2021

AbstractThe untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with Molecular Dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5’ UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in the stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel antiviral agents.
Structural characterization of the antimicrobial peptides myxinidin and WMR in bacterial membrane mimetic micelles and bicelles
Authors: Cherniavskyi Yevhen K. , Oliva Rosario , Stellato Marco , Vecchio Pompea Del , Galdiero Stefania , Falanga Annarita , Dames Sonja A. , Tieleman D. Peter 
Published: March 2021

AbstractAntimicrobial peptides are a promising class of alternative antibiotics that interact selectively with negatively charged lipid bilayers. This paper presents the structural characterization of the antimicrobial peptides myxinidin and WMR associated with bacterial membrane mimetic micelles and bicelles by NMR, CD spectroscopy, and Molecular Dynamics simulations. Both peptides adopt a different conformation in the lipidic environment than in aqueous solution. The location of peptides in micelles and bicelles has been studied by paramagnetic relaxation enhancement experiments with paramagnetic tagged 5- and 16-doxyl stearic acid (5-/16-SASL). Multi-microsecond long molecular dynamics simulations of multiple copies of the peptides were used to gain an atomic level of detail on membrane-peptide and peptide-peptide interactions. Our results highlight an essential role of the negatively charged membrane mimetic in the structural stability of both myxinidin and WMR. The peptides localize predominantly in the membrane’s headgroup region and have a noticeable membrane thinning effect on the overall bilayer structure. Myxinidin and WMR show different tendency to selfaggregate, which is also influenced by the membrane composition (DOPE/DOPG versus DOPE/DOPG/CL) and can be related to the previously observed difference in the ability of the peptides to disrupt different types of model membranes.
A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection
Authors: Zhou Panpan , Yuan Meng , Song Ge , Beutler Nathan , Shaabani Namir , Huang Deli , He Wan-ting , Zhu Xueyong , Callaghan Sean , Yong Peter , Anzanello Fabio , Peng Linghang , Ricketts James , Parren Mara , Garcia Elijah , Rawlings Stephen A. , Smith Davey M. , Nemazee David , Teijaro John R. , Rogers Thomas F. , Wilson Ian A. , Burton Dennis R. , Andrabi Raiees 
Published: March 2021

ABSTRACTBroadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and, importantly, as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a coronavirus disease 2019 (COVID-19)-convalescent donor that exhibits broad reactivity with human beta-coronaviruses (β-CoVs). Here, we showed that CC40.8 targets the conserved S2 stem-helix region of the coronavirus spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem-peptide at 1.6 Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted CC40.8-like bnAbs are relatively rare in human COVID-19 infection and therefore their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan-β-CoV vaccines.SUMMARYA human mAb isolated from a COVID-19 donor defines a protective cross-neutralizing epitope for pan-β-CoV vaccine design strategies
Cellular variability of nonsense-mediated mRNA decay
Authors: Sato Hanae , Singer Robert H. 
Published: March 2021

AbstractNonsense-mediated mRNA decay (NMD) is an mRNA degradation pathway that eliminates transcripts containing premature termination codons (PTCs). Half-lives of the mRNAs containing PTCs demonstrate that a small percent escape surveillance and do not degrade. It is not known whether this escape represents variable mRNA degradation within cells or, alternatively cells within the population are resistant. Here we demonstrate a single-cell approach with a bi-directional reporter, which expresses two β-globin genes with or without a PTC in the same cell, to characterize the efficiency of NMD in individual cells. We found a broad range of NMD efficiency in the population; some cells degraded essentially all of the mRNAs, while others escaped NMD almost completely. Characterization of NMD efficiency together with NMD regulators in single cells showed cell-to-cell variability of NMD reflects the differential level of surveillance factors, SMG1 and phosphorylated UPF1. A single-cell fluorescent reporter system that enabled detection of NMD using flow cytometry revealed that this escape occurred either by translational readthrough at the PTC or by a failure of mRNA degradation after successful translation termination at the PTC.
Memory specific to temporal features of sound is formed by cue-selective enhancements in temporal coding enabled by inhibition of an epigenetic regulator
Authors: Rotondo Elena K. , Bieszczad Kasia M. 
Published: March 2021

ABSTRACTRecent investigation of memory-related functions in the auditory system have capitalized on the use of memory-modulating molecules to probe the relationship between memory and its substrates in auditory system coding. For example, epigenetic mechanisms, which regulate gene expression necessary for memory consolidation, are powerful modulators of learning-induced neuroplasticity and long-term memory formation (LTM). Inhibition of the epigenetic regulator histone deacetylase 3 (HDAC3) promotes LTM that is highly specific forspectralfeatures of sound. The present work demonstrates for the first time that HDAC3 inhibition also enables memory fortemporalfeatures of sound. Rats trained in an amplitude modulation (AM) rate discrimination task and treated with a selective inhibitor of HDAC3 formed memory that was unusually specific to the AM rate paired with reward. Unusually sound-specific memory revealed behaviorally was associated with a signal-specific enhancement in temporal coding in the auditory system: stronger phase-locking that was specific to the rewarded AM rate was revealed in both the surface-recorded frequency following response (FFR) and auditory cortical multiunit activity in rats treated with the HDAC3-inhibitor. Furthermore, HDAC3inhibition increased trial-to-trial cortical response consistency (relative to naïve and trained vehicle-treated rats) that generalized across different AM rates. Stronger signal-specific phase-locking correlated with individual behavioral differences in memory specificity for the AM signal. Together, these findings support that epigenetic mechanisms regulate activity-dependent processes that enhance discriminability of sensory cues encoded into LTM in both spectral and temporal domains, which may be important for remembering spectrotemporal features of sounds, e.g., as in human voices and speech.SIGNIFICANCE STATEMENTEpigenetic mechanisms have recently been implicated in memory and information processing. Here, we use a pharmacological inhibitor of histone deacetylase 3 (HDAC3) in a sensory model of learning to reveal, for the first time, its ability to enable unusually precise memory for amplitude modulated sound cues. In so doing, we uncover neural substrates for memory’s “specificity” for temporal sound cues. Memory specificity was supported by auditory cortical changes in temporal coding, including greater response consistency and stronger phase-locking. HDAC3 appears to regulate effects across domains that determine specific cue saliency for behavior. Thus, epigenetic players may gate how sensory information is stored in long-term memory and can be leveraged to reveal the neural substrates of sensory details stored in memory.
A flash-based thermal simulation of scanning paths in LPBF additive manufacturing
Authors: Ettaieb Kamel , Lavernhe Sylvain , Tournier Christophe 
Published: March 2021

Purpose
This paper aims to propose an analytical thermal three-dimensional model that allows an efficient evaluation of the thermal effect of the laser-scanning path. During manufacturing by laser powder bed fusion (LPBF), the laser-scanning path influences the thermo-mechanical behavior of parts. Therefore, it is necessary to validate the path generation considering the thermal behavior induced by this process to improve the quality of parts.

Design/methodology/approach
The proposed model, based on the effect of successive thermal flashes along the scanning path, is calibrated and validated by comparison with thermal results obtained by FEM software and experimental measurements. A numerical investigation is performed to compare different scanning path strategies on the Ti6Al4V material with different stimulation parameters.

Findings
The simulation results confirm the effectiveness of the approach to simulate the thermal field to validate the scanning strategy. It suggests a change in the scale of simulation thanks to high-performance computing resources.

Originality/value
The flash-based approach is designed to ensure the quality of the simulated thermal field while minimizing the computational cost.
Amazonian mammal monitoring using aquatic environmental DNA
Authors: Coutant Opale , Richard‐Hansen Cécile , de Thoisy Benoit , Decotte Jean‐Baptiste , Valentini Alice , Dejean Tony , Vigouroux Régis , Murienne Jérôme , Brosse Sébastien 
Published: March 2021

AbstractEnvironmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi‐aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi‐aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi‐aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
“Protein aggregates” contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation
Authors: Shmookler Reis Robert J. , Atluri Ramani , Balasubramaniam Meenakshisundaram , Johnson Jay , Ganne Akshatha , Ayyadevara Srinivas 
Published: March 2021

AbstractAll neurodegenerative diseases feature aggregates, which usually contain disease‐specific diagnostic proteins; non‐protein constituents, however, have rarely been explored. Aggregates from SY5Y‐APPSw neuroblastoma, a cell model of familial Alzheimer's disease, were crosslinked and sequences of linked peptides identified. We constructed a normalized “contactome” comprising 11 subnetworks, centered on 24 high‐connectivity hubs. Remarkably, all 24 are nucleic acid‐binding proteins. This led us to isolate and sequence RNA and DNA from Alzheimer's and control aggregates. RNA fragments were mapped to the human genome by RNA‐seq and DNA by ChIP‐seq. Nearly all aggregate RNA sequences mapped to specific genes, whereas DNA fragments were predominantly intergenic. These nucleic acid mappings are all significantly nonrandom, making an artifactual origin extremely unlikely. RNA (mostly cytoplasmic) exceeded DNA (chiefly nuclear) by twofold to fivefold. RNA fragments recovered from AD tissue were ~1.5‐to 2.5‐fold more abundant than those recovered from control tissue, similar to the increase in protein. Aggregate abundances of specific RNA sequences were strikingly differential between cultured SY5Y‐APPSw glioblastoma cells expressing APOE3 vs. APOE4, consistent with APOE4 competition for E‐box/CLEAR motifs. We identified many G‐quadruplex and viral sequences within RNA and DNA of aggregates, suggesting that sequestration of viral genomes may have driven the evolution of disordered nucleic acid‐binding proteins. After RNA‐interference knockdown of the translational‐procession factor EEF2 to suppress translation in SY5Y‐APPSw cells, the RNA content of aggregates declined by >90%, while reducing protein content by only 30% and altering DNA content by ≤10%. This implies that cotranslational misfolding of nascent proteins may ensnare polysomes into aggregates, accounting for most of their RNA content.
The correlates and extent of prescribing of medications for alcohol relapse prevention in England
Authors: Donoghue Kim 
Published: March 2021

AbstractAimsTo determine the pattern and extent of prescribing of medications for alcohol relapse prevention (ARP) in England.DesignCross‐sectional.SettingSpecialist drug and alcohol treatment providers in England reporting to the National Drug Treatment Monitoring System.ParticipantsService users aged 18+, with alcohol the primary substance of dependence, completing a treatment journey between April 2013 and March 2016 (n = 188 152).MeasurementsPrescription of medications for ARP during a treatment journey. Data on service users’ demographics, treatment and clinical characteristics were extracted.FindingsThe rate of prescribing medications for ARP was 2.1% in 2013/14, 6.8% in 2014/15 and 7.8% in 2015/16. A greater likelihood of prescription was associated with treatment journey year [2014/15; adjusted odds ratio (aOR) = 3.269, 95% confidence intervals (CI) = 3.044–3.510, 2015/16; aOR = 3.823, CI = 3.560–4.106], age (25–34; aOR = 1.622, CI = 1.380–1.907, 35–54; aOR = 1.901, CI = 1.628–2.220 or 55+; aOR = 1.700, CI = 1.446–1.999), female gender (aOR = 1.129, CI = 1.077–1.184), white ethnicity (aOR = 1.219, CI = 1.077–1.380), regional prevalence of alcohol dependence (middle rate; aOR = 1.121, CI = 1.024–1.228), severity of alcohol dependence (moderate dependence without complex needs; aOR = 1.329, CI = 1.244–1.419, severe dependence without complex needs; aOR = 1.308, CI = 1.188–1.441, moderate/severe dependence with complex needs; aOR = 1.131, CI = 1.020–1.255), treatment setting (inpatient; aOR = 10.512, CI = 9.950–11.104, primary care; aOR = 2.264, CI = 2.050–2.500, residential; aOR = 3.216, CI = 2.807–3.685), prior treatment for alcohol dependence (aOR = 1.242, CI = 1.183–1.304), longer treatment journey (aOR = 1.002, CI = 1.002–1.002), more drinking days in the prior 28 days (aOR = 1.021, CI = 1.018–1.024) and drinking a higher number of alcohol units in the prior 28 days (aOR = 1.002 CI = 1.001–1.004). Living in a region of England with the lowest alcohol prevalence was associated with a lower likelihood of prescription of medication for aRP (AOR = 0.491, CI = 0.436–0.552).ConclusionsIn England, medications for alcohol relapse prevention are rarely prescribed (e.g. 7.8% in 2015/16) and those prescriptions appear to be associated with specific service user demographics, treatment and clinical characteristics.