bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression plasticity and frontloading promote thermotolerance inPocilloporacorals
Authors: Brener-Raffalli K. , Vidal-Dupiol J. , Adjeroud M. , Rey O. , Romans P. , Bonhomme F. , Pratlong M. , Haguenauer A. , Pillot R. , Feuillassier L. , Claereboudt M. , Magalon H. , Gélin P. , Pontarotti P. , Aurelle D. , Mitta G. , Toulza E. 
Published: August 2018

ABSTRACTEcosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response inPocilloporacoral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.
Acetate and hypertonic stress stimulate organelle membrane fission using distinct phosphatidylinositol signals
Authors: Patel Dipti , Brett Christopher Leonard 
Published: August 2018

ABSTRACTOrganelle morphology reflects an equilibrium between membrane fusion and fission that determines size, shape and copy number. By studying the yeast vacuole as a model, the conserved molecular mechanisms responsible for organelle fusion have been revealed. However, a detailed understanding of vacuole fission and how these opposing processes respond to the cell cycle, osmoregulation or metabolism to change morphology remain elusive. Thus, herein we describe a new fluorometric assay to measure vacuole fission in vitro. For proof-of-concept, we use this assay to confirm that acetate, a key intermediary metabolite, triggers vacuole fission in vitro and show that it also blocks homotypic vacuole fusion. The basis of this effect is distinct from hypertonic stress, a known trigger of fission and inhibitor of fusion that inactivates the Rab-GTPase Ypt7: Treatment with the phosphatidylinositol-kinase inhibitor wortmannin or the catalytic domain of the Rab-GAP (GTPase Activating Protein) Gyp1 reveal that fission can be triggered by Ypt7 inactivation alone in absence of hypertonic stress, placing it upstream of PI-3,5-P2synthesis and osmosis required for membrane scission. Whereas acetate seems to block PI-4-kinase to possibly increase the pool of PI on vacuole membranes needed to synthesize sufficient PI-3,5-P2for fission. Thus, we speculate that both PI-4-P and PI-3-P arms of PI-P signaling drive changes in membrane fission and fusion responsible altering vacuole morphology in response to cellular metabolism or osmoregulation.GRAPHICAL ABSTRACT
Origins and geographic diversification of African rice (Oryza glaberrima)
Authors: Veltman Margaretha A. , Flowers Jonathan M. , van Andel Tinde R. , Schranz M. Eric 
Published: August 2018

AbstractRice is a staple food for the majority of our world’s growing population. Whereas Asian rice (Oryza sativaL.) has been extensively studied, the exact origins of African rice (Oryza glaberrimaSteud.) are still contested. Previous studies have supported either a centric or a non-centric origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice – either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest - suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.
Spatio-temporal variability of soil nutrients and the responses of growth during growth stages of winter wheat in the north of China
Authors: Bao-wei Su , Geng-xing Zhao , Chao Dong 
Published: August 2018

AbstractStudy on soil nutrient variability and its effect on the growth and development of crop under traditional tillage mode is the foundation to comprehensively implement the precision agriculture policy on the field scale and crop excellent management. In this paper, a winter wheat field of 28.5 hm2 under traditional cultivation model in Tianzhuang town of Huantai county was selected as the research area. Sampling by mesh point method (60×60m), the variation characteristics of soil available nitrogen (AN), available phosphorus (AP) and available potassium (AK) in the before sowing, reviving stage, jointing stage, filling stage of winter wheat were analyzed by the method of geostatistics and GIS. At the same time, Pearson correlation analysis was used to study the response of wheat growth and development to soil nutrient variation. As the growth period goes by, 1) each nutrient showed low-high-low and moderate variability. AN and AK had the highest content at reviving stage, while AP at jointing stage, as turning point. The order of variability of each nutrient was AN>AP>AK. 2) The difference of nutrient variation first increased and then decreased, and showed medium to strong spatial correlation.Three nutrients in the before sowing stage were strong spatial correlation, and the reviving stage was medium spatial correlation, to the jointing and filling stages, AN was medium spatial correlation, AP and AK were strong spatial correlation. The spatial correlation of each nutrients was the weakest in the reviving stage, and AN was the strongest in the before sowing stage, while AP and AK were strongest in the jointing stage. The spatial correlation of each soil nutrients decreased from before sowing to reviving stage, jointing stage to filling stage, and the spatial correlation increased from reviving stage to jointing stage. 3) Soil nutrient content first increased and then decreased, and the grade of nutrient gradually decreased. 4) The correlation between soil nutrients and wheat growth was gradually increasing. AN had the highest correlation with wheat growth, followed by AK and AP lowest. The effect of soil nutrients on the growth of wheat at the reviving stage was higher than that of the current nutrient, and the growth of wheat at jointing stage was mainly influenced by the current nutrient, while the growth of wheat at the filling period was both influenced by the nutrient content of the last and the current period; the date to supplement fertilizer should be postponed properly. In this study, the soil nutrient dynamics and its influence on the growth of wheat during the winter wheat growth period under the traditional field model were well understood, which could provide a theoretical basis for the precision management of soil nutrients in the northern winter wheat area with relatively uniform planting environment and cultivation management.
Quantitative Assessment of Colorectal Cancer Progression: a Comparative Study of Linear and Nonlinear Microscopy Techniques
Authors: Adur J. , Erbes L. , Bianchi M. , Ruff S. , Zeitoune A. , Izaguirre M.F. , Cesar C.L. , Carvahlo H.F. , Casco V.H. 
Published: August 2018

BACKGROUND AND AIMSColorectal cancer (CRC) is a disease that can be prevented if is diagnosed and treated at pre-invasive stages. Thus, the monitoring of colonic cancer progression can improve the early diagnosis and detection of malignant lesions in the colon. This monitoring should be performed with appropriate image techniques and be accompanied by proper quantification to minimize subjectivity. We have monitored the mice CRC progression by image deconvolution, two-photon emission fluorescence (TPEF) and second harmonic generation (SHG) microscopies and present different quantization indices for diagnosis.METHODSThe Azoxymethane (AOM) / dextran sodium sulfate (DSS) protocol was used. 35 eight-week old male BALB/cCmedc mice were used and distal colon segments were dissected at day zero and fourth, eighth, sixteen, and twenty weeks after injection. These segments were observed with linear and nonlinear optical microscopies and several parameters were used for quantification.RESULTSCrypt diameter higher than 0.08 mm and increased fluorescence signal intensity in linear images; as well as aspect relation above 0.7 and altered organization reflexed by high-energy values obtained from SHG images, away from those obtained in normal tissues.CONCLUSIONThe combination of linear and nonlinear signals improve the detection and classification of pathological changes in crypt morphology/distribution and collagen fiber structure/arrangement. In combination with standard screening approaches for CRC, the proposed methods improve the detection of the disease in its early stages, thereby increasing the chances of successful treatment.
Activation of TAp73 and inhibition of thioredoxin reductase for improved cancer therapy inTP53 mutant pancreatic tumors
Authors: Acedo Pilar , Fernandes Aristi , Zawacka-Pankau Joanna 
Published: August 2018

AbstractThe p73 is a tumor suppressor that compensates for p53 loss and induces apoptosis in tumors in response to genotoxic stress or small-molecule treatments.Pancreatic ductal adenocarcinoma (PDAC) has a late onset of the disease, responds poorly to the existing therapies and has very low overall survival rates.Here, using drug-repurposing approach, we found that protoporphyrin IX (PpIX) and benzoporphyrin derivative monoacid ring A (BPD) activate p73 and induce apoptosis in pancreatic cancer cells. PpIX and BPD induce reactive oxygen species and inhibit thioredoxin reductase 1 (TrxR1). Thus, PpIX and BPD target cancer cells’ vulnerabilities namely activate TAp73 tumor suppressor and inhibit oncogenic TrxR1. Our findings, may contribute to faster repurposing of PpIX and BPD to treat pancreatic tumors.Lay AbstractDespite the efforts, pancreatic cancer remains among the most aggressive tumors. Late diagnoses often linked with the asymptomatic disease progression make it extremely difficult to cure. We have used drugs that are already in clinics and applied in photodynamic therapy of cancer and showed that the compounds induce death of cancer cells. The mechanism is via activation of p73 tumor suppressor and inhibition oncogenic thioredoxin reductase. Molecules that in parallel induce two pathways leading to cell death might be very promising candidates for improved cancer therapy in pancreatic cancer patients.
Predicting protein-peptide interaction sites using distant protein complexes as structural templates
Authors: Johansson-Åkhe Isak , Mirabello Claudio , Wallner Björn 
Published: August 2018

ABSTRACTProtein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details of the interactions. However, because of peptide flexibility and the transient nature of protein-peptide interactions, peptides are difficult to study experimentally. Thus, computational methods for predicting structural information about protein-peptide interactions are needed. Here we present InterPep, a pipeline for predicting protein-peptide interaction sites. It is a novel pipeline that, given a protein structure and a peptide sequence, utilizes structural template matches, sequence information, random forest machine learning, and hierarchical clustering to predict what region of the protein structure the peptide is most likely to bind. When tested on its ability to predict binding sites, InterPep successfully pinpointed 255 of 502 (50.7%) binding sites in experimentally determined structures at rank 1 and 348 of 502 (69.3%) among the top five predictions using only structures with no significant sequence similarity as templates. InterPep is a powerful tool for identifying peptide-binding sites; with a precision of 80% at a recall of 20% it should be an excellent starting point for docking protocols or experiments investigating peptide interactions. The source code for InterPred is available athttp://wallnerlab.org/InterPep/
Anticancer Drug Impact on DNA – A Study by Neutron Spectrocopy, Synchrotron-based FTIR and EXAFS
Authors: de Carvalho Ana L.M. Batista , Mamede Adriana P. , Dopplapudi Asha , Sakai Victoria Garcia , Doherty James , Frogley Mark , Cinque Gianfelice , Gardner Peter , Gianolio Diego , de Carvalho Luís A.E. Batista , Marques Maria P.M. 
Published: August 2018

ABSTRACTA complementary structural and dynamical information on drug-DNA interplay has been achieved at a molecular level, for Pt/Pd-drugs, allowing a better understanding of their pharmacodynamic profile. The interaction of two cisplatin-like dinuclear Pt(II) and Pd(II) complexes with DNA was studied through a multidisciplinary experimental approach, using quasi-elastic neutron scattering (QENS) techniques coupled to synchrotron-based extended X-ray absorption fine structure (SR-EXAFS) and Fourier-Transform Infrared Spectroscopy-Attenuated Total Reflectance (SR-FTIR-ATR). The drug impact on DNA’s dynamical profile,viaits hydration layer, was provided by QENS, a drug-triggered enhanced mobility having been revealed. Additionally, an onset of anharmonicity was detected for dehydrated DNA, at room temperature. Far- and mid-infrared measurements allowed the first simultaneous detection of the drugs and its primary pharmacological target, as well as the drug-prompted changes in DNA’s conformation that mediate cytotoxicity in DNA extracted from drug-exposed human triple negative breast cancer cells (MDA-MB-231), a low prognosis type of cancer. The local environment of the absorbing Pd(II) and Pt(II) centers in the drugs’ adducts with adenine, guanine and glutathione was attained by EXAFS.
Mechanical vibration does not systematically reduce the tremor in Essential Tremor patients
Authors: Lora-Millán Julio Salvador , López-Blanco Roberto , Gallego Juan Álvaro , Benito-León Julián , de la Aleja Jesús González , Rocon Eduardo 
Published: August 2018

AbstractEssential tremor (ET) is a major cause of disability and is not effectively managed in half of the patients. We investigated whether mechanical vibration could reduce tremor in ET by selectively recruiting afferent pathways. We used piezoelectric actuators to deliver vibratory stimuli to the hand and forearm during long trials (4 min), while we monitored the tremor using inertial sensors. We analyzed the effect of four stimulation strategies, including different constant and variable vibration frequencies, in 18 ET patients. Although there was not a clear homogeneous response to vibration across patients and strategies, in most cases (50-72%) mechanical vibration was associated with an increase in the amplitude of their tremor. In contrast, the tremor was reduced in 5-22% of the patients, depending on the strategy. However, these results are hard to interpret given the intrinsic variability of the tremor: during equally long trials without vibration, the tremor changed significantly in 67% of the patients (increased in 45%; decreased in 22%). We conclude that mechanical vibration of the limb does not have a systematic effect on tremor in ET. Moreover, the observed intrinsic variability of the tremor should be taken into account when designing future experiments to assess tremor in ET and how it responds to any intervention.
The transmembrane protein Crb2a regulates cardiomyocyte apicobasal polarity and adhesion in zebrafish
Authors: Jiménez-Amilburu Vanesa , Stainier Didier Y.R. 
Published: August 2018

AbstractTissue morphogenesis requires changes in cell-cell adhesion as well as in cell shape and polarity. Cardiac trabeculation is a morphogenetic process essential to form a functional ventricular wall. Here we show that zebrafish hearts lacking Crb2a, a component of the Crumbs polarity complex, display compact wall integrity defects and fail to form trabeculae. Crb2a localization is very dynamic, at a time when other cardiomyocyte junctional proteins also relocalize. Before the initiation of cardiomyocyte delamination to form the trabecular layer, Crb2a is expressed in all ventricular cardiomyocytes colocalizing with the junctional protein ZO-1. Subsequently, Crb2a becomes localized all along the apical membrane of compact layer cardiomyocytes and is downregulated by those delaminating. We show that blood flow and Nrg/ErbB2 signaling regulate these Crb2a localization changes.crb2amutants display a multilayered wall with polarized cardiomyocytes, a unique phenotype. Our data further indicate that Crb2a regulates cardiac trabeculation by controlling the localization of tight and adherens junctions in cardiomyocytes. Importantly, transplantation data show that Crb2a controls trabeculation in a CM-autonomous manner. Altogether, our study reveals a critical role for Crb2a during cardiac development.Summary statementInvestigation of the Crumbs polarity protein Crb2a in zebrafish reveals a novel role in cardiac development via regulation of cell-cell adhesion and apicobasal polarity.
DART-ID increases single-cell proteome coverage
Authors: Chen Albert T. , Franks Alexander , Slavov Nikolai 
Published: August 2018

AbstractAnalysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30 – 50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://github.com/SlavovLab/DART-ID.Author SummaryIdentifying and quantifying proteins in single cells gives researchers the ability to tackle complex biological problems that involve single cell heterogeneity, such as the treatment of solid tumors. Mass spectrometry analysis of peptides can identify their sequence from their masses and the masses of their fragment ion, but often times these pieces of evidence are insufficient for a confident peptide identification. This problem is exacerbated when analyzing lowly abundant samples such as single cells. To identify even peptides with weak mass spectra, DART-ID incorporates their retention time – the time when they elute from the liquid chromatography used to physically separate them. We present both a novel method of aligning the retention times of peptides across experiments, as well as a rigorous framework for using the estimated retention times to enhance peptide sequence identification. Incorporating the retention time as additional evidence leads to a substantial increase in the number of samples in which proteins are confidently identified and quantified.
Parvalbumin loss following chronic sub-anesthetic NMDA antagonist treatment is age-dependent in the hippocampus: Implications for modeling NMDA hypofunction
Authors: Honeycutt Jennifer A. , Chrobak James J. 
Published: August 2018

AbstractA marked decrease in parvalbumin (PV), a calcium-binding protein specific to a subset of GABAergic neurons, is a consistent finding in postmortem schizophrenic brain tissue. This reduction is selective to PV and is regionally specific: occurring primarily in the prefrontal cortex and hippocampus (HPC) of patients. Rodent models of NMDA receptor hypofunction utilizing NMDA antagonist treatments – e.g. ketamine (KET) – show schizophrenia-like cognitive and behavioral impairments with parallel changes in PV. While decreased PV is considered a hallmark of neuropathology in schizophrenia, previous work elucidating the effects of KET administration on PV are contradictory, with findings suggesting decreased, increased, or no change in PV expression. Upon close examination of the procedures used across studies, there are two primary inconsistencies, including: 1) the age of animals used; and 2) the timeline of post-treatment tissue collection. To better understand whether these key differences impact observed PV changes, the present study investigated the impact of age and time of sacrifice on chronic KET-induced PV changes in the neocortex and HPC. Our findings suggest an effect of age, but not sacrifice timeline, on PV cell count following 14 days of sub-anesthetic KET treatment. We provide evidence that 1-month-old rats exhibit significant KET-induced HPC PV decreases, while adult rats show a modest increase in HPC PV following chronic KET. Taken together, we propose that PV is a dynamic marker, and that changes in cell counts - and their interpretation - following NDMA antagonist treatment should be considered in the context of age.