bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reevaluating the ability of cerebellum in associative motor learning
Authors: Li Da-bing , Yao Juan , Sun Lin , Wu Bing , Li Xuan , Liu Shu-lei , Hou Jing-ming , Liu Hong-liang , Sui Jian-feng , Wu Guang-yan 
Published: April 2019

AbstractIt has been well established that the cerebellum and its associated circuitry constitute the essential neuronal system for both delay and trace classical eyeblink conditioning (DEC and TEC). However, whether the cerebellum is sufficient to independently modulate the DEC, and TEC with a shorter trace interval remained controversial. Here, we used direct optogenetic stimulation of mossy fibers in the middle cerebellar peduncle (MCP) as a conditioned stimulus (CS) replacement for the peripheral CS (eg, a tone CS or a light CS) paired with a periorbital shock unconditioned stimulus (US) to examine the ability of the cerebellum to learn the DEC and the TEC with various trace intervals. Moreover, neural inputs to the pontine nucleus (PN) were pharmacological blocked to limit the associative motor learning inside the cerebellum. We show that all rats quickly acquired the DEC, indicating that direct optogenetic stimulation of mossy fibers in the left MCP is a very effective and sufficient CS to establish DEC and to limit the motor learning process inside the cerebellum. However, only five out of seven rats acquired the TEC with a 150-ms trace interval, three out of nine rats acquired the TEC with a 350-ms trace interval, and none of the rats acquired the TEC with a 500-ms trace interval. Moreover, pharmacological blocking glutamatergic and GABAergic inputs to the PN from the extra-cerebellar and cerebellar regions has no significant effect on the DEC and TEC learning with the optogenetic CS. These results indicate that the cerebellum has the ability to independently support both the simple DEC, and the TEC with a trace interval of 150 or 350 ms, but not the TEC with a trace interval of 500 ms. The present results are of great importance in our understanding of the mechanisms and ability of the cerebellum in associative motor learning and memory.
Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral
Authors: Lohr Kathryn E. , Khattri Ram B. , Guingab-Cagmat Joy , Camp Emma F. , Merritt Matthew E. , Garrett Timothy J. , Patterson Joshua T. 
Published: April 2019

AbstractGlobal threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.
Physiological stress levels in wild koala sub-populations facing anthropogenic induced environmental trauma and disease
Authors: Narayan Edward 
Published: April 2019

AbstractAustralian small mammals such as koalas must cope with immense pressure from anthropogenic induced stressors or trauma such as bushfires, vehicle collision impacts and habitat disturbance and land clearance. In addition, they must cope with diseases such as chlamydia. To date, there is no published literature on physiological stress levels in wild koala populations compared with identified environmental stressors. This study investigated physiological stress levels within sub-populations of wild koalas encountering environmental trauma and disease from New South Wales (NSW), Queensland (QLD) and South Australia (SA). Physiological stress was determined using a faecal glucocorticoid (or cortisol) metabolites (FGMs) enzyme-immunoassay (EIA) from 291 fresh faecal samples collected from wild koalas at the point of rescue. A healthy breeding sub-population from a forest reserve in QLD acted as a control group. Clearance of prime Eucalyptus habitat had the largest impact on FGMs, followed by bushfire related factors (e.g. flat demeanour, dehydration and burns injury). Koalas with other sources of physical injury (dog-attacks and vehicle collisions) and disease (chlamydia) also had higher FGMs compared to healthy wild koalas. Healthy wild koalas expressed the lowest median levels of FGMs. Overall, the results highlight that anthropogenic-induced stressors tend to increase physiological stress in wild koalas. Thus, the ultimate stressors such as habitat clearance and bush fire events could increase the incidences of proximate stressors such as dog attacks and vehicle collisions, and increase risks of foliage shortage, diseases and mortality. Therefore, there is need for ecological monitoring, conservation management actions and policy changes to curb the koala population crisis, especially within on-going and future land and road development programs.
Low fibrosis biomarker levels predict cardiac resynchronization therapy response
Authors: Massoullié Grégoire , Sapin Vincent , Ploux Sylvain , Rossignol Patrick , Mulliez Aurélien , Jean Frédéric , Marie Pierre-Yves , Merlin Charles , Pereira Bruno , Andronache Marius , Motreff Pascal , Chabin Xavier , Sellal Jean-Marc , Citron Bernard , Lusson Jean-René , Vorilhon Charles , Clerfond Guillaume , Bordachar Pierre , Zannad Faiez , Eschalier Romain 
Published: April 2019

AbstractCardiac fibrosis is associated with heart failure and poor prognosis. Fibrosis biomarkers have been poorly evaluated as a tool to predict cardiac resynchronization therapy (CRT) response generating conflicting results. The present study assessed the predictive value of cardiac fibrosis biomarkers on CRT response. Patients underwent clinical examination, echocardiography and blood fibrosis biomarker evaluation prior to CRT implantation. At six months, a positive response to CRT was defined by a composite endpoint of no death or hospitalization for heart failure, and presence of left ventricular (LV) reverse remodeling (decrease in LV end-systolic volume ≥15%). Sixty patients were included in a multicenter study. At 6 months, 38 were positive responders to CRT and reached the response criteria (63%). Compared to non-responders, CRT responders displayed lower concentration levels of the fibrosis biomarkers procollagen type I C-terminal propeptide [PICP 135[99–166] ng/ml vs. 179[142–226]ng/ml, p = 0.001)] and procollagen type III N-terminal propeptide [PIIINP 5.50[3.66–8.96] ng/ml vs. 8.01[5.01–11.86]ng/ml, p = 0.014)] at baseline. In multivariate analysis, a PICP ≤ 163 ng/ml was associated with a positive CRT response [OR = 7.8(1.3–46.7), p = 0.023] independently of the presence of LBBB, QRS duration, LV lead position or non-ischemic cardiomyopathy. Altogether, the present findings show that a lower degree of cardiac fibrosis is associated with a positive response after CRT implantation. PICP evaluation before CRT implantation could help improve patient selection.
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
Authors: Sieracki M. E. , Poulton N. J. , Jaillon O. , Wincker P. , de Vargas C. , Rubinat-Ripoll L. , Stepanauskas R. , Logares R. , Massana R. 
Published: April 2019

AbstractMarine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.
The Metabolomic Signature of Opa1 Deficiency in Rat Primary Cortical Neurons Shows Aspartate/Glutamate Depletion and Phospholipids Remodeling
Authors: Chao de la Barca Juan Manuel , Arrázola Macarena S. , Bocca Cinzia , Arnauné-Pelloquin Laetitia , Iuliano Olga , Tcherkez Guillaume , Lenaers Guy , Simard Gilles , Belenguer Pascale , Reynier Pascal 
Published: April 2019

AbstractPathogenic variants of OPA1, which encodes a dynamin GTPase involved in mitochondrial fusion, are responsible for a spectrum of neurological disorders sharing optic nerve atrophy and visual impairment. To gain insight on OPA1 neuronal specificity, we performed targeted metabolomics on rat cortical neurons with OPA1 expression inhibited by RNA interference. Of the 103 metabolites accurately measured, univariate analysis including the Benjamini-Hochberg correction revealed 6 significantly different metabolites in OPA1 down-regulated neurons, with aspartate being the most significant (p < 0.001). Supervised multivariate analysis by OPLS-DA yielded a model with good predictive capability (Q2cum = 0.65) and a low risk of over-fitting (permQ2 = −0.16, CV-ANOVA p-value 0.036). Amongst the 46 metabolites contributing the most to the metabolic signature were aspartate, glutamate and threonine, which all decreased in OPA1 down-regulated neurons, and lysine, 4 sphingomyelins, 4 lysophosphatidylcholines and 32 phosphatidylcholines which were increased. The phospholipid signature may reflect intracellular membrane remodeling due to loss of mitochondrial fusion and/or lipid droplet accumulation. Aspartate and glutamate deficiency, also found in the plasma of OPA1 patients, is likely the consequence of respiratory chain deficiency, whereas the glutamate decrease could contribute to the synaptic dysfunction that we previously identified in this model.
Mapping of apparent susceptibility yields promising diagnostic separation of progressive supranuclear palsy from other causes of parkinsonism
Authors: Sjöström Henrik , Surova Yulia , Nilsson Markus , Granberg Tobias , Westman Eric , van Westen Danielle , Svenningsson Per , Hansson Oskar 
Published: April 2019

AbstractThere is a need for methods that distinguish Parkinson’s disease (PD) from progressive supranuclear palsy (PSP) and multiple system atrophy (MSA), which have similar characteristics in the early stages of the disease. In this prospective study, we evaluate mapping of apparent susceptibility based on susceptibility weighted imaging (SWI) for differential diagnosis. We included 134 patients with PD, 11 with PSP, 10 with MSA and 44 healthy controls. SWI data were processed into maps of apparent susceptibility. In PSP, apparent susceptibility was increased in the red nucleus compared to all other groups, and in globus pallidus, putamen, substantia nigra and the dentate nucleus compared to PD and controls. In MSA, putaminal susceptibility was increased compared to PD and controls. Including all studied regions and using discriminant analysis between PSP and PD, 100% sensitivity and 97% specificity was achieved, and 91% sensitivity and 90% specificity in separating PSP from MSA. Correlations between putaminal susceptibility and disease severity in PD could warrant further research into using susceptibility mapping for monitoring disease progression and in clinical trials. Our study indicates that susceptibility in deep nuclei could play a role in the diagnosis of atypical parkinsonism, especially in PSP.
Timing of the Brunhes-Matuyama transition constrained by U-series disequilibrium
Authors: Ghaleb Bassam , Falguères Christophe , Carlut Julie , Pozzi Jean-Pierre , Mahieux Geoffroy , Boudad Larbi , Rousseau Louis 
Published: April 2019

AbstractU-series disequilibrium measurements carried out on thermogenic travertine samples from a 12.6 m-long core and a 10 m-thick section from southeastern Morocco yielded finite ages ranging from 500 ka to the present-day, as well as two clusters determined to be older than 500 ka. The calculation of initial 234U/238U activity ratios in all samples younger than 500 ka shows high, reasonably constant values, with an average of 5.172 ± 0.520 (one standard deviation). Assuming that this value prevailed for periods older than 500 ka, we derived ages of up to approximately 1.2 Ma using the initial 234U excess decay. Our results indicate that the two older clusters have ages of 776 ± 14 ka for samples from between 8 and 10.1 m and 1173 ± 22 ka for deeper samples respectively. The palaeomagnetic record of the core shows normal polarity inclinations from the surface to around 9 m followed by reverse polarity inclination and antipodal declinations. The inversion is attributed to the Brunhes-Matuyama transition. 234U excess ages for the interval corresponding to the part of the core where the polarity inversion occurred are in the range of 735 ± 51 to 794 ± 54 ka, with an arithmetic mean value of 776 ± 14 ka for the B-M transition. This age is in good agreement with that determined previously using other dating methods.
Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment
Authors: Pasari Nandita , Gupta Mayank , Eqbal Danish , Yazdani Syed Shams 
Published: April 2019

AbstractPaenibacillus polymyxa A18 was isolated from termite gut and was identified as a potential cellulase and hemicellulase producer in our previous study. Considering that members belonging to genus Paenibacillus are mostly free-living in soil, we investigated here the essential genetic features that helped P. polymyxa A18 to survive in gut environment. Genome sequencing and analysis identified 4608 coding sequences along with several elements of horizontal gene transfer, insertion sequences, transposases and integrated phages, which add to its genetic diversity. Many genes coding for carbohydrate-active enzymes, including the enzymes responsible for woody biomass hydrolysis in termite gut, were identified in P. polymyxa A18 genome. Further, a series of proteins conferring resistance to 11 antibiotics and responsible for production of 4 antibiotics were also found to be encoded, indicating selective advantage for growth and colonization in the gut environment. To further identify genomic regions unique to this strain, a BLAST-based comparative analysis with the sequenced genomes of 47 members belonging to genus Paenibacillus was carried out. Unique regions coding for nucleic acid modifying enzymes like CRISPR/Cas and Type I Restriction-Modification enzymes were identified in P. polymyxa A18 genome suggesting the presence of defense mechanism to combat viral infections in the gut. In addition, genes responsible for the formation of biofilms, such as Type IV pili and adhesins, which might be assisting P. polymyxa A18 in colonizing the gut were also identified in its genome. In situ colonization experiment further confirmed the ability of P. polymyxa A18 to colonize the gut of termite.
Single cell RNA-sequencing identified Dec2 as a suppressive factor for spermatogonial differentiation by inhibiting Sohlh1 expression
Authors: Makino Yoshinori , Jensen Niels H. , Yokota Naoko , Rossner Moritz J. , Akiyama Haruhiko , Shirahige Katsuhiko , Okada Yuki 
Published: April 2019

AbstractGonocyte-to-spermatogonia transition is a critical fate determination process to initiate sperm production throughout the lifecycle. However, the molecular dynamics of this process has not been fully elucidated mainly due to the asynchronized differentiation stages of neonatal germ cells. In this study, we employed single cell RNA sequencing analyses of P1.5–5.5 germ cells to clarify the temporal dynamics of gene expression during gonocyte-to-spermatogonia transition. The analyses identified transcriptional modules, one of which regulates spermatogonial gene network in neonatal germ cells. Among them, we identified Dec2, a bHLH-type transcription factor, as a transcriptional repressor for a spermatogonial differentiation factor Sohlh1. Deficiency of Dec2 in mice induces significant reduction of undifferentiated spermatogonia, and transplantation assay using Dec2-depleted cells also demonstrated the impaired efficiency of engraftment, suggesting its role in maintaining spermatogonial stem cells (SSCs). Collectively, this study revealed the intrinsic role of a new SSC factor Dec2, which protects germ cells from inadequate differentiation during neonatal testis development.
Differential Regulation of Gene Expression in Lung Cancer Cells by Diacyglycerol-Lactones and a Phorbol Ester Via Selective Activation of Protein Kinase C Isozymes
Authors: Cooke Mariana , Casado-Medrano Victoria , Ann Jihyae , Lee Jeewoo , Blumberg Peter M. , Abba Martin C. , Kazanietz Marcelo G. 
Published: April 2019

AbstractDespite our extensive knowledge on the biology of protein kinase C (PKC) and its involvement in disease, limited success has been attained in the generation of PKC isozyme-specific modulators acting via the C1 domain, the binding site for the lipid second messenger diacylglycerol (DAG) and the phorbol ester tumor promoters. Synthetic efforts had recently led to the identification of AJH-836, a DAG-lactone with preferential affinity for novel isozymes (nPKCs) relative to classical PKCs (cPKCs). Here, we compared the ability of AJH-836 and a prototypical phorbol ester (phorbol 12-myristate 13-acetate, PMA) to induce changes in gene expression in a lung cancer model. Gene profiling analysis using RNA-Seq revealed that PMA caused major changes in gene expression, whereas AJH-836 only induced a small subset of genes, thus providing a strong indication for a major involvement of cPKCs in their control of gene expression. MMP1, MMP9, and MMP10 were among the genes most prominently induced by PMA, an effect impaired by RNAi silencing of PKCα, but not PKCδ or PKCε. Comprehensive gene signature analysis and bioinformatics efforts, including functional enrichment and transcription factor binding site analyses of dysregulated genes, identified major differences in pathway activation and transcriptional networks between PMA and DAG-lactones. In addition to providing solid evidence for the differential involvement of individual PKC isozymes in the control of gene expression, our studies emphasize the importance of generating targeted C1 domain ligands capable of differentially regulating PKC isozyme-specific function in cellular models.
Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies
Authors: Lim Chia Chiu , Woo Patrick C. Y. , Lim Theam Soon 
Published: April 2019

AbstractAntibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.
Disorder and compositional dependences in Urbach-Martienssen tails in amorphous (GeTe)x(Sb2Te3)1−x alloys
Authors: Shportko K. V. 
Published: April 2019

AbstractThis work focuses on the compositional dependences in parameters that govern the optical properties of (GeTe)x(Sb2Te3)1−x amorphous alloys in the wide spectral range from above the phonons and to the inter-band electronic transitions. We studied the absorption edge fluctuations that are linked to the variations of the bandgap Eg, the width of Urbach-Martienssen tails EU, the Tauc parameter B1/2, and average halfwidth <FWHM> of Raman bands in amorphous (GeTe)x(Sb2Te3)1−x alloys at various temperatures. Obtained results reveal the compositional trends in the influence of the disordering on the absorption processes in studied alloys.
Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants
Authors: Nikkanen Lauri , Rintamäki Eevi 
Published: April 2019

Abstract
Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light energy could be used for production of sugars instead of dissipation as heat and down-regulation of carbon fixation. The plant chloroplast has a high number of regulatory proteins called thioredoxins (TRX), which control the function of chloroplasts from biogenesis and assembly of chloroplast machinery to light and carbon fixation reactions as well as photoprotective mechanisms. Here, we review the current knowledge of regulation of photosynthesis by chloroplast TRXs and assess the prospect of improving plant photosynthetic efficiency by modification of chloroplast thioredoxin systems.