bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depletion of microbiome-derived molecules in the host using Clostridium genetics
Authors: Guo Chun-Jun , Allen Breanna M. , Hiam Kamir J. , Dodd Dylan , van Treuren Will , Higginbottom Steven , Fischer Curt R. , Sonnenburg Justin L. , Spitzer Matthew H. , Fischbach Michael A. 
Published: August 2018

ABSTRACTThe gut microbiota produce hundreds of molecules that are present at high concentrations in circulation and whose levels vary widely among humans. In most cases, molecule production has not been linked to specific bacterial strains or metabolic pathways, and unraveling the contribution of each molecule to host biology remains difficult. A general system to ‘toggle’ molecules in this pool on/off in the host would enable interrogation of the mechanisms by which they modulate host biology and disease processes. Such a system has been elusive due to limitations in the genetic manipulability of Clostridium and its relatives, the source of many molecules in this pool. Here, we describe a method for reliably constructing clean deletions in a model commensal Clostridium, C. sporogenes (Cs), including multiply mutated strains. We demonstrate the utility of this method by using it to ‘toggle’ off the production of ten Cs-derived molecules that accumulate in host tissues. By comparing mice colonized by wild-type Cs versus a mutant deficient in the production of branched short-chain fatty acids, we discover a previously unknown IgA-modulatory activity of these abundant microbiome-derived molecules. Our method opens the door to interrogating and sculpting a highly concentrated pool of chemicals from the microbiome.
Zinc Boosts EGCG’s hIAPP Amyloid Inhibition Both in Solution and Membrane
Authors: Lee Young-Ho , Lin Yuxi , Cox Sarah J. , Kinoshita Misaki , Sahoo Bikash R. , Ivanova Magdalena , Ramamoorthy Ayyalusamy 
Published: August 2018

AbstractAmyloid aggregation of human islet amyloid polypeptide (hIAPP) is linked to insulin-producing islet cell death in type II diabetes. Previous studies have shown the amyloid inhibiting effects of zinc (Zn) and insulin that are co-present with hIAPP in islet cells, and the lipid membrane has been shown to significantly influence the aggregation kinetics. Increasing number of studies report the importance of developing small molecule inhibitors to suppress the hIAPP’s toxicity. Particularly, the ability of epigallocatechin-gallate (EGCG) to inhibit amyloid aggregation of a variety of amyloid peptide/proteins including hIAPP initiated numerous studies including the development of compounds to potentially treat amyloid diseases. In this study, by using a combination of thioflavin-T fluorescence and transmission electron microscopy experiments, we demonstrate a significant enhancement in EGCG’s efficiency, when mixed with Zn, to significantly suppress hIAPP amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of EGCG:Zn complex. Our results also reveal the ability of EGCG or EGCG:Zn to suppress hIAPP’s cellular toxicity and that the ability of EGCG to chelate with Zn suppresses zinc’s cellular toxicity. We suggest that the reported results would be useful to develop strategies to trap hIAPP intermediates for further biophysical and structural studies, and also to devise approaches to abolish amyloid aggregation and cellular toxicity.
Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
Authors: Jurisic Anamarija , Robin Chloe , Tarlykov Pavel , Siggens Lee , Schoell Brigitte , Jauch Anna , Ekwal Karl , Sørensen Claus Storgaard , Lipinski Marc , Shoaib Muhammad , Ogryzko Vasily 
Published: August 2018

ABSTRACTAnalysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions.
Activation of innate immune responses by a CpG oligonucleotide sequence composed entirely of threose nucleic acid
Authors: Lange Margaret J. , Burke Donald H. , Chaput John C. 
Published: August 2018

AbstractRecent advances in synthetic biology have led to the development of nucleic acid polymers with backbone structures distinct from those found in nature, termed xeno-nucleic acids (XNAs). Several unique properties of XNAs make them attractive as nucleic acid therapeutics, most notably their high resistance to serum nucleases and ability to form Watson-Crick base-pairing with DNA and RNA. The ability of XNAs to induce immune responses has not been investigated. Threose nucleic acid (TNA), a type of XNA, is recalcitrant to nuclease digestion and capable of undergoing Darwinian evolution to produce high affinity aptamers; thus, TNA is an attractive candidate for diverse applications, including nucleic acid therapeutics. Here, we evaluated a TNA oligonucleotide derived from a CpG oligonucleotide sequence known to activate TLR9-dependent immune signaling in B cell lines. We observed a slight induction of relevant mRNA signals, robust B cell line activation, and negligible effects on cellular proliferation.
Whole genome sequencing for drug resistance profile prediction inMycobacterium tuberculosis
Authors: Gygli Sebastian M. , Keller Peter M. , Ballif Marie , Blöchliger Nicolas , Hömke Rico , Reinhard Miriam , Loiseau Chloé , Ritter Claudia , Sander Peter , Borrell Sonia , Loo Jimena Collantes , Avihingsanon Anchalee , Gnokoro Joachim , Yotebieng Marcel , Egger Matthias , Gagneux Sebastien , Böttger Erik C. 
Published: August 2018

AbstractWhole genome sequencing allows rapid detection of drug-resistantM. tuberculosisisolates. However, high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been lacking.We determined drug resistance profiles of 176 genetically diverse clinicalM. tuberculosisisolates from Democratic Republic of the Congo, Ivory Coast, Peru, Thailand and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD BACTEC MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared phenotypic drug susceptibility results with predicted drug resistance profiles inferred by whole genome sequencing.Both phenotypic DST methods identically classified the strains into resistant/susceptible in 73-99% of the cases, depending on the drug. Changes in minimal inhibitory concentrations were readily explained by mutations identified by whole genome sequencing. Using the whole genome sequences we were able to predict quantitative drug resistance levels where wild type and mutant MIC distributions did not overlap. The utility of genome sequences to predict quantitative levels of drug resistance was partially limited due to incompletely understood mechanisms influencing the expression of phenotypic drug resistance. The overall sensitivity and specificity of whole genome-based DST were 86.8% and 94.5%, respectively.Despite some limitations, whole genome sequencing has high predictive power to infer resistance profiles without the need for time-consuming phenotypic methods.One sentence summaryWhole genome sequencing of clinicalM. tuberculosisisolates accurately predicts drug resistance profiles and may replace culture-based drug susceptibility testing in the future.
The RNA-Binding Protein DND1Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming
Authors: Ruthig Victor A. , Friedersdorf Matthew B. , Garness Jason A. , Munger Steve C. , Bunce Corey , Keene Jack D. , Capel Blanche 
Published: August 2018

AbstractThe adult spermatogonial stem cell population arises from pluripotent primordial germ cells (PGCs) that enter the fetal testis around embryonic day 10.5 (E10.5). These cells undergo rapid mitotic proliferation, then enter a prolonged period of cell cycle arrest (G1/G0) during which they transition to pro-spermatogonia. In mice homozygous for theTermutation in the RNA-binding proteinDND1(DND1Ter/Ter), many germ cells fail to enter G1/G0, and give rise to teratomas, tumors in which many embryonic cell types are represented. To investigate the origin of these tumors, we sequenced the transcriptome of male germ cells inDND1Ter/Termutants at E12.5, E13.5, and E14.5, just prior to the formation of teratomas, and correlated this information with direct targets of DND1identified by DO-RIP-Seq. Consistent with previous results, we found that DND1controls the down regulation of many genes associated with pluripotency and active cell cycle, including elements of the mTor, Hippo and Bmp/Nodal signaling pathways. However, DND1targets also include genes associated with male differentiation including a large group of chromatin regulators activated in wild type but not mutant germ cells during the transition between E13.5and E14.5. These results suggest multiple functions of DND1, and link DND1to the initiation of epigenetic modifications in male germ cells.
Description of novel marine bioflocculant-producing bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds
Authors: Che Hashim Nurul Fakriah , Ghazali Nurarina Ayuni , Amin Nakisah Mat , Ismail Noraznawati , Kasan Nor Azman 
Published: August 2018

AbstractDescription of marine bioflocculant-producing bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds was prompted to explore the bacteria that enhanced bioflocculation process in aquaculture wastewater treatment. Certain marine bacteria were potentially secreted extracellular polymeric substances (EPS) which response to the physiological stress encountered in the natural environment that can act as bioflocculants. This study aimed to identify marine bioflocculant-producing bacteria isolated from biofloc; to evaluate their flocculating activities; and to characterize their protein in EPS. Phenotypic and genotypic identification of the bacteria including morphological and molecular approaches were employed, while their flocculating activities were examined via Kaolin clay suspension method and statistically analyzed. The EPS that acted as bioflocculants were extracted using cold ethanol precipitation method. Protein concentration was determined by Bradford assay and protein profiling was finally completed with Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) method. Six species of marine bacteria known asHalomonas venusta, Bacillus cereus, Bacillus subtilis, Bacillus pumilus, Nitratireductor aquimarinusandPseudoalteromonassp. were successfully identified as bioflocculant-producing bacteria. The highest flocculating activity was exhibited byBacillus cereusat 93%, whileHalomonas venustashowed the lowest record at 59%. All bioflocculant-producing bacteria species showed different protein concentration that ranged between 1.377 μg/mL to 1.455 μg/mL. Several protein bands with different molecular weight that ranged between 16 kDa to 100 kDa were observed. This study revealed that all the identified bacteria species have high potential characteristics to initiate aquaculture wastewater treatment and may play important roles in bioflocculation process.ImportanceSix species of marine bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds were identified as bioflocculant-producing bacteria. Among those six species,Bacillus cereus,Bacillus pumilus,Nitratireductor aquimarinusandPseudoalteromonassp. were highly potential to be used as booster for rapid formation of biofloc due to their high flocculating activities. Protein content in EPS of novel marine biofocculant-producing bacteria has beneficial consequences on degradation process of organic substances, denitrification of wastes and ions elimination from aquaculture wastes.
Screening Mycobacterium tuberculosis secreted proteins identifies Mpt64 as eukaryotic membrane-binding virulence factor
Authors: Stamm Chelsea E. , Pasko Breanna L. , Chaisavaneeyakorn Sujittra , Franco Luis H. , Nair Vidhya R. , Weigele Bethany A. , Alto Neal M. , Shiloh Michael U. 
Published: August 2018

AbstractMycobacterium tuberculosis(Mtb), the causative agent of tuberculosis, is one of the most successful human pathogens. One reason for its success is that Mtb can reside within host macrophages, a cell type that normally functions to phagocytose and destroy infectious bacteria. However, Mtb is able to evade macrophage defenses in order to survive for prolonged periods of time. Many intracellular pathogens secret virulence factors targeting host membranes and organelles to remodel their intracellular environmental niche. We hypothesized that Mtb exported proteins that target host membranes are vital for Mtb to adapt to and manipulate the host environment for survival. Thus, we characterized 200 exported proteins from Mtb for their ability to associate with eukaryotic membranes using a unique temperature sensitive yeast screen and to manipulate host trafficking pathways using a modified inducible secretion screen. We identified five Mtb exported proteins that both associated with eukaryotic membranes and altered the host secretory pathway. One of these secreted proteins, Mpt64, localized to the endoplasmic reticulum during Mtb infection of murine and human macrophages and was necessary for Mtb survival in primary human macrophages. These data highlight the importance of exported proteins in Mtb pathogenesis and provide a basis for further investigation into their molecular mechanisms.ImportanceAdvances have been made to identify exported proteins ofMycobacterium tuberculosisduring animal infections. These data, combined with transposon screens identifying genes important forM. tuberculosisvirulence, have generated a vast resource of potentialM. tuberculosisvirulence proteins. However, the function of many of these proteins inM. tuberculosispathogenesis remains elusive. We have integrated three cell biological screens to characterize nearly 200M. tuberculosisexported proteins for eukaryotic membrane binding, host subcellular localization and interactions with host vesicular trafficking. In addition, we observed the localization of one exported protein, Mpt64, duringM. tuberculosisinfection of macrophages. Interestingly, although Mpt64 is exported by the Sec pathway, its delivery into host cells was dependent upon the action of the Type VII Secretion System. Finally, we observed that Mpt64 contributes to the virulence ofM. tuberculosisduring infection of primary human macrophages.
Epigenetic signatures of starting and stopping smoking
Authors: McCartney Daniel L , Stevenson Anna J , Hillary Robert F , Walker Rosie M , Bermingham Mairead L , Morris Stewart W , Clarke Toni-Kim , Campbell Archie , Murray Alison D , Whalley Heather C , Porteous David J , Visscher Peter M , McIntosh Andrew M , Evans Kathryn L , Deary Ian J , Marioni Riccardo E 
Published: August 2018

AbstractBackgroundMultiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well-established. Here, we assess DNA methylation patterns in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers.MethodsDimensionality reduction was applied to DNA methylation data at 90 previously identified smoking-associated CpG sites for over 4,900 individuals in the Generation Scotland cohort. K-means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day).ResultsTwo clusters were specified, corresponding to never smokers (97.5% of whom were assigned to Cluster 1) and current smokers (81.1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to thesmoker-enrichedcluster varied between 5-9 years in heavier smokers and between 15-19 years in lighter smokers. Low-dose former smokers were more likely to be assigned to thenever smoker-enrichedcluster from the first year following cessation. In contrast, a period of at least two years was required before the majority of former high-dose smokers were assigned to the never smoker-enriched cluster.ConclusionsOur findings suggest that smoking-associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation-based signatures of smoking status be predictive of smoking-related health outcomes, our findings may provide an additional criterion on which to stratify risk.
Establishment of baseline sensitivity ofRhizoctonia solanito thifluzamide in corn and its field application
Authors: Shang Dianlong , Yao Chentao , He Falin , Sun Xiao , Sun Shiang , Tan Haili , Li Xiangdong , Zhang Jiwang , Jiang Xingyin 
Published: August 2018

AbstractIn recent years, banded leaf sheath blight in corn has become an important disease in corn that seriously affects quality and yield. This paper aims to evaluate the sensitivity ofRhizoctonia solanito thifluzamide in corn, to clarify the effect of seed coating using a thifluzamide suspension agent on safety and physiological indicators and to determine banded leaf sheath blight in corn control effectiveness in the field, thereby providing a basis for the application of thifluzamide suspension agent as a seed coating. In this study, the thifluzamide sensitivity of 102 strains ofR. solaniin corn in different regions of Shandong was determined using the mycelial growth rate method, and the average half-maximal effective concentration value (EC50) was 0.086±0.004 μg/mL. The sensitivity was consistent with a continuous and skewed normal distribution, and the sensitivity distribution frequency exhibited a continuous, unimodal curve, indicating that thifluzamide had strong inhibitory activity on the mycelial growth ofR. solaniin corn. The impacts of using a thifluzamide suspension agent for seed coating on safety and physiological indicators as well as the control effect in corn were evaluated by combining seed coating, an indoor pot test, and a field trial. The root activities under 24 g a.i. 100 kg-1seed and 12 g a.i. 100 kg-1seed were found to increase by 78.01% and 77.40%, respectively, compared with that under the blank control; the chlorophyll content of corn increased most significantly at a dosage of 24 g a.i. 100 kg-1, which was a 32.32% increase compared to the blank control. Thifluzamide (FS) could significantly increase the hundred-grain weight of corn and the per-plot yield. Among the examined dosages, 24 g a.i. 100 kg-1seed had the most significant treatment effect, with the hundred-grain weight increasing by 12.47% and the yield rate increasing by 15.72% compared to the control in 2016, Simultaneously, the hundred-grain weight increasing by 13.44% and the yield rate increasing by 14.11% compared to the control in 2017. Three dosages of 24% thifluzamide (FS) increased the emergence rate and seedling growth of corn to varying extents. The field control effectiveness against banded leaf sheath blight in corn was best at the dosage of 24 g a.i. 100 kg-1seed for seed dressing with thifluzamide (FS); in 2016 and 2017, the control effects in the small bell stage, large bell stage, tasseling and pollen-shedding stage, silking stage, milk-ripening stage, and wax-ripening stage were 100%, 66.73%, 52.8%, 67.81%, 68.48%, and 62.68% (2016), respectively, and 74.97%, 63.17%, 50.90%, 53.60%, 61.42%, and 55.88% (2017). These results indicated that thifluzamide had enormous potential for controlling banded leaf sheath blight in corn.
Small Data Challenge: Structural Analysis and Optimization of Convolutional Neural Networks with a Small Sample Size
Authors: D’souza Rhett N. , Huang Po-Yao , Yeh Fang-Cheng 
Published: August 2018

AbstractDeep neural networks have gained immense popularity in the Big Data problem; however, the availability of training samples can be relatively limited in certain application domains, particularly medical imaging, and consequently leading to overfitting problems. This “Small Data” challenge may need a mindset that is entirely different from the existing Big Data paradigm. Here, under the small data setting, we examined whether the network structure has a substantial influence on the performance and whether the optimal structure is predominantly determined by sample size or data nature. To this end, we listed all possible combinations of layers given an upper bound of the VC-dimension to study how structural hyperparameters affected the performance. Our results showed that structural optimization improved accuracy by 27.99%, 16.44%, and 13.11% over random selection for a sample size of 100, 500, and 1,000 in the MNIST dataset, respectively, suggesting that the importance of the network structure increases as the sample size becomes smaller. Furthermore, the optimal network structure was mostly determined by the data nature (photographic, calligraphic, or medical images), and less affected by the sample size, suggesting that the optimal network structure is data-driven, not sample size driven. After network structure optimization, the conventional convolutional neural network could achieve 91.13% in accuracy with only 500 samples, 93.66% in accuracy with only 1000 samples for the MNIST dataset and 94.10% in accuracy with only 3300 samples for the Mitosis (microscopic) dataset. These results indicate the primary importance of the network structure and the nature of the data in facing the Small Data challenge.