bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nonsense mutation inTFECis the likely cause of the recessive piebald phenotype in ball pythons (Python regius)
Authors: Garcia-Elfring Alan , Roffey Heather L. , Hendry Andrew P. , Barrett Rowan D. H. 
Published: November 2020

AbstractCaptive-bred ball pythons (Python regius) represent a powerful model system for studying the genetic basis of colour variation and Mendelian phenotypes in vertebrates. Although hundreds of Mendelian phenotypes (colour morphs) affecting colouration and patterning have been described for ball pythons, the genes causing these colour morphs remain unknown. Here, we used crowdsourcing of samples from commercial ball python breeders to investigate the genetic basis of a classic phenotype found in the pet trade, the piebald [characterized by dorsolateral patches of unpigmented (white) skin]. We used whole-genome sequencing of pooled samples followed by population genetic methods to delineate the genomic region containing the causal gene. We identifiedTFECof the MIT-family of transcription factors as a candidate gene. Functional annotation of SNPs identified a nonsense mutation inTFEC, which we conclude is the likely causal variant for the piebald phenotype. Our work shows that ball python colour morphs have the potential to be an excellent model system for studying the genetic basis of pigment variation in vertebrates, and highlights how collaborations with commercial breeders can accelerate discoveries.
Natural isotope correction improves analysis of protein modification dynamics
Authors: Dietze Jörn , van Pijkeren Alienke , Egger Anna-Sophia , Ziegler Mathias , Kwiatkowski Marcel , Heiland Ines 
Published: November 2020

AbstractStable isotope labelling in combination with high resolution mass spectrometry approaches are increasingly used to analyse both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.
Evaluation of azithromycin or hydroxychloroquine plus azithromycin combination therapy on cardiac conduction and function in guinea pigs
Authors: Li Xiang , Tan Weijiang , Zheng Shuang , Sun Huan , Zhang Xiaoshen , Li Xiaohui , Chen Honghua , Ren Xuecong , He Tianzhen , Zhu Caiyi , Zhang Yu , Yang Feng Hua 
Published: November 2020

AbstractBackgroundIn the early stages of the coronavirus disease pandemic, the anti-malarial drug hydroxychloroquine (HCQ) and the antibiotic drug azithromycin (AZM) were widely used as emerging treatments. However, controversial cardiac toxicity results obtained from clinical trials and epidemic studies suggest that the cardiotoxicity of these two drugs should be re-evaluated. In the present study, we aimed to assess the impact of a short course of AZM or HCQ + AZM combination treatment on ECG and cardiac function in healthy guinea pigs.MethodsThirty-two male guinea pigs were randomly divided into four groups: control; AZM; HCQ; and HCQ + AZM groups. At 3, 6, and 9 days after treatment, electrocardiograms (ECGs) and echocardiographic techniques were used to determine important ECG parameters and cardiac functional parameters of the left ventricle (including posterior wall thickness, end systolic/end diastolic volume, ejection fraction, and fractional shortening).ResultsAlthough AZM decreased the heart rates of guinea pigs on day 9 (under anesthetized conditions), HCQ + AZM decreased heart rates on days 3, 6, and 9. The corrected QT intervals of guinea pigs after AZM and HCQ + AZM treatments were significantly increased, compared with CON and HCQ treatment respectively, on days 3, 6, and 9. However, QRS complex durations were not significantly different between the groups. AZM significantly decreased left ventricular ejection fraction (LVEF) and left ventricular fraction shortening (LVFS) on days 3, 6, and 9, whereas HCQ + AZM only decreased LVEF and LVFS on day 9. Posterior wall thickness and of the left ventricle in the diastolic and systolic states were not significantly different between these groups. In addition, compared with CON, AZM and HCQ decreased the EDV. And, in comparison with HCQ treatment, HCQ + AZM treatment increased ESV on day 9.ConclusionsAccording to our study, AZM significantly prolongs the QT interval and damages cardiac function. Moreover, HCQ + AZM treatment increased the risk of cardiac dysfunction compared with HCQ treatment.
Structural Basis of Stu2 Recruitment to Yeast Kinetochores
Authors: Zahm Jacob A. , Stewart Michael G. , Carrier Joseph S. , Harrison Stephen C. , Miller Matthew P. 
Published: November 2020

ABSTRACTAccurate chromosome segregation during cell division requires engagement of the kinetochores of sister chromatids with microtubules emanating from opposite poles of the mitotic spindle. In yeast, these “bioriented” metaphase sister chromatids experience tension as the corresponding microtubules (one per sister chromatid) shorten. Spindle-assembly checkpoint signaling appears to cease from a kinetochore under tension, which also stabilizes kinetochore-microtubule attachment in single-kinetochore experiments in vitro. The microtubule polymerase, Stu2, the yeast member of the XMAP215/ch-TOG protein family, associates with kinetochores in cells and contributes to tension-dependent stabilization, both in vitro and in vivo. We show here that a C-terminal segment of Stu2 binds the four-way junction of the Ndc80 complex (Ndc80c) and that amino-acid residues conserved both in yeast Stu2 orthologs and in their metazoan counterparts make specific contacts with Ndc80 and Spc24. Mutations that perturb this interaction prevent association of Stu2 with kinetochores, impair cell viability, produce biorientation defects, and delay cell-cycle progression. Ectopic tethering of the mutant Stu2 species to the Ndc80c junction restores wild-type function. These findings show that the role of Stu2 in tension sensing depends on its association with kinetochores by binding with Ndc80c.
Structure of Gcn1 bound to stalled and colliding 80S ribosomes
Authors: Pochopien Agnieszka A. , Beckert Bertrand , Kasvandik Sergo , Berninghausen Otto , Beckmann Roland , Tenson Tanel , Wilson Daniel N. 
Published: November 2020

AbstractProtein synthesis is essential to cells and requires a constant supply of nutrients. Amino acid starvation leads to accumulation of uncharged tRNAs that promote ribosomal stalling, which is sensed by the protein kinase Gcn2, together with its effector proteins, Gcn1 and Gcn20. Activation of Gcn2 phosphorylates eIF2, leading to a global repression of translation. Fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, which is a negative regulator of Gcn2. Despite the wealth of biochemical data, structures of Gcn proteins on the ribosome have remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the A-site region of the lead ribosome. The lead ribosome is stalled in a non-rotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, as well as Rbg2/Gir2 located in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings provide a structural basis for Rbg2/Gir2 repression of Gcn2, and also reveal that colliding disomes are the substrate for Gcn1 binding, which has important implications not only for Gcn2-activated stress responses, but also for general ribosome quality control (RQC) pathways.
CHARACTERISATION OF FUNGI OF STORED COMMON BEAN CULTIVARS GROWN IN MENOUA DIVISION, CAMEROON
Authors: Akwa Teh Exodus , Maingi John M , Birgen Jonah K. 
Published: November 2020

AbstractCommon bean is a legume grown globally especially in developing countries including Cameroon for human consumption. In Cameroon it is grown in a wide variety of agro ecological zones in quantities enough to last through the off growing season after harvest. Stored common bean after harvest in Cameroon are prone to fungal spoilage which contributes to post harvest losses. This study aimed at characterising storage fungi on cultivars of stored common bean using morphological and molecular techniques. Fungi were isolated from six stored cultivars of common bean; Kidney bean, Black bean, Navy bean, Pinto bean, Pea bean and Large seeded bean plated on potato dextrose agar media. Cultural, micro-morphological and molecular techniques were used to characterise the isolates. A total of four fungi isolates resulted. Homology matches of the gene sequences in the Genbank databases identified the isolates to be;Xylaria hypoxylon, Aspergillus flavus, Penicillium aethiopicumandFusarium oxysporium. Phylogenetic analysis and multiple sequence alignment showed these isolates were of distinct species. The species of fungi recovered from the stored cultivars signified poor preservation methods carried out after harvest. Effective management and control of these fungal species in common bean at storage will help reduce post-harvest losses and increase seed health.
Beauty and the brain: Investigating the neural and musical attributes of beauty during a naturalistic music listening experience
Authors: Brattico E. , Brusa A. , Dietz M.J. , Jacobsen T. , Fernandes H.M. , Gaggero G. , Toiviainen P. , Vuust P. , Proverbio A.M. 
Published: November 2020

ABSTRACTEvaluative beauty judgments are very common, but in spite of this commonality, are rarely studied in cognitive neuroscience. Here we investigated the neural and musical attributes of musical beauty using a naturalistic free-listening paradigm applied to behavioral and neuroimaging recordings and validated by experts’ judgments. In Study 1, 30 Western healthy adult participants rated continuously the perceived beauty of three musical pieces using a motion sensor. This allowed us to identify the passages in the three musical pieces that were inter-subjectively judged as beautiful or ugly. This informed the analysis for Study 2, where additional 36 participants were recorded with functional magnetic resonance imaging (fMRI) while they listened attentively to the same musical pieces as in Study 1. In Study 3, in order to identify the musicological features characterizing the passages that were consistently rated as beautiful or ugly in Study 1, we collected post-hoc questionnaires from 12 music-composition experts. Results from Study 2 evidenced focal regional activity in the orbitofrontal brain structure when listening to beautiful passages of music, irrespectively of the subjective reactions and individual listening biographies. In turn, the moments in the music that were consistently rated as ugly were associated with bilateral supratemporal activity. Effective connectivity analysis also discovered inhibition of auditory activation and neural communication with orbitofrontal cortex, especially in the right hemisphere, during listening to beautiful musical passages as opposed to intrinsic activation of auditory cortices and decreased coupling to orbitofrontal cortex during listening to ugly musical passages. Experts’ questionnaires indicated that the beautiful passages were more melodic, calm, sad, slow, tonal, traditional and simple than the ones negatively valenced. In sum, we identified a neural mechanism for inter-subjective beauty judgments of music in the supratemporal-orbitofrontal circuit, irrespectively of individual taste and listening biography. Furthermore, some invariance in objective musical attributes of beautiful and ugly passages was evidenced. Future studies might address the generalizability of the findings to non-Western listeners.
Fast inactivation of Na+current in rat adrenal chromaffin cells involves two independent inactivation pathways
Authors: Martinez-Espinosa Pedro L. , Neely Alan , Ding Jiuping , Lingle Christopher J. 
Published: November 2020

AbstractVoltage-dependent sodium (Nav) current in adrenal chromaffin cells (CCs) is rapidly inactivating and TTX-sensitive. The fractional availability of CC Nav current has been implicated in regulation of action potential (AP) frequency and the occurrence of slow-wave burst firing. To ascertain whether features of CC Nav inactivation might influence AP firing, we recorded Nav current in rat CCs, primarily from adrenal medullary slices. A key feature of CC Nav current is that recovery from inactivation, even following brief (5 ms) inactivation steps, exhibits two exponential components of generally similar amplitude. Variations of standard paired pulse protocols support the view that entry into the fast and slower recovery processes result from largely independent, competing inactivation pathways, both of which occur with similar onset times at depolarizing potentials. Over voltages from −120 to −80 mV, faster recovery varies from ~3 to 30 ms, while slower recovery from about 50-400 ms. At strong activation voltages (+0 mV and more positive), the relative entry into slow or fast recovery pathways is similar and independent of voltage. Trains of brief inactivating steps result in cumulative increases in the slower recovery fraction. This supports idea that brief recovery intervals preferentially allow recovery of channels from fast recovery pathways, thereby increasing the fraction of channels in the slow recovery pathway with each subsequent inactivation step. This provides a mechanism whereby differential rates of recovery produce use-dependent accumulation in slower recovery pathways. Consistent with use-dependent accumulation of channels in slow recovery pathways, repetitive AP clamp waveforms at 1-10 Hz frequencies reduce Nav availability to 10-20% of initial amplitude dependent on holding potential. The results indicate that there are two distinct pathways of fast inactivation, one that leads to normal fast recovery and the other with a slower time course, which together are well-suited to mediate use-dependent changes in Nav availability.
Neural responses to sensory novelty with and without conscious access
Authors: Osorio Sergio , Irani Martín , Herrada Javiera , Aboitiz Francisco 
Published: November 2020

AbstractDetection of novel stimuli that violate statistical regularities in the sensory scene is of paramount importance for the survival of biological organisms. Event-related potentials, phasic increases in pupil size, and evoked changes in oscillatory power in the theta (4-8 Hz) frequency range have been proposed as markers of sensory novelty detection. However, how conscious access to novelty modulates these different brain responses is not well understood. Here, we studied the neural responses to sensory novelty in the auditory modality with and without conscious access. We identified individual thresholds for conscious auditory discrimination and presented to our participants sequences of tones, where the last stimulus could be another standard, a subthreshold target or a suprathreshold target. Participants were instructed to report whether the last tone of each sequence was the same or different from those preceding it. Results indicate that stimulus evaluation and overt decision-making mechanisms, indexed by the P3 event-related response and reaction times, best predict whether a novel stimulus will be consciously accessed or not. In contrast, increased pupil size does not predict conscious access to novelty but reflects unexpected sensory uncertainty. These results highlight the interplay between bottom-up and top-down mechanisms and how the brain weights neural responses to novelty and uncertainty during perception and goal-directed behavior.
CryoET structures of immature HIV Gag reveal a complete six-helix bundle and stabilizing small molecules distinct from IP6
Authors: Mendonça Luiza , Sun Dapeng , Ning Jiying , Liu Jiwei , Kotecha Abhay , Olek Mateusz , Frosio Thomas , Fu Xiaofeng , Himes Benjamin A , Kleinpeter Alex B. , Freed Eric O. , Zhou Jing , Aiken Christopher , Zhang Peijun 
Published: November 2020

AbstractGag is the major HIV-1 structural polyprotein precursor. The Gag SP1 domain with the last residues of CA have been hypothesized to form a six-helix bundle necessary for particle assembly, but this bundle has not been fully resolved. Here, we determined the structures of complete CA-SP1 six-helix bundle connecting to the NC domain, from bothin vitroGag assemblies and viral-like particles (VLPs) carrying a T8I mutation in SP1, to near-atomic resolutions using cryoET and subtomogram averaging. The structures revealed novel densities, however distinct from IP6, inside the six-helix bundle of Gag assemblies, stabilizing the immature lattice. Interestingly, the T8I mutation impaired proteolytic cleavage of Gag at both SP1 boundaries. Our findings signify the involvement of small molecules in immature Gag assembly and provide the structural basis for development of small molecule inhibitors that stabilize SP1 helix, thus interfere with PR-mediated virus maturation.
Nav1.3 and fibroblast growth factor homologous factor 14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells
Authors: Martinez-Espinosa P.L. , Yang C. , Xia X.M. , Lingle C.J. 
Published: November 2020

AbstractAdrenal chromaffin cells (CCs) in rodents express a rapidly inactivating, TTX-sensitive sodium current. The current has generally been attributed to Nav1.7, although a possible role for Nav1.3 has also been suggested. Nav channels in rat CCs rapidly inactivate into two separable pathways, which differ in their time course of recovery from inactivation. One population recovers with time constants similar to traditional fast inactivation and the other about 10-fold slower. Inactivation properties suggest that the two pathways result from a single homogenous population of channels. Here we probe the properties and molecular components of the Nav current present in mouse CCs. We first confirm that functional properties of Nav current in rat and mouse cells are generally similar in terms of activation range, steady-state inactivation, and dual pathway fast inactivation. The results then show that all inward Nav current is absent in CCs from Nav1.3 KO mice. Subsequently, in a mouse with KO of fibroblast growth factor homology factor 14 (FGF14), we find that the slow component of recovery from fast inactivation is completely absent in most CCs, with no change in the time constant of fast recovery. Experiments probing the use-dependence of Nav current diminution between WT and FGF14 KO mice directly demonstrate a role of slow recovery from inactivation in determination of Nav current availability. Overall, the results indicate that the FGF14-mediated inactivation is the major determinant in defining use-dependent changes in Nav availability in CCs. We also consider the potential impact that inactivating FGF’s with different recovery kinetics can exert on differential use-dependent changes in Nav availability.
MINSTED fluorescence localization and nanoscopy
Authors: Weber Michael , Leutenegger Marcel , Stoldt Stefan , Jakobs Stefan , Mihaila Tiberiu S. , Butkevich Alexey N. , Hell Stefan W. 
Published: November 2020

AbstractWe introduce MINSTED, a stimulated-emission-depletion (STED) based fluorescence localization and super-resolution microscopy concept providing spatial precision and resolution down to the molecular scale. In MINSTED, the intensity minimum of the STED donut, and hence the point of minimal STED, serves as a movable reference coordinate for fluorophore localization. As the STED rate, the background, and the required number of fluorescence detections are low compared to most other STED microscopy and localization methods, MINSTED entails substantially less fluorophore bleaching. In our implementation, 200-1000 detections per fluorophore provide a localization precision of 1-3 nm in standard deviation, which in conjunction with independent single fluorophore switching translates to a ~100-fold improvement of far-field microscopy resolution over the diffraction limit. The performance of MINSTED nanoscopy is demonstrated by imaging the distribution of Mic60 proteins in the mitochondrial inner membrane of human cells.
Catestatin induces glycogenesis by stimulating phosphoinositide 3-kinase-AKT pathway
Authors: Bandyopadhyay Gautam , Tang Kechun , Webster Nicholas J.G. , van den Bogaart Geert , Mahata Sushil K. 
Published: November 2020

AbstractAimDefects in hepatic glycogen synthesis contribute to postprandial hyperglycemia in type 2 diabetic (T2D) patients. Chromogranin A (CgA) peptide Catestatin (CST: hCgA352-372) has been shown to improve glucose tolerance in insulin-resistant mice. Here, we seek to determine whether CST also reduces hyperglycemia by increasing hepatic glycogen synthesis.MethodsWe determined liver glycogen, glucose-6-phosphate (G6P), uridine diphosphate glucose (UDPG), and glycogen synthase (GYS2) activities; plasma insulin, glucagon, norepinephrine (NE), and epinephrine (EPI) levels in fed and fasted liver of lean and obese mice as well as in CST knockout (CST-KO) mice after treatments with saline, CST, or insulin. We also determined glycogen synthesis and glycogenolysis in primary hepatocytes. In addition, we analyzed phosphorylation signals of Insulin receptor (IR), insulin receptor substrate-1 (IRS-1), phosphatidylinositol dependent kinase-1 (PDK-1), GYS2, glycogen synthase kinase-3β (GSK-3β), AKT (an enzyme in AKR mouse that produces Thymoma)/PKB (protein kinase B) and mTOR (mammalian/mechanistic target of rapamycin) by immunoblotting.ResultsCST stimulated glycogen accumulation in fed and fasted liver and in primary hepatocytes. CST reduced plasma NE and EPI levels, suggesting that CST promotes glycogenesis by inhibiting catecholamine-induced glycogenolysis. CST also directly stimulated glycogenesis and inhibited NE and EPI-induced glycogenolysis in hepatocytes. CST elevated the levels of UDPG and increased GYS2 activity, thus redirecting G6P to the glycogenic pathway. CST-KO mice had decreased liver glycogen that was restored by treatment with CST, reinforcing the crucial role of CST in hepatic glycogenesis. CST can improve insulin signals downstream of insulin receptor IR and IRS-1 by enhancing phospho-AKT signals through stimulation of PDK-1 and mTORC2 (mTOR complex 2) activities.ConclusionsWe conclude that CST directly promotes the glycogenic pathway and reduces plasma glucose levels in insulin-resistant mice by (i) reducing glucose production, (ii) increasing glycogen synthesis from UDPG, and (iii) reducing glycogenolysis. This is achieved by enhancing downstream insulin signaling.