bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California
Authors: Suttner Brittany J. , Johnston Eric R. , Orellana Luis H. , Rodriguez-R Luis M. , Hatt Janet K. , Carychao Diana , Carter Michelle Q. , Cooley Michael B. , Konstantinidis Konstantinos T.
Published: August 2019

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from agricultural activities such as Shiga Toxin-producingE. coli(STEC) in such sediments remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (~4 Gbp per library), we were unable to detect any pathogenicEscherichia coliin the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low pathogen abundance. Further, no significant differences were detected in the abundance of human- or cow-specific gut microbiome sequences compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high baseline level of metagenomic reads encoding antibiotic resistance genes (ARGs) was found in all samples and was significantly higher compared to ARG reads in metagenomes from other environments, suggesting that these communities may be natural reservoirs of ARGs. Overall, our metagenomic results revealed that creek sediments are not a major sink for anthropogenic runoff and the public health risk associated with these sediment microbial communities may be low.

IMPORTANCE

Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium,E. coli. However, the accuracy of these traditional methods (e.g., low quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.
The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes
Authors: Lv Xiaokang , Chai Jianmin , Diao Qiyu , Huang Wenqin , Zhuang Yimin , Zhang Naifeng
Published: August 2019

The feeding regime of early supplementary solid diet improved rumen development and ruminant production. However, the signature microbiota linking dietary regimes to rumen function shifts and hosts are still unclear. We analyzed the rumen microbiome and functions affected by supplementation of solid diet using a combination of machine learning algorithms. The volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes increased significantly in the supplementary solid diet groups. The predominant genera altered significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups) RandomForest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acids production. The nutrient specific bacteria for carbohydrate and protein were also identified. According to FishTaco analysis, a set of intersecting core species contributed with rumen function shifts by solid diet. The core community structures consisted of specific signature microbiota and their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanism of microbiome governing by solid diet and highlights the signatures microbiota for animal health and production.

Importance

Small ruminants are essential protein sources for human, so keeping them health and increasing their production are important. The microbial communities resided in rumen play key roles to convert fiber resources to human food. Moreover, rumen physiology experience huge changes after birth, and understanding its microbiome roles could provide insights for other species. Recently, our studies and others have shown that diet changed rumen microbial composition and goat performance. In this study, we identified core community structures that were affected by diet and associated to the rumen development and goat production. This outcome could potentially allow us to select specific microbiome to improve rumen physiology and functions, maintain host health and benefit animal production. Therefore, it gives a significant clue that core microbiome manipulation by feeding strategies can increase animal products. To our knowledge, we firstly used FishTaco for determination of link between signatures abundances and rumen function shifts.
Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection
Authors: Brümmer Anneke , Dreos Rene , Marques Ana Claudia , Bergmann Sven
Published: August 2019

Long intergenic non-coding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as non-coding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated.

Here, we analysed signatures of repressed translation in lincRNA sequences from six eukaryotes. In species under stronger selection, i.e. fission yeast and worm, we detected significantly shorter ORFs than in intronic and non-transcribed control regions, a suboptimal sequence context around start codons for translation initiation, and trinucleotides (“codons”) corresponding to less abundant tRNAs than codons in control regions, potentially impeding translation elongation.

We verified that varying tRNA expression levels affect ribosome-binding to lincRNAs by analyzing data from five human cell lines. Notably, for three cell lines, codons in abundant cytoplasmic lincRNAs corresponded to lower expressed tRNAs than control codons, substantiating cell type-specific repression of lincRNA translation in human. Finally, comparing non-coding with peptide-encoding ORFs suggested that codon usage at the start of ORFs to be of particular relevance for ribosome-binding.

The identified sequence signatures may assist distinguishing peptide- from real non-coding lincRNAs in a cell.
Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction
Authors: Català-Moll Francesc , Weichenhan Dieter , Lutsik Pavlo , Álvarez-Prado Ángel F. , Rodríguez-Ubreva Javier , Klemann Christian , Speckmann Carsten , Abolhassani Hassan , Martínez-Gallo Mónica , Dieli-Crimi Romina , Soler-Palacín Pere , Kracker Sven , Hammarström Lennart , Durandy Anne , Grimbacher Bodo , Plass Christoph , Ballestar Esteban
Published: August 2019

Mutations in activation induced deaminase (AID) lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated cytosine deamination has been proposed as mediating active demethylation, although evidences both support and cast doubt on such a role. We here made use of HIGM2 B cells to investigate direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation defects, of which approximately 25% of these defects correspond to active events. For genes that undergo active demethylation that is impaired in HIGM2 individuals, we did not observe AID involvement but a participation of TET enzymes. DNA methylation alterations in HIGM2 naïve B cells are related to premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data supports a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.
Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach
Authors: Crotti M. , Adams C.E. , Elmer K.R.
Published: August 2019

Epigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses.

We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we compared the number of SNPs retained, population genetic summary statistics, and population genetic structure between data drawn from ddRADseq and epiRADseq library preparations.

We find that SNPs drawn from epiRADseq are similar in number to those drawn from ddRADseq, with a 55-83% of SNPs being identified by both methods. Genotyping error rate was <5% in both approaches. For summary statistics such as heterozygosity and nucleotide diversity, there is a strong correlation between methods (Spearman’s rho > 0.88). Furthermore, identical patterns of population genetic structure were recovered using SNPs from epiRADseq and ddRADseq approaches.

We show that SNPs obtained from epiRADseq are highly similar to those from ddRADseq and are equivalent for estimating genetic diversity and population structure. This finding is particularly relevant to researchers interested in genetics and epigenetics on the same individuals because using a single epigenomic approach to generate two datasets greatly reduces the time and financial costs compared to using these techniques separately. It also efficiently enables correction of epigenetic estimates with population genetic data. Many studies will benefit from a combinatorial approach with genetic and epigenetic markers and this demonstrates a single, efficient method to do so.
A personalised approach for identifying disease-relevant pathways in heterogeneous diseases
Authors: Somani Juhi , Ramchandran Siddharth , Lähdesmäki Harri
Published: August 2019

Numerous time-course gene expression datasets have been curated for studying the biological dynamics that drive disease progression; and nearly as many methods have been proposed to analyse them. However, barely any method exists that can appropriately model time-course data and at the same time account for heterogeneity that entails many complex diseases. Most methods manage to fulfil either one of those qualities, but not both. The lack of appropriate methods hinders our capability of understanding the disease process and pursuing preventive or curative treatments. Here, we present a method that models time-course data in a personalised manner, i.e. for each case-control pair individually, using Gaussian processes in order to identify differentially expressed genes (DEGs); and combines the lists of DEGs on a pathway-level using a permutation-based empirical hypothesis testing in order to overcome gene-level variability and inconsistencies prevalent to heterogeneous datasets from complex diseases. Our method can be applied to study the time-course dynamics as well as specific time-windows of heterogeneous diseases. We apply our personalised approach on two longitudinal type 1 diabetes (T1D) datasets to determine perturbations that take place during early prognosis of the disease as well as in time-windows before seroconversion and clinical onset of T1D. By comparing to non-personalised methods, we demonstrate that our approach is biologically motivated and can reveal more insights into progression of heterogeneous diseases. With its robust capabilities of identifying immunologically interesting and disease-relevant pathways, our approach could be useful for predicting certain events in the progression of heterogeneous diseases and even biomarker identification.

Availability

The implemented code of our personalised approach will be available online upon publication.
The euchromatic histone mark H3K36me3 preserves heterochromatin through sequestration of an acetyltransferase complex in fission yeast
Authors: Georgescu Paula R. , Capella Matías , Fischer-Burkart Sabine , Braun Sigurd
Published: August 2019

Maintaining the identity of chromatin states requires mechanisms that ensure their structural integrity through the concerted actions of histone modifiers, readers, and erasers. Histone H3K9me and H3K27me are hallmarks of repressed heterochromatin, whereas H3K4me and H3K36me are associated with actively transcribed euchromatin. Paradoxically, several studies have reported that loss of Set2, the methyltransferase responsible for H3K36me, causes de-repression of heterochromatin. Here we show that unconstrained activity of the acetyltransferase complex Mst2C, which antagonizes heterochromatin, is the main cause of the silencing defects observed in Set2-deficient cells. As previously shown, Mst2C is sequestered to actively transcribed chromatin via binding to H3K36me3 that is recognized by the PWWP domain protein Pdp3. We demonstrate that combining deletions ofset2+andpdp3+results in an epistatic silencing phenotype. In contrast, deletingmst2+, or other members of Mst2C, fully restores silencing in Set2-deficient cells. Suppression of the silencing defect inset2Δ cells is specific for pericentromeres and subtelomeres, which are marked by H3K9me, but not seen for loci that lack genuine heterochromatin. Although Mst2 catalyzes acetylation of H3K14, this modification is likely not involved in the Set2-dependent pathway due to redundancy with the HAT Gcn5. Moreover, while Mst2 is required for acetylation of the H2B ubiquitin ligase Brl1 in euchromatin, we find that its role in heterochromatin silencing is not affected by Brl1 acetylation. We propose that it targets another, unknown substrate critical for heterochromatin silencing. Our findings demonstrate that maintenance of chromatin states requires spatial constraint of opposing chromatin activities.
Hingepoints and neural folds reveal conserved features of primary neurulation in the zebrafish forebrain
Authors: Werner Jonathan M. , Negesse Maraki Y. , Brooks Dominique L. , Caldwell Allyson R. , Johnson Jafira M. , Brewster Rachel M.
Published: August 2019

Primary neurulation is the process by which the neural tube, the central nervous system precursor, is formed from the neural plate. Incomplete neural tube closure occurs frequently, yet underlying causes remain poorly understood. Developmental studies in amniotes and amphibians have identified hingepoint and neural fold formation as key morphogenetic events and hallmarks of primary neurulation, the disruption of which causes neural tube defects. In contrast, the mode of neurulation in teleosts such as zebrafish has remained highly debated. Teleosts are thought to have evolved a unique pattern of neurulation, whereby the neural plate infolds in absence of hingepoints and neural folds (NFs), at least in the hindbrain/trunk where it has been studied. We report here on zebrafish forebrain morphogenesis where we identify these morphological landmarks. Our findings reveal a deeper level of conservation of neurulation than previously recognized and establish the zebrafish as a model to understand human neural tube development.
Exploiting epistasis to perturb the evolution of antibiotic resistance
Authors: Lukačišinová Marta , Fernando Booshini , Bollenbach Tobias
Published: August 2019

New ways of curbing the ability of bacteria to evolve spontaneous resistance could mitigate the looming antibiotic resistance crisis. Progress toward this goal requires a comprehensive understanding of the key factors that contribute to resistance evolvability. Here, we present a systematic approach to identify cellular functions that affect the evolvability of resistance. Using a robotic lab-evolution platform that keeps population size and selection pressure under tight control for hundreds ofEscherichia colipopulations evolving in parallel, we quantified the effects of a genome-wide selection of pre-existing gene deletions on resistance evolution. Initial resistance of strains with gene deletions differed by more than tenfold but converged toward a hard upper bound for resistance during the evolution experiment, reflecting a global pattern of diminishing returns epistasis. We identified specific cellular functions that drastically curtail the evolvability of resistance; beyond DNA repair, these include membrane transport, LPS biosynthesis, and chaperones. Perturbations of efflux pumps prevented resistance evolution completely or forced evolution on inferior mutational paths, not explored in the wild type. We show that strong negative epistasis generally underlies these phenomena. The identified functions provide new targets for adjuvants tailored to block evolutionary paths to resistance when combined with antibiotics.
Unexpected differences in the pharmacokinetics of N-acetyl-DL-leucine enantiomers after oral dosing and their clinical relevance
Authors: Churchill Grant C. , Strupp Michael , Galione Antony , Platt Frances M.
Published: August 2019

These results suggest that during chronic administration of the racemate, the D-enantiomer would accumulate, which could have negative effects. The enantiomers of many chiral drugs not only exhibit different pharmacological effects in regard to targets that dictate therapeutic and toxic effects, but are also handled differently in the body due to pharmacokinetic effects. We investigated the pharmacokinetics of the enantiomers of N-acetyl-leucine after administration of the racemate (N-acetyl-DL-leucine) or purified, pharmacologically active L-enantiomer (N-acetyl-L-leucine). Compounds were administered orally to mice. Plasma and tissue samples were collected at predetermined time points (0.25 to 8 h), quantified with liquid chromatography/mass spectrometry, and pharmacokinetic constants were calculated using a noncompartmental model. When administered as the racemate, both the maximum plasma concentration (Cmax) and the area under the plasma drug concentration over time curve (AUC) were much greater for the D-enantiomer relative to the L-enantiomer. When administered as the L-enantiomer, the dose proportionality was greater than unity compared to the racemate, suggesting saturable processes affecting uptake and/or metabolism. Elimination (keand T1/2) was similar for both enantiomers. These results are most readily explained by inhibition of uptake at an intestinal carrier of the L-enantiomer by the D-enantiomer, and by first-pass metabolism of the L-, but not D-enantiomer, likely by deacetylation. In brain and muscle, N-acetyl-L-leucine levels were lower than N-acetyl-D-leucine, consistent with rapid conversion into L-leucine and utilization by normal leucine metabolism. In summary, the enantiomers of N-acetyl-leucine exhibit large, unexpected differences in pharmacokinetics due to both unique handling and/or inhibition of uptake and metabolism of the L-enantiomer by the D-enantiomer. Taken together, these results have clinical implications supporting the use of N-acetyl-L-leucine instead of the racemate or N-acetyl-D-leucine, and support the research and development of isolated N-acetyl-L-leucine.
Formate induces a metabolic switch in nucleotide and energy metabolism
Authors: Oizel Kristell , Tait-Mulder Jacqueline , Fernandez-de-Cossio-Diaz Jorge , Pietzke Matthias , Brunton Holly , Dhayade Sandeep , Athineos Dimitris , Lilla Sergio , Blanco Giovanny Rodriguez , Sumpton David , Mackay Gillian M , Blyth Karen , Zanivan Sara , Meiser Johannes , Vazquez Alexei
Published: August 2019

Formate is a precursor for the de novo synthesis of purine and deoxythymidine nucleotides. Formate also interacts with energy metabolism by promoting the synthesis of adenine nucleotides. Here we use theoretical modelling together with metabolomics analysis to investigate the link between formate, nucleotide and energy metabolism. We uncover that endogenous or exogenous formate induces a metabolic switch from low to high adenine nucleotide levels, increasing the rate of glycolysis and repressing the AMPK activity. Formate also induces an increase in the pyrimidine precursor orotate and the urea cycle intermediate argininosuccinate, in agreement with the ATP dependent activities of carbamoyl-phosphate and argininosuccinate synthetase. In vivo data for mouse and human cancers confirms the association between increased formate production, nucleotide and energy metabolism. Finally, the in vitro observations are recapitulated in mice following intraperitoneal injection of formate. We conclude that formate is a potent regulator of purine, pyrimidine and energy metabolism.
Cryo-EM structures of α-synuclein fibrils with the H50Q hereditary mutation reveal new polymorphs
Authors: Boyer David R. , Li Binsen , Sun Chuanqi , Fan Weijia , Sawaya Michael R. , Jiang Lin , Eisenberg David S.
Published: August 2019

Abstract

Deposits of amyloid fibrils of α-synuclein are the histological hallmarks of Parkinson’s disease, multiple system atrophy, and dementia with Lewy bodies. Although most cases of these diseases are sporadic, autosomal-dominant hereditary mutations have been linked to Parkinson’s disease and dementia with Lewy bodies. Seeing the changes to the structure of amyloid fibrils bearing these mutations may help to understand these diseases. To this end, we determined the cryo-EM structures of α-synuclein fibrils containing the H50Q hereditary mutation. We find that the H50Q mutation results in two new polymorphs of α-synuclein, which we term Narrow and Wide Fibrils. Both polymorphs recapitulate the conserved kernel formed by residues 50-77 observed in wild-type structures; however, the Narrow and Wide Fibrils reveal that H50Q disrupts a key interaction between H50-E57 on the opposing protofilament, abolishing the extensive protofilament interface formed by preNAC residues in the wild-type “rod” structure. Instead, the Narrow Fibril is formed from a single protofilament and the two protofilaments of the Wide protofilament are held together by only a pair of atoms – the Cɣ atoms from the two threonine 59 sidechains. Further, we find that H50Q forms an intramolecular hydrogen bond with K45 leading to the formation of a novel β-arch formed by residues 36-46 that features an extensive hydrogen-bond network between Y39, T44, and E46. The structures of the H50Q polymorphs help to rationalize the faster aggregation kinetics, higher seeding capacity in biosensor cells, and greater cytotoxicity we observe for H50Q compared to wild-type α-synuclein.
Head Mesoderm Tissue Growth, Dynamics and Neural Crest Cell Migration
Authors: McKinney Mary Cathleen , McLennan Rebecca , Giniunaite Rasa , Baker Ruth E. , Maini Philip K. , Othmer Hans G. , Kulesa Paul M
Published: August 2019

Vertebrate head morphogenesis involves orchestrated cell growth and tissue movements of the mesoderm and neural crest to form the distinct craniofacial pattern. To better understand structural birth defects, it is important that we learn how these processes are controlled. Here, we examine this question during chick head morphogenesis using time-lapse imaging, computational modeling, and experiment. We find that head mesodermal cells are inherently dynamic in culture and alter cell behaviors in the presence of either ectoderm or neural crest cells. Mesodermal cells in vivo display large-scale whirling motions that rapidly transition to lateral, directed movements after neural crest cells emerge. Computer model simulations predict distinct changes in neural crest migration as the spatio-temporal growth profile of the mesoderm is varied. BrdU-labeling and photoconversion combined with cell density measurements then reveal non-uniform mesoderm growth in space and time. Chemical inhibition of head mesoderm proliferation or ablation of premigratory neural crest alters mesoderm growth and neural crest migration, implying a dynamic feedback between tissue growth and neural crest cell signaling to confer robustness to the system.

Summary Statement

Dynamic feedback between tissue growth and neural crest cell migration ensures robust neural crest stream formation and head morphogenesis shown by time-lapse microscopy, mathematical modeling and embryo perturbations.
A negative autoregulation network motif is required for synchronizedMyxococcus xanthusdevelopment
Authors: McLaughlin Maeve , Higgs Penelope I.
Published: August 2019

Transcription factor autoregulation is a simple network motif (recurring circuit) built into genetic regulatory networks that direct cell behavior. Negative autoregulation (NAR) network motifs are particularly abundant in bacteria and provide specific functions, such as buffering against transcriptional noise. Here, we investigate the phenotypic consequence of perturbing NAR of a major transcription factor, MrpC, that controls the multicellular development program of the bacteriumMyxococcus xanthus. Launch of the developmental program directs certain cells in the population to first aggregate into haystack-shaped mounds, and then to differentiate into environmentally resistant spores to form mature fruiting bodies. Perturbation of MrpC NAR causes a striking phenotype in which cells lose synchronized transition from aggregation to sporulation. Instead, some cells abruptly exit aggregation centers and remain locked in a cohesive swarming state, while the remaining cells transition to spores inside residual fruiting bodies. As predicted, disruption of MrpC NAR led to an increased and broadened population distribution ofmrpCexpression. Examination of MrpC levels in developmental subpopulations duringin situdevelopment demonstrated cells locked in the swarms contained intermediate MrpC levels insufficient to promote sporulation. These results suggest an inherent property of NAR motifs that function in multicellular developmental programs is to facilitate synchronized responses.

Significance Statement

All organisms use regulatory networks for cellular homeostasis, mediating appropriate responses to environmental changes, or to direct animal development. Understanding how the basic building blocks (motifs) of regulatory networks contribute to these processes is essential to mitigate the effects of mutations in regulatory networks (i.e.cancers) or to synthesize beneficial organisms. In this study, we demonstrate that a common regulatory motif, a transcription factor that represses its own expression, helps synchronize cells that engage in collective behaviors.
Assessing digital phenotyping to enhance genetic studies of human diseases
Authors: DeBoever Christopher , Tanigawa Yosuke , Aguirre Matthew , McInnes Greg , Lavertu Adam , Rivas Manuel A.
Published: August 2019

Population-scale biobanks that combine genetic data and high-dimensional phenotyping for a large number of participants provide an exciting opportunity to perform genome-wide association studies (GWAS) to identify genetic variants associated with diverse quantitative traits and diseases. A major challenge for GWAS in population biobanks is ascertaining disease cases from heterogeneous data sources such as hospital records, digital questionnaire responses, or interviews. In this study, we use genetic parameters including genetic correlation to evaluate whether GWAS performed using cases in the UK Biobank ascertained from hospital records, questionnaire responses, and family history of diseases implicate similar disease genetics across a range of effect sizes. We find that hospital record and questionnaire GWAS largely identify similar genetic effects for many complex phenotypes and that combining together both phenotyping methods improves power to detect genetic associations. We also show that family GWAS using cases ascertained on family history of disease agrees with combined hospital record/questionnaire GWAS and that family history GWAS has better power to detect genetic associations for some phenotypes. Overall, this work demonstrates that digital phenotyping and unstructured phenotype data can be combined with structured data such as hospital records to identify cases for GWAS in biobanks and improve the ability of such studies to identify genetic associations.
Quantitative profiling of 1-Carbon Metabolites, Amino Acids and Precursors, and Plasmalogens in human plasma using Ultra-High-Pressure Liquid Chromatography coupled with Tandem Mass Spectrometry and robotic compound extraction
Authors: Andraos Stephanie , Goy Michael , Albert Ben , Kussmann Martin , Thorstensen Eric B. , O’Sullivan Justin M.
Published: August 2019

Amino acids (AAs) and one-carbon (1-C) compounds are involved in a range of key metabolic pathways, and mediate numerous health and disease processes in the human body. Previous assays have quantified a limited selection of these compounds. Here, we describe an analytical method for the simultaneous quantification of 37 1-C metabolites, amino acids, precursors, and plasmalogens using reversed-phase ultra-high pressure liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). Compound extraction from human plasma was tested manually before being robotically automated. The final analytical panel was validated on human plasma samples. Our automated and multiplexed method holds promise for application to large cohort studies.
Assessment of computational methods for the analysis of single-cell ATAC-seq data
Authors: Chen Huidong , Lareau Caleb , Andreani Tommaso , Vinyard Michael E. , Garcia Sara P. , Clement Kendell , Andrade-Navarro Miguel A , Buenrostro Jason D. , Pinello Luca
Published: August 2019

Background

Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges. scATAC-seq experiments sample DNA, which, due to low copy numbers (diploid in humans) lead to inherent data sparsity (1-10% of peaks detected per cell) compared to transcriptomic (scRNA-seq) data (20-50% of expressed genes detected per cell). Such challenges in data generation emphasize the need for informative features to assess cell heterogeneity at the chromatin level.

Results

We present a benchmarking framework that was applied to 10 computational methods for scATAC-seq on 13 synthetic and real datasets from different assays, profiling cell types from diverse tissues and organisms. Methods for processing and featurizing scATAC-seq data were evaluated by their ability to discriminate cell types when combined with common unsupervised clustering approaches. We rank evaluated methods and discuss computational challenges associated with scATAC-seq analysis including inherently sparse data, determination of features, peak calling, the effects of sequencing coverage and noise, and clustering performance. Running times and memory requirements are also discussed.

Conclusions

This reference summary of scATAC-seq methods offers recommendations for best practices with consideration for both the non-expert user and the methods developer. Despite variation across methods and datasets, SnapATAC,Cusanovich2018, and cisTopic outperform other methods in separating cell populations of different coverages and noise levels in both synthetic and real datasets. Notably, SnapATAC was the only method able to analyze a large dataset (> 80,000 cells).
The differences between rewilding and restoring an ecologically degraded landscape
Authors: du Toit Johan T. , Pettorelli Nathalie
Published: August 2019

Rewilding is a developing concept in ecosystem stewardship that involves reorganizing and regenerating wildness in an ecologically degraded landscape, with present and future ecosystem function being of higher consideration than historical benchmark conditions. This approach differs from ecosystem restoration but the two concepts are often conflated because (a) they both rely on similar management actions (at least initially) and (b) it can be erroneously assumed that they both aim for similar states of wildness.

Rewilding and restoring both influence biodiversity, and common management actions such as species reintroductions (e.g. beavers or wolves) can be integral to a rewilding project. However, in contrast with restoration, rewilding has lower fidelity to taxonomic precedent and promotes taxonomic substitutions for extinct native species that once underpinned the delivery of key ecological functions.

We suggest the adaptive cycle as the appropriate conceptual framework in which to distinguish rewilding from ecosystem restoration. The focus of restoration ecology is to return an ecosystem to as close to its former state as is possible after a major disturbance, by directly reinstating it on the ‘foreloop’ of the adaptive cycle. In contrast, rewilding draws from the ‘backloop’ by promoting reorganization and redevelopment of the ecosystem under changing environmental conditions. If environmental conditions have changed so significantly that a regime shift is inevitable, then rewilding can facilitate the development of a novel ecosystem to sustain the provision of ecosystem services.

Synthesis and applications. Rewilding and restoring both have their places in biodiversity conservation. In each case, their respective merits should be weighed in relation to stakeholder priorities, prevailing and predicted environmental conditions, the level of biological organization targeted for management, and existing and future management capacity. We provide simple schematic decision‐pathways to assist in exploring whether an ecologically degraded landscape might be a candidate for restoration, active rewilding, or passive rewilding.
The relationship between adult height and diabetes in India: A countrywide cross‐sectional study
Authors: Al Ssabbagh Majd , Geldsetzer Pascal , Bärnighausen Till , Deckert Andreas
Published: August 2019

Background

One major aspect of the epidemiological transition happening in India is the increased diabetes prevalence. Poor environmental conditions in early childhood potentially can increase the risk of developing diabetes in adulthood. Adults' height as an indirect indicator might reflect such conditions. In this paper, we investigate the relationship between adult height as a proxy for early childhood conditions and the risk of developing diabetes in India.

Methods

This cross‐sectional study used national representative data of the latest National Family Health Survey (2015‐2016), comprising 512 616 women aged 20 to 49 and 87 281 men aged 20 to 54. We applied the multivariable fractional polynomials approach in logistic regression models to allow for nonlinear relationships between height and diabetes, separated by sex. Additionally, we fitted logistic regression models with height categories. Fixed effects linear probability models were used to control for potential confounding.

Results

The study revealed a linear relationship between increasing height and increasing diabetes risk among men. Among women, the shortest were at the highest risk (not significant).

Conclusions

Among Indian men, being taller increases the risk of developing diabetes, which contradicts findings from other countries. In contrast, the shortest women seem to be at the greatest risk. Hence, public health interventions in India might be well advised to focus more on the nutrition status of young girls.
Maximizing Impact in Anthropology and Education: Capitulations, Linkages, and Publics
Authors: Demerath Peter
Published: August 2019

This article describes several ways that anthropologists of education can maximize impact on knowledge projects, policies, and practices. The approaches discussed here are all anchored in powerful and distinctive qualities of our field, and include: (1) Centering our disciplinary authority by refusing to capitulate to dominant forms of knowledge, (2) adopting the sensibilities of public anthropology, and (3) being as expansive in our collaborations and networks as we are in our considerations of context.
Re‐Framing Master Narratives of Dis/ability through an Affective Lens: Sophia Cruz’s LD Story at Her Intersections
Authors: Hernández‐Saca David I.
Published: August 2019

Learning disabilities (LD) researchers have produced a knowledge base about the academic side of LD. A gap exists concerning the experiences of individuals with LD, particularly their feeling‐meaning‐making about having LDs. Based on a three‐year qualitative study using critical ethnographic methods, I center Sophia Cruz’s experiences with LD and the label. Sophia experienced the hegemony of smartness and disability micro‐aggressions, and voiced the idea that LD is a complex multifaceted construct. I discuss implications for the LD field.
Intrauterine inhibition of chemokine receptor 4 signaling modulates local and systemic inflammation in ovine pregnancy
Authors: McIntosh Stacia Z. , Maxam Clara J. , Maestas Marlie M. , Quinn Kelsey E. , Ashley Ryan L.
Published: August 2019

Problem

Chemokines help coordinate inflammation within the fetal‐maternal microenvironment during gestation. The chemokine CXCL12 signaling through its receptor CXCR4 regulates inflammatory activity, but this phenomenon is not well understood during pregnancy, and there are no reports exploring the role of this pair in peripheral immune tolerance during gestation. Herein, we hypothesize that intrauterine CXCL12‐CXCR4 signaling governs local and systemic immunomodulatory dynamics during early gestation in ewes.

Method of study

Osmotic pumps were surgically installed for intrauterine infusion of a CXCR4 inhibitor, AMD3100, beginning on day 12 post‐breeding in sheep. Endometrial tissues were collected on day 35 of gestation and evaluated for inflammatory potential, Akt pathway activation, and autophagy induction. Demonstrative of peripheral immune activity, levels of select cytokines were assessed in daily blood samples collected throughout the study, as well as in corpus luteum and spleen on day 35.

Results

Anti‐inflammatory IL10 was primarily localized to endometrial glandular epithelium with lower abundance when CXCR4 was antagonized. Inhibition of CXCR4 at the fetal‐maternal interface resulted in less activation of Akt in endometrium, while evidence of autophagy induction was greater. Corpora lutea from ewes receiving intrauterine AMD3100 exhibited lower interferon‐gamma (IFNG) expression. Blood inflammatory potential was differentially altered in a temporal fashion throughout infusion. IL10 abundance in spleen was greater following CXCR4 inhibition at the fetal‐maternal interface, while IFNG was less.

Conclusion

Intrauterine CXCL12‐CXCR4 signaling governs endometrial and systemic inflammation; disruption of this axis may have detrimental impacts on offspring and maternal health.
Peripapillary border tissue of the choroid and peripapillary scleral flange in human eyes
Authors: Jonas Rahul A. , Holbach Leonard
Published: August 2019

Purpose

To assess dimensions and associations of the peripapillary border tissue of the choroid (PBT‐C) and peripapillary scleral flange (PBT‐S).

Methods

The histomorphometric investigation included histological sections of enucleated eyes of Caucasian patients. Using light microscopy, the PBT dimensions were measured.

Results

The study included 85 eyes (85 patients) with an age of 62.0 years (14.1 years) (mean (SD)) (range:37–87 years) and mean axial length of 26.7 mm (3.5 mm) (range:21.0–37.0 mm). Thicker PBT‐C thickness (mean: 68.8 μm (35.7 μm)) was associated with shorter axial length (p < 0.001; standardized regression coefficient beta: −0.50), and longer PBT‐C length (mean: 531 μm (802 μm)) was correlated with longer axial length (p < 0.001;beta:0.66). PBT‐C cross‐sectional area (mean 17 050 μm2 (10 420 μm2)) was not significantly associated with axial length (p = 0.37). Decreasing with longer axial length (p < 0.001;beta:0.64), the angle between PBT‐C and Bruch's membrane was approximately 90° in non‐highly myopic eyes without overhanging Bruch's membrane (BM), it ranged between 100° and 180° in eyes with BM overhanging into the intrapapillary region, and it was close to 0° in eyes with parapapillary gamma zone. Thicker thickness of PBT‐S (mean:83 μm (21 μm)) was correlated with presence of glaucoma (p = 0.02). Optic nerve pia mater thickness (mean:109 μm (44 μm)) increased with glaucoma presence (p = 0.046;beta:0.31) but not with axial length (p = 0.34).

Conclusions

Peripapillary border tissue of the choroid (PBT‐C) and PBT‐S as continuation of the optic nerve pia mater are distinct structures, with PBT‐C remodelling during myopic axial elongation and PBT‐S being mostly independent of axial elongation. PBT‐C and PBT‐S may be of importance for the optic nerve head biomechanics and PBT‐C for separation of the choroidal space from the intrapapillary compartment.
MMPs, TIMPs and BMP‐4 in medial rectus muscle obtained from intermittent exotropia patients and their clinical correlations
Authors: Lee Yoon Pyo , Choi Dong Gyu
Published: August 2019

Background

To measure the amounts of matrix metalloproteinase (MMP)‐2, MMP‐9, tissue inhibitor of metalloproteinase (TIMP)‐1, TIMP‐2 and bone morphogenetic protein (BMP)‐4 in medial rectus muscle (MR) tissue obtained from intermittent exotropia (IXT) patients and to investigate the correlation between each protein amount and the clinical features of IXT including angles of deviation, age at surgery, duration of IXT and postoperative recurrence.

Methods

The protein amounts were measured by enzyme‐linked immunosorbent assay (ELISA) in MR collected during surgery for 78 IXT patients.

Results

The mean amount of MMP‐2 per mm of resected MR was 0.86 ng, of MMP‐9, 2.72 ng, of TIMP‐1, 1.99 ng, of TIMP‐2, 0.92 ng and of BMP‐4, 0.82 pg. MMP‐2 showed a positive correlation with angle of deviation at distance and at near, age at surgery and duration of IXT (p = 0.000, p = 0.000, p = 0.000, p = 0.022, respectively, Spearman's rank correlation analysis). MMP‐9 showed a positive correlation with angle of deviation at distance and at near (p = 0.001, p = 0.024) and BMP‐4 showed a positive correlation with angle of deviation at distance (p = 0.012). TIMP‐1 showed a negative correlation with angle of deviation at distance and at near (p = 0.003, p = 0.000).

Conclusion

In IXT patients, MMPs and BMP‐4 tended to increase and TIMPs to decrease with increasing angle of deviation, greater age at surgery and longer duration of IXT.
Tumour size criteria for Group D and E eyes in the International Classification System for Retinoblastoma: effects on rates of globe salvage and high‐risk histopathologic features
Authors: Kim Jonathan W. , Shah Sona N. , Green Sarah , O'Fee John , Tamrazi Benita , Berry Jesse L.
Published: August 2019

Purpose

To determine the significance of large tumour size as a criteria for classifying advanced intraocular retinoblastoma, analysing rates of globe survival and high‐risk (HE) histopathologic features.

Methods

Retrospective chart review of 212 eyes diagnosed with Group D (111 eyes) or Group E (101 eyes) retinoblastoma in at least one eye from January 1, 2006 to December 31, 2016 using the Los Angeles (LA) Classification System (no tumour size criteria for Group E). The 111 Group D tumours were then reclassified to Group E using 10, 12, 14, 16, 18 mm tumour size criteria, as determined by ultrasound or magnetic resonance imaging dimensions.

Results

For eyes in the original LA classification, 66.7% of Group D and 10.5% of Group E eyes undergoing globe preservation therapy avoided enucleation or radiotherapy (p < 0.0001; median follow‐up of 33.0 months). In the LA classification, 8.5% of Group D and 26.3% of Group E enucleated globes had HE histopathologic features (p = 0.0065). When Group D eyes with tumours meeting the size criteria were reclassified to Group E, 65.7–74.4% of Group D and 16.1–36.7% of Group E eyes avoided enucleation or radiotherapy. Applying the tumour size criteria, 0–10.9% of Group D and 20.7–23.8% of Group E eyes had HE histopathologic features.

Conclusion

Our retrospective analysis suggests that a large tumour size criteria for Group E retinoblastoma have no clinical basis, given that the LA classification system provided the greatest separation in globe salvage rates between Group D and E eyes. The LA classification system was also able to show a statistically significant difference in the rates of HE histopathologic features between Group D and E eyes. To avoid discrepancies in the literature, we recommend that centres use one uniform system for classifying advanced intraocular retinoblastoma.
Prediction of late displacement of the globe in orbital blowout fractures
Authors: Ji Yongrong , Zhou Yixiong , Shen Qin , Xu Wei , Ge Shengfang , Gu Lixu , Fan Xianqun
Published: August 2019

Purpose

To establish a linear measuring method in computed tomographic (CT) images to predict the displacement of the globe late after orbital blowout fracture.

Methods

Subjects were retrospectively included. Inclusion criteria were as follows: (1) adult subjects (≥18 years old at the time of trauma); (2) unilateral orbital medial‐wall and/or floor fractures; (3) CT examination at least 30 days after trauma. Exclusion criteria were as follows: (1) facial or orbital fracture extending to other parts of the orbit than medial‐wall and/or floor; (2) history of orbital or ocular abnormality other than the orbital trauma; (3) severe ocular trauma accompanied by the orbital trauma; (4) orbital fracture treated surgically before the CT examination. A co‐ordinate system was built based on the orbital CT scans. Displacements of orbital walls, displacement of the globe and relative location of the fracture site were measured. Correlations between the variables were investigated.

Results

Ninety‐nine per cent of fracture sites of the medial wall and 100% of fracture sites of the floor were posterior to the centre of the unaffected globe. The affected globe moved significantly medially (p < 0.001) and backwards (p < 0.001) in pure medial‐wall fracture; backwards (p < 0.001) and downwards (p = 0.017) in pure floor fracture; and medially (p < 0.001), backwards (p < 0.001) and downwards (p < 0.001) in medial‐wall and floor fractures. Displacement of the globe was correlated with displacements of the orbital walls, and the regression formulae were therefore fitted. Application of the formulae revealed that the same extent of orbital wall displacement caused more displacement of the globe in female patients than in male patients.

Conclusions

A linear measuring method in a three‐dimensional co‐ordinate system was established to identify the displacements of orbital walls and the displacement of the globe in orbital blowout fractures. The regression formulae generated in this study might be used in clinical practice to predict late displacement of the globe by measuring the displacements of orbital walls.