bluuebunny/crossref_metadata_2025 huggingface dataset:
In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species
Authors: Bauwens Eva , Joosten Myrthe , Taganna Joemar , Rossi Mirko , Debraekeleer Ayla , Tay Alfred , Peters Fanny , Backert Steffen , Fox James , Ducatelle Richard , Remaut Han , Haesebrouck Freddy , Smet Annemieke
Published: October 2018

Helicobacter (H.) pylori is an important risk factor for gastric malignancies worldwide. Its outer membrane proteome takes an important role in colonization of the human gastric mucosa. However, in zoonotic non-H. pylori helicobacters (NHPHs) also associated with human gastric disease, the composition of the outer membrane (OM) proteome and its relative contribution to disease remain largely unknown. By means of a comprehensive survey of the diversity and distribution of predicted outer membrane proteins (OMPs) identified in all known gastric Helicobacter species with fully annotated genome sequences, we found genus- and species-specific families known or thought to be implicated in virulence. Hop adhesins, part of the Helicobacter-specific family 13 (Hop, Hor and Hom) were restricted to the gastric species H. pylori, H. cetorum and H. acinonychis. Hof proteins (family 33) were putative adhesins with predicted Occ- or MOMP-family like 18-stranded β-barrels. They were found to be widespread amongst all gastric Helicobacter species only sporadically detected in enterohepatic Helicobacter species. These latter are other members within the genus Helicobacter, although ecologically and genetically distinct. LpxR, a lipopolysaccharide remodeling factor, was also detected in all gastric Helicobacter species but lacking as well from the enterohepatic species H. cinaedi, H. equorum and H. hepaticus. In conclusion, our systemic survey of Helicobacter OMPs points to species and infection-site specific members that are interesting candidates for future virulence and colonization studies.
The Competition of Homophily and Popularity in Growing and Evolving Social Networks
Authors: Liu Yezheng , Li Lingfei , Wang Hai , Sun Chunhua , Chen Xiayu , He Jianmin , Jiang Yuanchun
Published: October 2018

Previous studies have used several models to investigate the mechanisms for growing and evolving real social networks. These models have been widely used to simulate large networks in many applications. In this paper, based on the evolutionary mechanisms of homophily and popularity, we propose a new generation model for growing and evolving social networks, namely, the Homophily-Popularity model. In this new model, new links are added, and old links are deleted based on the link probabilities between every node pair. The results of our simulation-based experimental studies provide evidence that the proposed model is capable of modelling a variety of real social networks.
Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea
Authors: Deng Wenchao , Peng Lulu , Jiao Nianzhi , Zhang Yao
Published: October 2018

Methanol (MOH) and monomethylamine (MMA) are two typical one-carbon (C1) compounds found in natural environments. They play an important role in marine and atmospheric chemistry, cloud formation, and global climate. The main biological sink of MOH and MMA is rapid consumption by marine microbes. Here, field-based time-series incubations with supplemental 13C-labelled MOH and MMA and isotope ratio analyses were performed. A substantial difference in the MOH and MMA incorporation rates and bacterial taxa were observed between the South China Sea (SCS) and the Pearl River estuary. C1 substrates were assimilated more quickly in the estuary than the SCS shelf where MOH and MMA had similar bio-availability. However, microbial responses to MMA may be faster than to MOH in the coastal and basin surface water of the SCS despite similar active bacterial populations. Three ecological types of bacteria, in terms of response to supplemented MOH and MMA, were identified: rapid incorporation (I, dominant C1-incorporating group), slow incorporation (II, minor C1-incorporating group), and no incorporation (III, C1-non-incorporating group). Members of the families Methylophilaceae (β-Proteobacteria) and Piscirickettsiaceae (γ-Proteobacteria) belonged to type I and actively incorporated substrates in the estuary and SCS, respectively. Diverse MOH and MMA-incorporating type II bacteria were identified by stable isotope probing in the SCS, and could play a more important role in the transformation of C1 compounds in marine environments than hitherto assumed.
Regulatory elements in vectors containing the ctEF-1α first intron and double enhancers for an efficient recombinant protein expression system
Authors: Lee Chi-Pin , Ko Albert Min-Shan , Chiang Shang-Lun , Lu Chi-Yu , Tsai Eing-Mei , Ko Ying-Chin
Published: October 2018

To establish a stable and scalable transient protein production system, we modified the EF-1 first intron size and verified the order of two recombinant enhancers downstream of the SV40 polyA sequence. This new vector was named pHH-Gemini (pHH-GM1) and was used to express alpha kinase 1 (ALPK1) and various other proteins, NLRP3, F-actin, Camodulin, PP2A, URAT1, Rab11a and myosin IIA. The results showed that, compared with six commercial plasmids, pHH-GM1 significantly enhanced His-HA-ALPK1 expression in a western blot analysis of transfected HEK293T cells. The expression of various other genes was also successful using the pHH-GM1 vector. In addition, we inserted turbo green florescence protein (tGFP) into the pHH-GM1 vector, and an improvement in fluorescence intensity was observed after transient transfection of HEK293T cells. For large-scale production, protein production was tested by standard supplementation with one volume of medium, and volumetric yields of 2 and 2.3 mg/L were achieved with pHH-GM1-ALPK1 in HEK293-F and CHO-S cells, respectively. We found that cell viability was more than 70% 11 days after cells were transfected with the pHH-GM1 vector. The pHH-GM1 vector with the ctEF-1α first intron and double enhancers, Simian virus 40 and Cytomegalovirus (SV40 and CMV) is an efficient CMV promoter-based gene expression system that can potentially be applied to study genes of interest and improve protein production.
Nighttime activities and peripheral clock oscillations depend on Wolbachia endosymbionts in flies
Authors: Morioka Eri , Oida Minami , Tsuchida Tsutomu , Ikeda Masayuki
Published: October 2018

Wolbachia are ubiquitous bacterial endosymbionts of arthropods and affect host gene expression. Although Wolbachia infections were suggested to modulate sleep in flies, their influence on the circadian clock remained obscure. Here, we screened bacterial symbionts in a laboratory Drosophila melanogaster colony, and observed widespread infections of wMel strain Wolbachia. We established a Wolbachia-free strain from a clock gene reporter strain, period-luciferase (per-luc). Temperature (19–29 °C)-compensated free-running periods were detected regardless of infections which may reflect the lack of wMel infections in central circadian pacemaker neurons. However, locomotor activity levels during the night or subjective night were significantly amplified in uninfected flies. Moreover, the behavioral phenotype of F1 offspring of an uninfected female and infected male resembled that of uninfected flies. This trait is consistent with maternal transmission of Wolbachia infection. Interestingly, per-luc activities in headless bodies, as an index of peripheral circadian oscillators, were severely damped in uninfected flies. Additionally, circadian amplitudes of PER immunoreactivities in Malpighian tubules were reduced in uninfected flies. These results demonstrate that Wolbachia boost fly peripheral clock oscillations and diurnal behavioral patterns. Genetic mechanisms underlying behavioral rhythms have been widely analyzed using mutant flies whereas screening of Wolbachia will be necessary for future studies.
The role of functional and structural interhemispheric auditory connectivity for language lateralization - A combined EEG and DTI study
Authors: Steinmann Saskia , Amselberg Rom , Cheng Bastian , Thomalla Götz , Engel Andreas K. , Leicht Gregor , Mulert Christoph
Published: October 2018

Interhemispheric connectivity between auditory areas is highly relevant for normal auditory perception and alterations are a major factor for the development of auditory verbal hallucinations. Surprisingly, there is no combined EEG-DTI study directly addressing the role of functional and structural connectivity in the same group of subjects. Accordingly, nothing is known about the relationship between functional connectivity such as gamma-band synchrony, structural integrity of the interhemispheric auditory pathways (IAPs) and language lateralization as well as whether the gamma-band synchrony is configured on the backbone of IAPs. By applying multimodal imaging of 64-channel EEG and DTI tractography, we investigated in 27 healthy volunteers the functional gamma-band synchrony between either bilateral primary or secondary auditory cortices from eLORETA source-estimation during dichotic listening, as well as the correspondent IAPs from which fractional anisotropy (FA) values were extracted. Correlation and regression analyses revealed highest values for gamma-band synchrony, followed by FA for secondary auditory cortices, which were both significantly related to a reduced language lateralization. There was no such association between the white-matter microstructure and gamma-band synchrony, suggesting that structural connectivity might also be relevant for other (minor) aspects of information transfer in addition to gamma-band synchrony, which are not detected in the present coupling analyses. The combination of multimodal EEG-DTI imaging provides converging evidence of neural correlates by showing that both stronger pathways and increased gamma-band synchrony within one cohort of subjects are related to a reduced leftward-lateralization for language.
Nocturnal spawning as a way to avoid egg exposure to diurnal predators
Authors: Šmejkal Marek , Souza Allan T. , Blabolil Petr , Bartoň Daniel , Sajdlová Zuzana , Vejřík Lukáš , Kubečka Jan
Published: October 2018

Animals that do not provide parental care have to secure the survival of their offspring by ensuring a safe reproductive environment or smart timing tactics. Nocturnal spawning behaviour of many fish species is an example of the latter behaviour in the animal kingdom and is hypothesized to provide a survival advantage to the eggs spawned during the night. In order to test the efficiency of the smart timing tactics in a freshwater fish, a study was carried out of the interaction of the rheophilic spawner (asp Leuciscus aspius) and the predator of its drifting eggs (bleak Alburnus alburnus) using passive telemetry. According to a model based on acquired data, asp laid 63% of its eggs at night, while vision-oriented bleak was present in 92% of the time during the day. This study gives support to the predator avoidance hypothesis, which expects animals to reproduce in a period when the probability of offspring predation is at its lowest.
Characteristics of phantom upper limb mobility encourage phantom-mobility-based prosthesis control
Authors: Touillet Amélie , Peultier-Celli Laetitia , Nicol Caroline , Jarrassé Nathanaël , Loiret Isabelle , Martinet Noël , Paysant Jean , De Graaf Jozina B
Published: October 2018

There is an increasing need to extend the control possibilities of upper limb amputees over their prosthetics, especially given the development of devices with numerous active joints. One way of feeding pattern recognition myoelectric control is to rely on the myoelectric activities of the residual limb associated with phantom limb movements (PLM). This study aimed to describe the types, characteristics, potential influencing factors and trainability of upper limb PLM. Seventy-six below- and above-elbow amputees with major amputation underwent a semi-directed interview about their phantom limb. Amputation level, elapsed time since amputation, chronic pain and use of prostheses of upper limb PLM were extracted from the interviews. Thirteen different PLM were found involving the hand, wrist and elbow. Seventy-six percent of the patients were able to produce at least one type of PLM; most of them could execute several. Amputation level, elapsed time since amputation, chronic pain and use of myoelectric prostheses were not found to influence PLM. Five above-elbow amputees participated in a PLM training program and consequently increased both endurance and speed of their PLM. These results clearly encourage further research on PLM-associated muscle activation patterns for future PLM-based modes of prostheses control.
Effect of diversity on growth, mortality, and loss of resilience to extreme climate events in a tropical planted forest experiment
Authors: Hutchison Chantal , Gravel Dominique , Guichard Frédéric , Potvin Catherine
Published: October 2018

A pressing question is whether biodiversity can buffer ecosystem functioning against extreme climate events. However, biodiversity loss is expected to occur due to climate change with severe impacts to tropical forests. Using data from a ca. 15 year-old tropical planted forest, we construct models based on a bootstrapping procedure to measure growth and mortality among different species richness treatments in response to extreme climate events. In contrast to higher richness mixtures, in one-species plots we find growth is strongly regulated by climate events and we also find increasingly higher mortality during a consecutive three year dry event. Based on these results together with indicators of loss of resilience, we infer an effect of diversity on critical slowing down. Our work generates new methods, concepts, and applications for global change ecology and emphasises the need for research in the area of biodiversity-ecosystem functioning along environmental stress gradients.
Definition of Fiducial Points in the Normal Seismocardiogram
Authors: Sørensen Kasper , Schmidt Samuel E. , Jensen Ask S. , Søgaard Peter , Struijk Johannes J.
Published: October 2018

The purpose of this work is to define fiducial points in the seismocardiogram (SCG) and to correlate them with physiological events identified in ultrasound images. For 45 healthy subjects the SCG and the electrocardiogram (ECG) were recorded simultaneously at rest. Immediately following the SCG and ECG recordings ultrasound images of the heart were also obtained at rest. For all subjects a mean SCG signal was calculated and all fiducial points (peaks and valleys) were identified and labeled in the same way across all signals. Eight physiologic events, including the valve openings and closings, were annotated from ultrasound as well and the fiducial points were correlated with those physiologic events. A total of 42 SCG signals were used in the data analysis. The smallest mean differences (±SD) between the eight events found in the ultrasound images and the fiducial points, together with their correlation coefficients (r) were: atrial systolic onset: −2 (±16) ms, r = 0.75 (p < 0.001); peak atrial inflow: 13 (±19) ms, r = 0.63 (p < 0.001); mitral valve closure: 4 (±11) ms, r = 0.71 (p < 0.01); aortic valve opening: −3 (±11) ms, r = 0.60 (p < 0.001); peak systolic outflow: 13 (±23) ms, r = 0.42 (p < 0.01); aortic valve closure: −5 (±12) ms, r = 0.94 (p < 0.001); mitral valve opening: −7 (±19) ms, r = 0.87 (p < 0.001) and peak early ventricular filling: −18 (±28 ms), r = 0.79 (p < 0.001). In conclusion eight physiologic events characterizeing the cardiac cycle, are associated with reproducible, well-defined fiducial points in the SCG.
Plasmid-normalized quantification of relative mitochondrial DNA copy number
Authors: Fazzini Federica , Schöpf Bernd , Blatzer Michael , Coassin Stefan , Hicks Andrew A. , Kronenberg Florian , Fendt Liane
Published: October 2018

Alterations of mitochondrial DNA (mtDNA) copy number have been associated with a wide variety of phenotypes and diseases. Unfortunately, the literature provides scarce methodical information about duplex targeting of nuclear and mtDNA that meets the quality criteria for qPCR. Therefore, we established a method for mtDNA copy number quantification using a quantitative PCR assay that allows for simultaneous targeting of a single copy nuclear gene (beta-2-microglobulin) and the t-RNALeu gene on the mtDNA. We include a plasmid containing both targets in order to normalize against differences in emission intensities of the fluorescent dyes Yakima Yellow and FAM. Applying the plasmid calibrator on an internal control reduced the intra-assay variability from 21% (uncorrected) to 7% (plasmid-corrected). Moreover, we noted that DNA samples isolated with different methods revealed different numbers of mtDNA copies, thus highlighting an important influence of the pre-analytical procedures. In summary, we developed a precise assay for mitochondrial copy number detection relative to nuclear DNA. Our method is applicable to comparative mitochondrial DNA copy number studies since the use of the dual insert plasmid allows correcting for the unequal emission intensities of the different fluorescent labels of the two targets.
In-season performance of European Union wheat forecasts during extreme impacts
Authors: van der Velde M. , Baruth B. , Bussay A. , Ceglar A. , Garcia Condado S. , Karetsos S. , Lecerf R. , Lopez R. , Maiorano A. , Nisini L. , Seguini L. , van den Berg M.
Published: October 2018

Here we assess the quality and in-season development of European wheat (Triticum spp.) yield forecasts during low, medium, and high-yielding years. 440 forecasts were evaluated for 75 wheat forecast years from 1993–2013 for 25 European Union (EU) Member States. By July, years with median yields were accurately forecast with errors below ~2%. Yield forecasts in years with low yields were overestimated by ~10%, while yield forecasts in high-yielding years were underestimated by ~8%. Four-fifths of the lowest yields had a drought or hot driver, a third a wet driver, while a quarter had both. Forecast accuracy of high-yielding years improved gradually during the season, and drought-driven yield reductions were anticipated with lead times of ~2 months. Single, contrasting successive in-season, as well as spatially distant dry and wet extreme synoptic weather systems affected multiple-countries in 2003, ’06, ’07, ’11 and 12’, leading to wheat losses up to 8.1 Mt (>40% of total EU loss). In these years, June forecasts (~ 1-month lead-time) underestimated these impacts by 10.4 to 78.4%. To cope with increasingly unprecedented impacts, near-real-time information fusion needs to underpin operational crop yield forecasting to benefit from improved crop modelling, more detailed and frequent earth observations, and faster computation.
MicroRNA induction by copy number gain is associated with poor outcome in squamous cell carcinoma of the lung
Authors: Xia Endi , Kanematsu Sotaro , Suenaga Yusuke , Elzawahry Asmaa , Kondo Hitomi , Otsuka Noriko , Moriya Yasumitsu , Iizasa Toshihiko , Kato Mamoru , Yoshino Ichiro , Yokoi Sana
Published: October 2018

Copy number gains in cancer genomes have been shown to induce oncogene expression and promote carcinogenesis; however, their role in regulating oncogenic microRNAs (onco-miRNAs) remains largely unknown. Our aim was to identify onco-miRNAs induced by copy number gains in human squamous cell carcinoma (Sq) of the lung. We performed a genome-wide screen of onco-miRNAs from 245 Sqs using data sets from RNA-sequencing, comparative genomic hybridization, and the corresponding clinical information from The Cancer Genome Atlas. Among 1001 miRNAs expressed in the samples, 231 were correlated with copy number alternations, with only 11 of these being highly expressed in Sq compared to adenocarcinoma and normal tissues. Notably, miR-296-5p, miR-324-3p, and miR-3928-3p expression was significantly associated with poor prognosis. Multivariate analysis using the Cox proportional hazards model showed that miRNA expression and smoking were independent prognostic factors and were associated with poor prognosis. Furthermore, the three onco-miRNAs inhibited FAM46C to induce MYC expression, promoting proliferation of Sq cells. We found that copy number gains in Sq of the lung induce onco-miRNA expression that is associated with poor prognosis.
Variants in the 14q32 miRNA cluster are associated with osteosarcoma risk in the Spanish population
Authors: Martin-Guerrero Idoia , Bilbao-Aldaiturriaga Nerea , Gutierrez-Camino Angela , Santos-Zorrozua Borja , Dolžan Vita , Patiño-Garcia Ana , Garcia-Orad Africa
Published: October 2018

Association studies in osteosarcoma risk found significant results in intergenic regions, suggesting that regions which do not codify for proteins could play an important role. The deregulation of microRNAs (miRNAs) has been already associated with osteosarcoma. Consequently, genetic variants affecting miRNA function could be associated with risk. This study aimed to evaluate the involvement of all genetic variants in pre-miRNAs described so far in relationship to the risk of osteosarcoma. We analyzed a total of 213 genetic variants in 206 pre-miRNAs in two cohorts of osteosarcoma patients (n = 100) and their corresponding controls (n = 256) from Spanish and Slovenian populations, using Goldengate Veracode technology (Illumina). Four polymorphisms in pre-miRNAs at 14q32 miRNA cluster were associated with osteosarcoma risk in the Spanish population (rs12894467, rs61992671, rs58834075 and rs12879262). Pathway enrichment analysis including target genes of these miRNAs pointed out the WNT signaling pathways overrepresented. Moreover, different single nucleotide polymorphism (SNP) effects between the two populations included were observed, suggesting the existence of population differences. In conclusion, 14q32 miRNA cluster seems to be a hotspot for osteosarcoma susceptibility in the Spanish population, but not in the Slovenian, which supports the idea of the existence of population differences in developing this disease.
Genetic enhancement of Ras-ERK pathway does not aggravate L-DOPA-induced dyskinesia in mice but prevents the decrease induced by lovastatin
Authors: Ruiz-DeDiego Irene , Fasano Stefania , Solís Oscar , Garcia-Montes José-Rubén , Brea José , Loza María I. , Brambilla Riccardo , Moratalla Rosario
Published: October 2018

Increasing evidence supports a close relationship between Ras-ERK1/2 activation in the striatum and L-DOPA-induced dyskinesia (LID). ERK1/2 activation by L-DOPA takes place through the crosstalk between D1R/AC/PKA/DARPP-32 pathway and NMDA/Ras pathway. Compelling genetic and pharmacological evidence indicates that Ras-ERK1/2 inhibition prevents LID onset and may even revert already established dyskinetic symptoms. However, it is currently unclear whether exacerbation of Ras-ERK1/2 activity in the striatum may further aggravate dyskinesia in experimental animal models. Here we took advantage of two genetic models in which Ras-ERK1/2 signaling is hyperactivated, the Nf1+/− mice, in which the Ras inhibitor neurofibromin is reduced, and the Ras-GRF1 overexpressing (Ras-GRF1 OE) transgenic mice in which a specific neuronal activator of Ras is enhanced. Nf1+/− and Ras-GRF1 OE mice were unilaterally lesioned with 6-OHDA and treated with an escalating L-DOPA dosing regimen. In addition, a subset of Nf1+/− hemi-parkinsonian animals was also co-treated with the Ras inhibitor lovastatin. Our results revealed that Nf1+/− and Ras-GRF1 OE mice displayed similar dyskinetic symptoms to their wild-type counterparts. This observation was confirmed by the lack of differences between mutant and wild-type mice in striatal molecular changes associated to LID (i.e., FosB, and pERK1/2 expression). Interestingly, attenuation of Ras activity with lovastatin does not weaken dyskinetic symptoms in Nf1+/− mice. Altogether, these data suggest that ERK1/2-signaling activation in dyskinetic animals is maximal and does not require further genetic enhancement in the upstream Ras pathway. However, our data also demonstrate that such a genetic enhancement may reduce the efficacy of anti-dyskinetic drugs like lovastatin.
A Real-Time PCR based assay for determining parasite to host ratio and parasitaemia in the clinical samples of Bovine Theileriosis
Authors: Dandasena Debabrata , Bhandari Vasundhra , Sreenivasamurthy G. S. , Murthy Shweta , Roy Sonti , Bhanot Vandna , Arora Jaspreet Singh , Singh Satparkash , Sharma Paresh
Published: October 2018

Theileria annulatais an intracellular parasite that causes active and latent forms of bovine theileriosis. Diagnosis of the disease is primarily based on traditional methods such as microscopy, however, PCR based methods have proven to be superior in the absence of clear disease symptoms. However, diagnosis is difficult in cases of lower parasitaemia by conventional PCR. Hence, a rapid and sensitive method which can detect early infection and low parasite load is required. Therefore, we have developed an absolute quantification based real-time PCR (qPCR) assay. Reference standard curve using recombinant plasmids of a host (hprt) and a parasite gene (tasp) was constructed, and the assay was initially standardised usingin vitro T. annulatacell lines. Further, 414 blood samples from suspected theileriosis cases were also evaluated using qPCR. The assay can estimate host to parasite ratios, calculate parasitaemia and treatment effectiveness in the clinical cases of theileriosis. In comparison with the conventional PCR results, 44 additional positive cases were found. Therefore, the assay holds importance in a clinical setting due to its ability to quantify the parasite load in clinical samples. It may be further used in distinguishing active and latent theileriosis infections and detection of drug resistance in the field.
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase
Authors: Ezewudo Matthew , Borens Amanda , Chiner-Oms Álvaro , Miotto Paolo , Chindelevitch Leonid , Starks Angela M. , Hanna Debra , Liwski Richard , Zignol Matteo , Gilpin Christopher , Niemann Stefan , Kohl Thomas Andreas , Warren Robin M. , Crook Derrick , Gagneux Sebastien , Hoffner Sven , Rodrigues Camilla , Comas Iñaki , Engelthaler David M. , Alland David , Rigouts Leen , Lange Christoph , Dheda Keertan , Hasan Rumina , McNerney Ruth , Cirillo Daniela M. , Schito Marco , Rodwell Timothy C. , Posey James
Published: October 2018

Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
smarce1 mutants have a defective endocardium and an increased expression of cardiac transcription factors in zebrafish
Authors: Castillo-Robles Jorge , Ramírez Laura , Spaink Herman P. , Lomelí Hilda
Published: October 2018

SWI/SNF or BAF chromatin-remodeling complexes are polymorphic assemblies of homologous subunit families that remodel nucleosomes and facilitate tissue-specific gene regulation during development. BAF57/SMARCE1 is a BAF complex subunit encoded in animals by a single gene and is a component of all mammalian BAF complexes. In vivo, the loss of SMARCE1 would lead to the formation of deficient combinations of the complex which might present limited remodeling activities. To address the specific contribution of SMARCE1 to the function of the BAF complex, we generated CRISPR/Cas9 mutations of smarce1 in zebrafish. Smarce1 mutants showed visible defects at 72 hpf, including smaller eyes, abnormal body curvature and heart abnormalities. Gene expression analysis revealed that the mutant embryos displayed defects in endocardial development since early stages, which led to the formation of a misshapen heart tube. The severe morphological and functional cardiac problems observed at 4 dpf were correlated with the substantially increased expression of different cardiac transcription factors. Additionally, we showed that Smarce1 binds to cis-regulatory regions of the gata5 gene and is necessary for the recruitment of the BAF complex to these regions.
Stem cell enriched-epithelial spheroid cultures for rapidly assaying small intestinal radioprotectors and radiosensitizers in vitro
Authors: de la Cruz Bonilla Marimar , Stemler Kristina M. , Taniguchi Cullen M. , Piwnica-Worms Helen
Published: October 2018

Radiation therapy is one of the main treatment options for many cancer patients. Although high doses of radiation may maximize tumor cell killing, dose escalation is limited by toxicity to neighboring normal tissues. This limitation applies particularly to the small intestine, the second most radiosensitive organ in the body. Identifying small intestinal (SI) radioprotectors could enable dose escalation in the treatment of abdominopelvic malignancies. However, the only assay currently available to identify effects of radiomodulating drugs on the regenerating capacity of SI stem cells is the Withers-Elkind microcolony assay, which requires large numbers of mice, making it a costly and low throughput method. Here, we describe a novel spheroid formation assay (SFA) that utilizes SI stem cell-enriched three-dimensional epithelial spheroid cultures to identify gastrointestinal radiomodulators ex vivo. The SFA is scalable for high throughput screening and can be used to identify both radioprotectors and radiosensitizers.
Genetic diversities and phylogenetic analyses of three Chinese main ethnic groups in southwest China: A Y-Chromosomal STR study
Authors: Chen Pengyu , He Guanglin , Zou Xing , Zhang Xin , Li Jida , Wang Zhisong , Gao Hongyan , Luo Li , Zhang Zhongqing , Yu Jian , Han Yanyan
Published: October 2018

Short tandem repeats (STRs) located on the Y chromosome with the properties of male-specific inheritance and haploidy are widely used in forensics to analyze paternal genealogies and match male trace donors to evidence. Besides, Y-chromosomal haplotypes play an important role in providing breathtaking insights into population genetic history. However, the genetic diversity and forensic characteristics of Y-STRs in Guizhou main ethnic groups (Hans, Miaos and Bouyeis) remain uncharacterized. Here, we obtained Y-chromosomal 23-marker haplotypes in three Guizhou populations and submitted the first batch of Y-STR haplotype data to the YHRD. The HD in the aforementioned three populations are 0.99990, 0.99983, and 0.99979, respectively, and DC values are 0.9902, 0.9908, and 0.97959, respectively. Subsequently, genetic differentiation between our newly studied populations and reference groups along ethnic/administrative divisions, as well as national/continental boundaries were investigated via AMOVA, MDS, and phylogenetic relationship reconstruction. Significant genetic differentiations from our subjects and other groups are identified in ethnically, linguistically and geographically diverse populations, including most prominently Tibetans and Uyghurs among 30 mainland Chinese populations, Taiwanese groups and others among 58 Asian populations, as well as African groups and others among 89 worldwide populations. Qiannan Bouyei has a close genetic relationship with Guangxi Zhuang, and Zunyi Han and Qiandongnan Miao have close genetic affinity with Hunan Han and Guizhou Shui, respectively. Collectively, this new-generation Y-STR amplification system can be used as a supplementary tool in forensic identification and male parentage testing and even pedigree search.
The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics
Authors: Wang Aijun , Pang Linxiu , Wang Na , Ai Peng , Yin Desuo , Li Shuangcheng , Deng Qiming , Zhu Jun , Liang Yueyang , Zhu Jianqing , Li Ping , Zheng Aiping
Published: October 2018

Tilletia horrida is a soil-borne, mononucleate basidiomycete fungus with a biotrophic lifestyle that causes rice kernel smut, a disease that is distributed throughout hybrid rice growing areas worldwide. Here we report on the high-quality genome sequence of T. horrida; it is composed of 23.2 Mb that encode 7,729 predicted genes and 6,973 genes supported by RNA-seq. The genome contains few repetitive elements that account for 8.45% of the total. Evolutionarily, T. horrida lies close to the Ustilago fungi, suggesting grass species as potential hosts, but co-linearity was not observed between T. horrida and the barley smut Ustilago hordei. Genes and functions relevant to pathogenicity were presumed. T. horrida possesses a smaller set of carbohydrate-active enzymes and secondary metabolites, which probably reflect the specific characteristics of its infection and biotrophic lifestyle. Genes that encode secreted proteins and enzymes of secondary metabolism, and genes that are represented in the pathogen-host interaction gene database genes, are highly expressed during early infection; this is consistent with their potential roles in pathogenicity. Furthermore, among the 131 candidate pathogen effectors identified according to their expression patterns and functionality, we validated two that trigger leaf cell death in Nicotiana benthamiana. In summary, we have revealed new molecular mechanisms involved in the evolution, biotrophy, and pathogenesis of T. horrida.
Intra- and inter-protein couplings of backbone motions underlie protein thiol-disulfide exchange cascade
Authors: Zhang Wenbo , Niu Xiaogang , Ding Jienv , Hu Yunfei , Jin Changwen
Published: October 2018

The thioredoxin (Trx)-coupled arsenate reductase (ArsC) is a family of enzymes that catalyzes the reduction of arsenate to arsenite in the arsenic detoxification pathway. The catalytic cycle involves a series of relayed intramolecular and intermolecular thiol-disulfide exchange reactions. Structures at different reaction stages have been determined, suggesting significant conformational fluctuations along the reaction pathway. Herein, we use two state-of-the-art NMR methods, the chemical exchange saturation transfer (CEST) and the CPMG-based relaxation dispersion (CPMG RD) experiments, to probe the conformational dynamics of B. subtilis ArsC in all reaction stages, namely the enzymatic active reduced state, the intra-molecular C10–C82 disulfide-bonded intermediate state, the inactive oxidized state, and the inter-molecular disulfide-bonded protein complex with Trx. Our results reveal highly rugged energy landscapes in the active reduced state, and suggest global collective motions in both the C10–C82 disulfide-bonded intermediate and the mixed-disulfide Trx-ArsC complex.
Dual Inhibition of Bcl-2/Bcl-xL and XPO1 is synthetically lethal in glioblastoma model systems
Authors: Shang Enyuan , Zhang Yiru , Shu Chang , Ishida Chiaki Tsuge , Bianchetti Elena , Westhoff Mike-Andrew , Karpel-Massler Georg , Siegelin Markus D.
Published: October 2018

XPO1 has recently emerged as a viable treatment target for solid malignancies, including glioblastoma (GBM), the most common primary malignant brain tumor in adults. However, given that tumors become commonly resistant to single treatments, the identification of combination therapies is critical. Therefore, we tested the hypothesis that inhibition of anti-apoptotic Bcl-2 family members and XPO1 are synthetically lethal. To this purpose, two clinically validated drug compounds, the BH3-mimetic, ABT263, and the XPO1 inhibitor, Selinexor, were used in preclinical GBM model systems. Our results show that inhibition of XPO1 reduces cellular viability in glioblastoma cell cultures. Moreover, addition of ABT263 significantly enhances the efficacy of XPO1 inhibition on the reduction of cellular viability, which occurs in a synergistic manner. While selinexor inhibits the proliferation of glioblastoma cells, the combination treatment of ABT263 and selinexor results in substantial induction of cell death, which is accompanied by activation of effector- initiator caspases and cleavage of PARP. Mechanistically we find that XPO1 inhibition results in down-regulation of anti-apoptotic Mcl-1 and attenuates ABT263 driven Mcl-1 up-regulation. Consistently, siRNA mediated silencing of Mcl-1 sensitizes for ABT263 mediated cell death and partially for the combination treatment. By using a human patient-derived xenograft model of glioblastoma in mice, we demonstrate that the combination treatment of ABT263 and Selinexor reduces tumor growth significantly more than each compound alone. Collectively, these results suggest that inhibition of XPO1 and Bcl-2/Bcl-xL might be a potential strategy for the treatment of malignant glial tumors.
Novel detection of provenance in the illegal wildlife trade using elemental data
Authors: Brandis Kate J. , Meagher Phoebe J. B. , Tong Lydia J. , Shaw Michelle , Mazumder Debashish , Gadd Patricia , Ramp Daniel
Published: October 2018

Despite being the fourth largest criminal market in the world, no forensic tools have been sufficiently developed to accurately determine the legal status of seized animals and their parts. Although legal trading is permissible for farmed or captive-bred animals, many animals are illegally removed from the wild and laundered by masquerading them as captive bred. Here we present high-resolution x-ray fluorescence (XRF) as a non-invasive and cost-effective tool for forensic classification. We tested the efficacy of this technique by using machine learning on a training set of zoo specimens and wild-caught individuals of short-beaked echidnas (Tachyglossus aculeatus), a small insectivorous monotreme in Australia. XRF outperformed stable isotope analysis (δ13C, δ15N), reducing overall classification error below 4%. XRF has the added advantage of providing samples every 200 μm on a single quill, enabling 100% classification accuracy by taking the consensus of votes per quill. This accurate and cost-effective forensic technique could provide a much needed in situ solution for combating the illegal laundering of wildlife, and conversely, assist with certification of legally bred animals.
Whole-volume ADC Histogram and Texture Analyses of Parotid Glands as an Image Biomarker in Evaluating Disease Activity of Primary Sjögren’s Syndrome
Authors: Chu Chen , Wang Fengxian , Zhang Huayong , Zhu Yun , Wang Chun , Chen Weibo , He Jian , Sun Lingyun , Zhou Zhengyang
Published: October 2018

Diffusion weighted imaging (DWI) has proven to be sensitive for detecting early injury to the parotid gland in pSS (primary Sjögren’s syndrome). Here, we explored the application of ADC histogram and texture analyses for evaluating the disease activity of pSS. A total of 55 patients with pSS who met the classification criteria of the 2002 AECG criteria prospectively underwent 3.0-T magnetic resonance imaging (MRI) including DWI (b = 0 and 1000 s/mm2). According to the ESSDAI score, 35 patients were categorized into the low-activity group (ESSDAI < 5) and 20 into the moderate-high-activity group (ESSDAI ≥ 5). Via analysis of the whole-volume ADC histogram, the ADCmean, skewness, kurtosis, and entropy values of the bilateral parotid glands were determined. Multivariate analysis was used to identify independent risk factors for predicting disease activity. The diagnostic performance of the indexes was evaluated via receiver operating characteristic (ROC) analysis. ROC analysis showed that the anti-SSB, lip biopsy, MRI morphology, ADC, ADCmean, and entropy values were able to categorize the disease into two groups, particularly the entropy values. The multivariate model, which included anti-SSB, MRI morphology and entropy, had an area under the ROC curve of 0.923 (P < 0.001). The parotid entropy value distinguished disease activity in patients with pSS, especially combined with anti-SSB and MRI morphology.
Recovering distance information in spectral domain interferometry
Authors: Bradu Adrian , Israelsen Niels Møller , Maria Michael , Marques Manuel J. , Rivet Sylvain , Feuchter Thomas , Bang Ole , Podoleanu Adrian
Published: October 2018

This work evaluates the performance of the Complex Master Slave (CMS) method, that processes the spectra at the interferometer output of a spectral domain interferometry device without involving Fourier transforms (FT) after data acquisition. Reliability and performance of CMS are compared side by side with the conventional method based on FT, phase calibration with dispersion compensation (PCDC). We demonstrate that both methods provide similar results in terms of resolution and sensitivity drop-off. The mathematical operations required to produce CMS results are highly parallelizable, allowing real-time, simultaneous delivery of data from several points of different optical path differences in the interferometer, not possible via PCDC.
Surfactant protein D attenuates acute lung and kidney injuries in pneumonia-induced sepsis through modulating apoptosis, inflammation and NF-κB signaling
Authors: Du Juan , Abdel-Razek Osama , Shi Qiao , Hu Fengqi , Ding Guohua , Cooney Robert N. , Wang Guirong
Published: October 2018

Pneumonia and sepsis are major risk factors for acute kidney injury (AKI). Patients with pneumonia and AKI are at increased risk for morbidity and mortality. Surfactant protein D (SP-D) expressed in lung and kidney plays important roles in innate immunity. However, little is known about the role of organ-specific SP-D in the sepsis. The current study uses wild type (WT), SP-D knockout (KO), and humanized SP-D transgenic (hTG, lung-specific SP-D expression) mice to study organ-specific role of SP-D in pneumonia-induced sepsis. Analyses demonstrated differential lung and kidney injury among three-type mice infected with Pseudomonas aeruginosa. After infection, KO mice showed higher injurious scores in both lung and kidney, and decreased renal function than WT and hTG mice. hTG mice exhibited comparable lung injury but more severe kidney injury compared to WT mice. Increased renal tubular apoptosis, NF-κB activation and proinflammatory cytokines in the kidney of KO mice were found when compared with WT and hTG mice. Furthermore, in vitro primary proximal tubular epithelial cells from KO mice showed more apoptosis with higher level of activated caspase-3 than those from WT mice after LPS treatment. Collectively, SP-D attenuates AKI in the sepsis by modulating renal apoptosis, inflammation and NF-κB signaling.
Corticoefferent pathology distribution in amyotrophic lateral sclerosis: in vivo evidence from a meta-analysis of diffusion tensor imaging data
Authors: Gorges Martin , Del Tredici Kelly , Dreyhaupt Jens , Braak Heiko , Ludolph Albert C. , Müller Hans-Peter , Kassubek Jan
Published: October 2018

A sequential transaxonal disease spread of amyotrophic lateral sclerosis (ALS)-associated TDP-43 pathology in four stages has been defined bypost-mortemdata, which have been transferred toin vivoimaging by diffusion tensor imaging (DTI) studies. Here, we aimed to investigate whether DTI meta-data are consistent with this proposed pattern of progression in ALS. A systematic literature search using the search engines PubMed and Scopus yielded a total of 370 publications. Of these, 57 studies with cross-sectional data and 10 longitudinal studies of human whole-brain analyses of fractional anisotropy (FA) were included in the final data analysis. Statistical meta-analyses on coordinates of significant FA alterations were performed on a grand average alteration data set using a fixed-effect model. A widespread pattern of white matter impairment was identified from cross-sectional meta data (n = 2064 ALS patients vs.n = 1688 controls) and supported from longitudinal meta data (n = 266 ALS patients over 8 months). The results from cross-sectional meta-analyses corresponded to the brain regions and tract systems according to the sequential disease spread of ALS. Structural alterations in ALS patients vs. controls followed a power gradient, i.e., the most frequent alterations were observed along the corticospinal tract (CST, related to ALS stage 1), followed by frequent alterations along the corticorubral/-pontine tract (related to ALS stage 2), together with corticostriatal pathways (related to ALS stage 3), and, finally, alterations in the hippocampal regions adjacent to the proximal portion of the perforant path (related to ALS stage 4). The results from the DTI-based neuroimaging meta-analysis strongly support the model of the corticoefferent axonal disease progression in ALS and provides furtherin vivoevidence for the proposed staging scheme of ALS-associated pathology.
The developmental transcriptome of the human heart
Authors: Pervolaraki Eleftheria , Dachtler James , Anderson Richard A. , Holden Arun V.
Published: October 2018

The human heart develops through complex mechanisms producing morphological and functional changes during gestation. We have recently demonstrated using diffusion tensor MRI that over the relatively short space of 40 days, between 100–140 days gestational age, the ventricular myocardium transforms from a disorganised tissue to the ordered structure characteristic of mature cardiac tissue. However, the genetic basis underpinning this maturation is unclear. Herein, we have used RNA-Seq to establish the developmentally-regulated transcriptome of gene expression in the developing human heart across three gestational ages in the first and second trimester. By comparing 9 weeks gestational age (WGA) with 12 WGA, we find 288 genes show significant differential expression. 305 genes were significantly altered comparing 12 and 16 WGA, and 806 genes differentially expressed between 9 and 16 WGA. Network analysis was used to identify genetic interactions, node properties and gene ontology categories. In summary, we present a comprehensive transcriptomic analysis of human heart development during early gestation, and identify differentially expressed genes during heart development between 9 and 16 weeks, overlapping the first and early second trimester.