bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-term test-retest reliability of the human intrinsic functional connectome
Authors: Tozzi Leonardo , Fleming Scott L. , Taylor Zachary D. , Raterink Cooper D. , Williams Leanne M.
Published: September 2019

Functional connectivity is frequently used to quantify the complex synchronous distributed fluctuations in neuronal activity derived from functional Magnetic Resonance Imaging and to generate network representations of human brain function. Such “functional connectomes” have great promise for mechanistic studies and for clinical translation. However, we do not know to what extent a functional connectome is stable over time for an individual. In the present work, we evaluate the short-term test-retest reliability of functional connectomes in a large publicly available sample of healthy participants (N=833) scanned on two consecutive days. We also assess the consequences on reliability of three methodological procedures for which a clear guideline in the community is lacking: atlas choice, global signal regression and thresholding. By adopting the intraclass correlation coefficient as a reliability metric, we demonstrate that a relatively small portion of the intrinsic functional connectome is characterized by good (4-6%) to excellent (0.08-1%) stability over time. In particular, connectivity between prefrontal, parietal and temporal areas appears to be especially stable over short timescales. Also, while unreliable edges of the functional connectome are generally weak in terms of average functional connectivity, reliable edges are not necessarily strong. Methodologically, we demonstrate that multimodal parcellation and averaging of connections within known networks are practices that improve reliability. Harnessing this knowledge, for example by honing in on the reliable portion of the connectome, offers one way forward for studies of trait-like features within the normative connectome and for discovery of biomarkers in clinical cohorts.
Refining modules to determine functionally significant clusters in molecular networks
Authors: Kaalia Rama , Rajapakse Jagath C.
Published: September 2019

Module detection algorithms relying on modularity maximization suffer from an inherent resolution limit that hinders detection of small topological modules, especially in molecular networks where most biological processes are believed to form small and compact communities. We propose a novel modular refinement approach that helps finding functionally significant modules of molecular networks. The module refinement algorithm improves the quality of topological modules in protein-protein interaction networks by finding biologically functionally significant modules. The algorithm is based on the fact that functional modules in biology do not necessarily represent those corresponding to maximum modularity. Larger modules corresponding to maximal modularity are incrementally re-modularized again under specific constraints so that smaller yet topologically and biologically valid modules are recovered. We show improvement in quality and functional coverage of modules using experiments on synthetic and real protein-protein interaction networks. Results were also compared with six existing methods available for clustering biological networks. In conclusion, the proposed algorithm finds smaller but functionally relevant modules that are undetected by classical quality maximization approaches for modular detection. The refinement procedure helps to detect more functionally enriched modules in protein-protein interaction networks, which are also more coherent with functionally characterised gene sets.
Post-fire vegetation succession in the Siberian subarctic tundra over 45 years
Authors: Heim Ramona J. , Bucharova Anna , Brodt Leya , Kamp Johannes , Rieker Daniel , Soromotin Andrey V. , Yurtaev Andrey , Hölzel Norbert
Published: September 2019

Wildfires are relatively rare in subarctic tundra ecosystems, but they can strongly change ecosystem properties. Short-term fire effects on subarctic tundra vegetation are well documented, but long-term vegetation recovery has been studied less. The frequency of tundra fires will increase with climate warming. Understanding the long-term effects of fire is necessary to predict future ecosystem changes.

We used a space-for-time approach to assess vegetation recovery after fire over more than four decades. We studied soil and vegetation patterns on three large fire scars (>44, 28 and 12 years old) in dry, lichen-dominated forest tundra in Western Siberia. On 60 plots, we determined soil temperature and permafrost thaw depth, sampled vegetation and measured plant functional traits. We assessed trends in NDVI to support the field-based results on vegetation recovery.

Soil temperature, permafrost thaw depth and total vegetation cover had recovered to pre-fire levels after >44 years, as well as total vegetation cover. In contrast, after >44 years, functional groups had not recovered to the pre-fire state. Burnt areas had lower lichen and higher bryophyte and shrub cover. The dominating shrub species,Betula nana, exhibited a higher vitality (higher specific leaf area and plant height) on burnt compared with control plots, suggesting a fire legacy effect in shrub growth. Our results confirm patterns of shrub encroachment after fire that were detected before in other parts of the Arctic and Subarctic. In the so far poorly studied Western Siberian forest tundra we demonstrate for the first time, long-term fire-legacies on the functional composition of relatively dry shrub- and lichen-dominated vegetation.
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories
Authors: Munarko Yuda , Sarwar Dewan M. , Rampadarath Anand , Atalag Koray , Gennari John H. , Neal Maxwell L. , Nickerson David P.
Published: September 2019

Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends the use of the Resource Description Framework (RDF). This grounding in RDF provides the flexibility to enable searching for entities within models (e.g. variables, equations, or entire models) by utilising the RDF query language SPARQL. However, the rigidity and complexity of the SPARQL syntax and the nature of the tree-like structure of semantic annotations, are challenging for users. Therefore, we propose NLIMED, an interface that converts natural language queries into SPARQL. We use this interface to query and discover model entities from repositories of biosimulation models. NLIMED works with the Physiome Model Repository (PMR) and the BioModels database and potentially other repositories annotated using RDF. Natural language queries are first ‘chunked’ into phrases and annotated against ontology classes and predicates utilising different natural language processing tools. Then, the ontology classes and predicates are composed as SPARQL and finally ranked using our SPARQL Composer and our indexing system. We demonstrate that NLIMED’s approach for chunking and annotating queries is more effective than the NCBO Annotator for identifying relevant ontology classes in natural language queries. Comparison of NLIMED’s behaviour against historical query records in the PMR shows that it can adapt appropriately to queries associated with well-annotated models.
Fine-mapping of SNCA in REM sleep behavior disorder and overt synucleinopathies
Authors: Krohn Lynne , Wu Richard YJ , Heilbron Karl , Ruskey Jennifer A. , Laurent Sandra B. , Blauwendraat Cornelis , Alam Armaghan , Arnulf Isabelle , Hu Michele T.M. , Dauvilliers Yves , Högl Birgit , Toft Mathias , Bjørnarå Kari Anne , Stefani Ambra , Holzknecht Evi , Charley Monaca Christelle , Beatriz Abril , Plazzi Giuseppe , Antelmi Elena , Ferini-Strambi Luigi , Young Peter , Heidbreder Anna , Cochen De Cock Valérie , Mollenhauer Brit , Sixel-Döring Friederike , Trenkwalder Claudia , Sonka Karel , Kemlink David , Figorilli Michela , Puligheddu Monica , Dijkstra Femke , Viaene Mineke , Oertel Wolfang , Toffoli Marco , Gigli Gian Luigi , Valente Mariarosaria , Gagnon Jean-François , Nalls Mike A. , Singleton Andrew B. ,   23andMe Research Team, Desautels Alex , Montplaisir Jacques Y. , Cannon Paul , Ross Owen A. , Boeve Bradley F. , Dupré Nicolas , Fon Edward A. , Postuma Ronald B. , Pihlstrøm Lasse , Rouleau Guy A. , Gan-Or Ziv
Published: September 2019

Objective

REM-sleep behavior disorder (RBD) is a prodromal synucleinopathy, as >80% will eventually convert to overt synucleinopathy. We performed an in-depth analysis of the SNCA locus to identify RBD-specific risk variants.

Methods

Full sequencing and genotyping of SNCA was performed in isolated/idiopathic RBD (iRBD, n=1,076), Parkinson’s disease (PD, n=1,013), and dementia with Lewy bodies (DLB, n=415), and in control subjects (n=6,155). A replication cohort from 23andMe of PD patients with probable RBD (pRBD) was also analyzed (cases n=1,782, controls n=131,250). Adjusted logistic regression models and meta-analyses were performed. Effects on conversion rate were analyzed in 432 RBD patients with available data using Kaplan-Meier survival analysis.

Results

A 5’-region SNCA variant (rs10005233) was associated with iRBD (OR=1.43, p=1.1E-08), which was replicated in pRBD. This variant is in linkage disequilibrium (LD) with other 5’ risk variants across the different synucleinopathies. An independent iRBD-specific suggestive association (rs11732740) was detected at the 3’ of SNCA (OR=1.32, p=4.7E-04, not statistically significant after Bonferroni correction). Homozygous carriers of both iRBD-specific SNPs were at highly increased risk for iRBD (OR=5.74, p=2E-06). The known top PD-associated variant (3’ variant rs356182) had an opposite direction of effect in iRBD compared to PD.

Interpretation

There is a distinct pattern of association at the SNCA locus in RBD as compared to PD, with an opposite direction of effect at the 3’ of SNCA. Several 5’ SNCA variants are associated with iRBD and with pRBD in overt synucleinopathies, and may suggest a cognitive component to this region.
Single cell transcriptomics reveals a signaling roadmap coordinating endoderm and mesoderm diversification during foregut organogenesis
Authors: Han Lu , Chaturvedi Praneet , Kishimoto Keishi , Koike Hiroyuki , Nasr Talia , Iwasawa Kentaro , Giesbrecht Kirsten , Witcher Phillip C , Eicher Alexandra , Haines Lauren , Lee Yarim , Shannon John M , Morimoto Mitsuru , Wells James M , Takebe Takanori , Zorn Aaron M
Published: September 2019

Visceral organs, such as the lungs, stomach, liver and pancreas, are derived from the fetal foregut through a series of inductive interactions between the definitive endoderm (DE) and the surrounding splanchnic mesoderm (SM). While patterning of DE lineages has been fairly well studied, paracrine signaling controlling SM regionalization and how this is coordinated with the epithelial identity during organogenesis is obscure. Here we used single cell transcriptomics to generate a high-resolution cell state map of the embryonic mouse foregut. This uncovered an unexpected diversity in the SM cells that developed in close register with the organ-specific epithelium. From these data, we inferred a spatiotemporal signaling roadmap of the combinatorial endoderm-mesoderm interactions that orchestrate foregut organogenesis. We validated key predictions with mouse genetics, showing the importance of endoderm-derived signals in mesoderm patterning. Finally, leveraging the signaling road map we generated different SM subtypes from human pluripotent stem cells (hPSCs), which previously have been elusive. The single cell data can be explored at:https://research.cchmc.org/ZornLab-singlecell.
Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization
Authors: Shinkai Soya , Sugawara Takeshi , Miura Hisashi , Hiratani Ichiro , Onami Shuichi
Published: September 2019

The 1-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in 3-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the micro-scale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose, to our knowledge, a new microrheology for Hi-C data to analyze the compliance property as a barometer of rigidness and flexibility of genomic regions along with the time evolution. Our method allows conversion of a Hi-C matrix into the spectrum of the rheological property along the genomic coordinate of a single chromosome. To demonstrate the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD region. The spectrum clearly shows the rheological property of the dynamic chromatin domain formations at an individual time scale. Furthermore, we characterized the appearance of synchronous and liquid-like inter-compartment interactions in differentiated cells. Together, our microrheology provides physical insights revealing the dynamic 3D genome organization from Hi-C data.

SIGNIFICANCE

Genomic DNA is hierarchically packed inside the eukaryotic cell nucleus, and the genome organization in 3D contributes to proper genome functions at the multiscale chromatin domains. Although thermal fluctuations inevitably drive movements of the genome molecules in the micro-scale cell environment, there is no method, as yet, to quantify such dynamic 3D genome organization of hierarchical and structural chromatin units. Here, we describe a method to calculate rheological properties as barometers of flexibility and liquid-like behavior of genomic regions. We show that biologically relevant boundaries between chromatin domains are more rigid than the inside at a particular time scale. Our method allows interpretation of static and population-averaged genome conformation data as dynamic and hierarchical 3D genome picture.
A conserved activity for cohesin in bridging DNA molecules
Authors: Gutierrez-Escribano Pilar , Newton Matthew D. , Llauró Aida , Huber Jonas , Tanasie Loredana , Davy Joseph , Aly Isabel , Aramayo Ricardo , Montoya Alex , Kramer Holger , Stigler Johannes , Rueda David S. , Aragon Luis
Published: September 2019

Essential processes such as accurate chromosome segregation, regulation of gene expression and DNA repair rely on protein-mediated DNA tethering. Sister chromatid cohesion requires the SMC complex cohesin to act as a protein linker that holds replicated chromatids together (1, 2). The molecular mechanism by which cohesins hold sister chromatids has remained controversial. Here, we used a single molecule approach to visualise the activity of cohesin complexes as they hold DNA molecules. We describe a DNA bridging activity that requires ATP and is conserved from yeast to human cohesin. We show that cohesin can form two distinct classes of bridges at physiological conditions, a “permanent bridge” able to resists high force (over 80pN) and a “reversible bridge” that breaks at lower forces (5-40pN). Both classes of bridges require Scc2/Scc4 in addition to ATP. We demonstrate that bridge formation requires physical proximity of the DNA segments to be tethered and show that “permanent” cohesin bridges can move between two DNA molecules but cannot be removed from DNA when they occur in cis. This suggests that separate physical compartments in cohesin molecules are involved in the bridge. Finally, we show that cohesin tetramers, unlike condensin, cannot compact linear DNA molecules against low force, demonstrating that the core activity of cohesin tetramers is bridging DNA rather than compacting it. Our findings carry important implications for the understanding of the basic mechanisms behind cohesin-dependent establishment of sister chromatid cohesion and chromosome architecture.
The Secretome of Liver X Receptor Agonist Treated Early Outgrowth Cells Decreases Atherosclerosis inLdlr-/- Mice
Authors: Rasheed Adil , Shawky Sarah , Tsai Ricky , Jung Richard G , Simard Trevor , Hibbert Benjamin , Rayner Katey J , Cummins Carolyn L
Published: September 2019

Objective

Endothelial progenitor cells (EPCs) promote the maintenance of the endothelium by the secretion of vasoreparative factors. A population of EPCs known as early outgrowth cells (EOCs) are currently being investigated as novel cell-based therapies for the treatment of cardiovascular disease. We previously demonstrated that the absence of liver x receptors (LXRs) is detrimental to the formation and function of EOCs under hypercholesterolemic conditions. Here, we investigate whether LXR gain-of-function in EOCs is beneficial for the treatment of atherosclerosis.

Approach and Results

EOCs were differentiated from the bone marrow of wildtype (WT) and LXR-knockout (Lxrαβ-/-) mice in the presence of vehicle or LXR agonist (GW3965). WT EOCs treated with GW3965 throughout differentiation showed reduced expression of endothelial lineage markers (Cd144, Vegfr2) compared to WT vehicle andLxrαβ-/- cells. GW3965-treated EOCs produced secreted factors that reduced monocyte adhesion to activated endothelial cells in culture. When injected into atherosclerosis-proneLdlr-/- mice, GW3965-treated EOCs and concentrated conditioned media (CM) from GW3965-treated EOCs, reduced plaque burden within the aortic sinus. Furthermore, when CM from human EOCs (obtained from patients with established CAD) were treated with GW3965, monocyte to endothelial adhesion was decreased suggesting the translatability of the results.

Conclusions

Ex vivoLXR agonist treatment of EOCs produces a secretome that decreases early atherosclerosis inLdlr-/- mice. CM from human EOCs significantly inhibits monocyte to endothelial adhesion. Thus, active factor(s) within the GW3965-treated EOC secretome have the potential to be useful for the treatment of atherosclerosis.
Normal human lymph node T follicular helper cells and germinal center B cells accessed via fine needle aspirations
Authors: Havenar-Daughton Colin , Newton Isabel G. , Zare Somaye Y , Reiss Samantha M. , Suh Min Ji , Hasteh Farnaz , Crotty Shane
Published: September 2019

Germinal centers (GC) are critically important for the maturation of the antibody response and the generation of memory B cells, which are the basis for long-term protection from pathogens. Germinal centers only occur in lymphoid tissue, such as lymph nodes, and are not present in blood. Therefore, cells of the germinal center, including GC B cells and GC T follicular helper (TFH) cells, are not well-studied in humans under normal healthy conditions, due to the limited availability of healthy lymph node samples. We used a minimally invasive, routine clinical procedure, lymph node fine needle aspirations (LN FNAs), to obtain lymph node cells from healthy human subjects to establish benchmarks of GC cells under noninflammatory conditions. This study of 50 lymph nodes demonstrates that human LN FNAs are a safe and feasible technique for immunological research, and defines benchmarks for human GC biology. The findings indicate that assessment of the GC response via LN FNAs will have application to the study of human vaccination, allergy, and autoimmune disease.
Presence of a D2 receptor truncated protein in the brain of the D2 receptor functional knockout mouse, revisiting its molecular and neurochemical features
Authors: Sánchez Natalia , Olivares-Costa Montserrat , González Marcela P , Escobar Angélica P , Meza Rodrigo , Munita Roberto , Herrera-Rojas Mauricio , Andrés María E
Published: September 2019

Null mice for the dopamine D2 receptor (D2R) have been instrumental in understanding the function of this protein in the central nervous system. Several lines of D2R knockout mice have been generated, which share some characteristics but differ in others. The D2R functional knockout mouse, first described in 1997, is functionally null for D2R-mediated signaling but the Drd2 gene was interrupted at the most extreme distal end leaving open the question about whether transcript and protein are produced. We decided to determine if there are D2R transcripts, the characteristics of these transcripts and whether they are translated in the brain of D2R functional knockout mice. Sequence analysis of 3’ Rapid Amplification of cDNA Ends showed that D2R functional knockout mice express transcripts that lack only the exon eight. Immunofluorescence showed D2R-like protein in the brain of the knockout mice. As previously reported, D2R functional knockout mice are hypoactive and insensitive to the D2R agonist quinpirole (QNP). However, the heterozygous showed locomotor activity and response to QNP similar to the wild-type mice. Intriguingly, microdialysis experiments showed that heterozygous mice, such as knockouts, have half the normal levels of synaptic dopamine in the striatum. However, heterozygous mice responded similarly to wild-type mice to an acute injection of QNP, showing a 50% decrease in synaptic dopamine. In conclusion, D2R functional knockout mice express transcripts that lead to a truncated D2R protein that lacks from the sixth transmembrane domain to the C-terminal end but retains the third intracellular loop. We discuss the implications of this truncated D2R coexisting with the native D2R that may explain the unexpected outcomes observed in the heterozygous. Finally, we suggest that the D2R functional knockout mouse can be a useful model for studying protein-protein interaction and trafficking of D2R.
Binding to m6A RNA promotes YTHDF2-mediated phase separation
Authors: Wang Jiahua , Wang Liyong , Diao Jianbo , Shi Yujiang Geno , Shi Yang , Ma Honghui , Shen Hongjie
Published: September 2019

As the most abundant modification on mRNA in mammal, N6-Methyladenosine (m6A) has been demonstrated to play important roles in various biological processes including mRNA splicing, translation and degradation. m6A reader proteins have been shown to play central roles in these processes. One of the m6A readers, YTHDF2 is localized to the P granules, which are liquid-like droplets where RNA degradation occurs. How YTHDF2 is localized to P granules is unknown. Here we provide evidence that YTHDF2 forms liquid droplets and phase separate, mediated by its low complexity (LC) domains. Interestingly, the ability to phase separate is robustly stimulated by m6A RNAs in vitro. In vivo, YTHDF2 phase separation may in fact be dependent on m6A RNA and YTHDF2 binding to m6A RNA, since a YTHDF2 m6A-binding defective mutant or a wildtype YTHDF2 assayed in cells lacking m6A RNAs, both fail to phase separate. The ability of phase separate is not limited to YTHDF2; we find other members of the YTH-domain m6A readers can also undergo phase separation. Our findings suggest that m6A RNA induced phase separation of m6A readers may play an important role in their distributions to different phase-separated compartments in cells.
Stimjim: open source hardware for precise electrical stimulation
Authors: Cermak Nathan , Wilson Matthew A. , Schiller Jackie , Newman Jonathan P.
Published: September 2019

Electrical stimulation is a simple and powerful tool to perturb and evoke neuronal activity in order to understand the function of neurons and neural circuits. Despite this, devices that can provide precise current or voltage stimulation are expensive and closed-source. Here, we introduce Stimjim, a capable and inexpensive ($200 USD) open-source instrument for electrical stimulation that combines both function generation and electrical isolation. Stimjim provides microsecond temporal resolution with microampere or millivolt scale precision on two electrically isolated output channels. We demonstrate Stimjim’s utility both in vitro by precisely stimulating brain slices, and in vivo by training mice to perform intracranial self-stimulation (ICSS) for brain stimulation reward. During ICSS, Stimjim enables the experimenter to smoothly tune the strength of reward-seeking behavior by varying either the output frequency or amplitude. We envision Stimjim will enable new kinds of experiments due to its open-source and scalable nature.
Drosophila melanogaster Peroxisome Biogenesis Factor 7plays a role in embryonic development
Authors: Pridie C , Simmonds AJ
Published: September 2019

Peroxisomes are organelles responsible for aspects of lipid metabolism and management of reactive oxygen species. Peroxisome Biogenesis Factor (Peroxin, Pex) genes encode proteins essential to peroxisome biogenesis or function. In yeast and mammals, PEROXIN7 acts as a cytosolic receptor protein that targets a subset of enzymes for peroxisome matrix import.

Proteins targeted by PEROXIN7 contain a peroxisome targeting sequence 2 (PTS2) motif. The PTS2 was not found in theD. melanogasterhomologs of proteins that are PEROXIN7 targets in yeast or mammals, however comparative genomics suggest aPex7homolog is present in theD. melanogastergenome. Herein we report novel, tissue-specific patterns for transcription and translation ofPex7in theD. melanogasterembryo that appear to be strongest in presumptive neuronal lineages. We also show that targeted somaticPex7knockout in neural precursors via targeted somatic CRISPR knockout affected survival of mutant embryos.Pex7over-expression via Gal4-UAS also reduced adult survival but was not deleterious at the embryo stage. Notably, targeted somatic rescue ofPex7in the neural precursors ofPex7homozygous mutants also impaired embryo survival. We conclude thatD. melanogasterhas tissue-specific developmental requirements ofPex7expression. This may be related to the requirement for peroxisome-mediated lipid synthesis in cells of the central nervous system.
The feedstock microbiome selectively steers process stability during the anaerobic digestion of waste activated sludge
Authors: Law Cindy Ka Y , De Henau Rens , De Vrieze Jo
Published: September 2019

Strategies to enhance process performance of anaerobic digestion remain of key importance to achieve further spreading of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e., organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process performance of the digesters fed sterile WAS, with a 92 ± 45 % decrease in methane production, compared to a 42 ± 31 % increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process performance between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L−1. Feedstock sterilisation strongly impacted the microbial community in the digesters. In conclusion, feedstock inoculation can be considered a cheap, yet, disturbance-specific strategy to enhance process stability in full-scale anaerobic digestion processes.
Trehalose recycling promotes energy-efficient mycomembrane reorganization in nutrient-limited mycobacteria
Authors: Pohane Amol Arunrao , Carr Caleb R. , Garhyan Jaishree , Swarts Benjamin M. , Siegrist M. Sloan
Published: September 2019

The mycomembrane layer of the mycobacterial cell envelope is a barrier to environmental, immune and antibiotic insults. We find that there is mycomembrane remodeling along the periphery of nutrient-starved, non-replicating mycobacterial cells. Remodeling is supported by recycling of trehalose, a non-mammalian disaccharide that shuttles long-chain mycolate lipids to the mycomembrane. In the absence of trehalose recycling, mycomembrane synthesis continues but mycobacteria experience ATP depletion, enhanced respiration and redox stress. Redox stress from depletion of the trehalose pool is suppressed in a mutant that lacks the OtsAB de novo trehalose synthesis pathway. Our data suggest that trehalose recycling alleviates the energetic burden of mycomembrane remodeling. Loss of trehalose salvage is known to attenuate M. tuberculosis during infection and render the bacterium more susceptible to a variety of drugs. Recycling pathways are emerging targets for sensitizing resource-limited bacterial pathogens to host and antibiotic stress.
Hallmarks of frailty and osteosarcopenia in prematurely aged PolgAD257A/D257Amice
Authors: Scheuren Ariane C. , D’Hulst Gommaar , Kuhn Gisela A. , Masschelein Evi , Wehrle Esther , De Bock Katrien , Müller Ralph
Published: September 2019

Background

Frailty is a geriatric syndrome characterized by increased susceptibility to adverse health outcomes. One major determinant thereof is the gradual weakening of the musculoskeletal system and the associated osteosarcopenia. To improve our understanding of the underlying pathophysiology and, more importantly, to test potential interventions aimed at counteracting frailty suitable animal models are needed.

Methods

To evaluate the relevance of prematurely aged PolgA(D257A/D257A)mice as a model for frailty and osteosarcopenia, we quantified the clinical mouse frailty index in PolgA(D257A/D257A)and wild type littermates (PolgA(+/+), WT) with age and concertedly assessed the quantity and quality of bone and muscle tissue. Lastly, the anabolic responsiveness of skeletal muscle, muscle progenitors and bone was assessed.

Results

PolgA(D257A/D257A)accumulated health deficits at a higher rate compared to WT, resulting in a higher frailty index at 40 and 46 weeks of age (+166%, +278%, p<0.0001), respectively, with no differences between genotypes at 34 weeks. Concomitantly, PolgA(D257A/D257A)displayed progressive musculoskeletal deterioration such as reduced bone and muscle mass as well as impaired functionality thereof. In addition to lower muscle weights (-14%, p<0.05, -23%, p<0.0001) and fiber area (-20%, p<0.05, -22%, p<0.0001) at 40 and 46 weeks, respectively, PolgA(D257A/D257A)showed impairments in grip-strength and concentric muscle forces (p<0.05). PolgA(D257A/D257A)mutation altered the acute response to various anabolic stimuli in skeletal muscle and muscle progenitors. While PolgA(D257A/D257A)muscles were hypersensitive to eccentric contractions as well as leucine administration, shown by larger downstream signaling response of the mechanistic target of rapamycin complex 1 (mTORC1), myogenic progenitors culturedin vitroshowed severe anabolic resistance to leucine and robust impairments in cell proliferation. Longitudinal micro-CT analysis of the 6thcaudal vertebrae showed that PolgA(D257A/D257A)had lower bone morphometric parameters (e.g. bone volume fraction, trabecular and cortical thickness, p<0.05) as well as reduced remodeling activities (e.g. bone formation and resorption rate, p<0.05) compared to WT. When subjected to 4 weeks of cyclic loading, young but not aged PolgA(D257A/D257A)caudal vertebrae showed load-induced bone adaptation suggesting reduced mechanosensitivity with age.

Conclusions

PolgA(D257A/D257A)mutation leads to hallmarks of age-related frailty and osteosarcopenia and provides a powerful model to better understand the relationship between frailty and the aging musculoskeletal system.
Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma using Large-scale Transcriptomics Data
Authors: Kaur Harpreet , Dhall Anjali , Kumar Rajesh , Raghava Gajendra P. S.
Published: September 2019

The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on a small dataset obtained from a specific platform or lack of their reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms; we have employed large scale transcriptomic profiling datasets containing a total of 2,306 HCC and 1,655 non-tumorous tissue samples. These samples were obtained from 29 studies generated by mainly four types of profiling techniques include Affymetrix, Illumina, Agilent and High-throughput-seq, which implemented a wide range of platforms. Firstly, we scrutinized 26 genes that are differentially expressed or regulated in uniform pattern among numerous datasets. Subsequently, we identified three genes (FCN3, CLEC1B, & PRC1) panel-based HCC biomarker using different machine learning techniques include Simple-threshold based approach, Extra Trees, Support Vector Machine, Random Forest, K Neighbors Classifier, Logistic Regression etc. Three-genes panel-based HCC biomarker classified HCC samples and non-tumorous samples of training and three external validation datasets with an accuracy between 93 to 98% and AUROC (Area Under Receiver Operating Characteristic curve) in a range of 0.97 to 1.0. Furthermore, the prognostic potential of these genes was evaluated on TCGA cohort and GSE14520 cohort using univariate survival analysis revealed that these genes are independent prognostic indicators for various types of the survivals, i.e. OS (Overall Survival), PFS (Progression-Free Survival), DFS/RFS (Disease-Free Survival/Recurrence-Free Survival) and DSS (Disease-Specific Survival) of HCC patients and significantly stratify high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three genes-based biomarker that can predict HCC patients with high precision; also possess significant prognostic potential. Eventually, to provide service to the scientific community, we developed a webserver HCCPred based on the above study (http://webs.iiitd.edu.in/raghava/hccpred/).
A Modular Master Regulator Landscape Determines the Impact of Genetic Alterations on the Transcriptional Identity of Cancer Cells
Authors: Paull Evan O. , Aytes Alvaro , Subramaniam Prem , Giorgi Federico M. , Douglass Eugene F. , Chu Brennan , Jones Sunny J. , Zheng Siyuan , Verhaak Roel , Abate-Shen Cory , Alvarez Mariano J. , Califano Andrea
Published: September 2019

Despite considerable pan-cancer efforts, the link between genomics and transcriptomics in cancer remains relatively weak and mostly based on statistical rather than mechanistic principles. By performing integrative analysis of transcriptomic and mutational profiles on a sample-by-sample basis, via regulatory/signaling networks, we identified a repertoire of 407 Master-Regulator proteins responsible for canalizing the genetics of 20 TCGA cohorts into 112 transcriptionally-distinct tumor subtypes. Further analysis highlighted a highly-recurrent regulatory architecture (oncotecture) with Master-Regulators organized into 24 modular MR-Blocks, regulating highly-specific tumor-hallmark functions and predictive of patient outcome. Critically, >50% of the somatic alterations identified in individual samples were in proteins affecting Master-Regulator activity, thus yielding novel insight into mechanisms linking tumor genetics and transcriptional identity and establishing novel non-oncogene dependencies. Experimental validation of functional mutations upstream of the most conserved MR-Block confirmed their ability to affect MR-protein activity, suggesting that the proposed methodology may effectively complement and extend current pan-cancer knowledge.
A Monte Carlo method to estimate cell population heterogeneity
Authors: Lambert Ben , Gavaghan David J. , Tavener Simon
Published: September 2019

1

Variation is characteristic of all living systems. Laboratory techniques such as flow cytometry can probe individual cells, and, after decades of experimentation, it is clear that even members of genetically identical cell populations can exhibit differences. To understand whether variation is biologically meaningful, it is essential to discern its source. Mathematical models of biological systems are tools that can be used to investigate causes of cell-to-cell variation. From mathematical analysis and simulation of these models, biological hypotheses can be posed and investigated, then parameter inference can determine which of these is compatible with experimental data. Data from laboratory experiments often consist of “snapshots” representing distributions of cellular properties at different points in time, rather than individual cell trajectories. These data are not straightforward to fit using hierarchical Bayesian methods, which require the number of cell population clusters to be chosena priori. Here, we introduce a computational sampling method named “Contour Monte Carlo” for estimating mathematical model parameters from snapshot distributions, which is straightforward to implement and does not require cells be assigned to predefined categories. Our method is appropriate for systems where observed variation is mostly due to variability in cellular processes rather than experimental measurement error, which may be the case for many systems due to continued improvements in resolution of laboratory techniques. In this paper, we apply our method to quantify cellular variation for three biological systems of interest and provide Julia code enabling others to use this method.
Structural basis of recruitment of RBM39 to DCAF15 by a sulfonamide molecular glue E7820
Authors: Du Xinlin , Volkov Oleg , Czerwinski Robert , Tan HuiLing , Huerta Carlos , Morton Emily , Rizzi Jim , Wehn Paul , Xu Rui , Nijhawan Deepak , Wallace Eli
Published: September 2019

E7820 and indisulam are two examples of aryl sulfonamides that recruit RBM39 to Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ligase complex, leading to its ubiquitination and degradation by the proteasome. In order to understand their mechanism of action, we carried out kinetic analysis on the recruitment of RBM39 to DCAF15 and solved a crystal structure of DDA1-DDB1-DCAF15 in complex with E7820 and the RRM2 domain of RBM39. E7820 packs in a shallow pocket on the surface of DCAF15 and the resulting modified interface binds RBM39 through the α1 helix of RRM2 domain. Our kinetic studies revealed that aryl sulfonamide and RBM39 bind to DCAF15 in a synergistic manner. The structural and kinetic studies confirm aryl sulfonamides as molecular glues in the recruitment of RBM39 and provide a framework for future efforts to utilize DCAF15 to degrade other protein of interests.
Phylogenomic Testing of Root Hypotheses
Authors: Tria Fernando D. K. , Landan Giddy , Picazo Devani Romero , Dagan Tal
Published: September 2019

Abstract

The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch - the root branch - of the true species tree, and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesised species tree and its rooting leads us to re-evaluate what phylogenetic signal is directly relevant to LCA inference, and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competinga-prioriLCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative datasets we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust.
Population-scale prediabetic assessment using HbA1c from menstrual blood
Authors: Srinivasan Lakshminarayan , Khilnani Reshma , Fung Philip , Low Melissa , Esquivel Urano , White Bridget , Sidhu Gurbir , Rangel Jesus , Lim Shion A. , Sudhof Leanna S. , Alemán José O.
Published: September 2019

CDC-recommended diabetes prevention programs aim to detect and reverse disease in the one-third of Americans with prediabetes, but high-compliance serial assessment of percent hemoglobin A1c (HbA1c) remains a barrier to delivering this vision at population scale. Venous phlebotomy is challenging for busy or resource-constrained patients.

In this paper, we introduce the first-ever quantitative diagnostic test based on menstrual fluid, which allows HbA1c quantification from self-collected mailed tampons.We demonstrate that menstrual HbA1c is comparable to venous HbA1c in the diagnosis of prediabetes with the standard threshold of 5.7. We also demonstrate accuracy, precision, stability, and interference testing. Finally, surveying subjects reveals strong preference for menstrual HbA1c in quarterly testing. These findings suggest that menstrual HbA1c can be a key tool in addressing prediabetes at population scale.
Biological insights from self-perceived facial aging data of the UKBB participants
Authors: Vigodner Simona , Khanin Raya
Published: September 2019

Genetic underpinnings of facial aging are still largely unknown. In this study, we leverage the statistical power of large-scale data from the UK Biobank and perform insilico analysis of genome-wide self-perceived facial aging. Functional analysis reveals significant over-representation of skin pigmentation and immune related pathways that are correlated with facial aging. For males, hair loss is one of the top categories that is highly significantly over-represented in the genetics data associated with self-reported facial aging. Our analysis confirms that genes coding for the extracellular matrix play important roles in aging. Overall, our results provide evidence that while somewhat biased, large-scale self-reported data on aging can be utilized for extracting useful insights into underlying biology, provide candidate skin aging biomarkers, and advance anti-aging skincare.
Chitosan biosynthesis and virulence in the human fungal pathogenCryptococcus gattii
Authors: Lam Woei C. , Upadhya Rajendra , Specht Charles A. , Ragsdale Abigail E. , Hole Camaron R , Levitz Stuart M. , Lodge Jennifer K.
Published: September 2019

Cryptococcus gattiiR265 is a hyper-virulent fungal strain responsible for the major outbreak of cryptococcosis in Vancouver Island of British Columbia in 1999. It differs significantly fromC. neoformansin its natural environment, its preferred site in the mammalian host, and in the nature and mode of pathogenesis. Our previous studies inC. neoformanshave shown that the presence of chitosan, the deacetylated form of chitin, in the cell wall attenuates inflammatory responses in the host, while its absence induces robust immune responses, which in turn facilitate clearance of the fungus and induces a protective response. The results of the present investigation reveal that the cell wall ofC. gattiiR265 contains 2-3-fold higher amount of chitosan compared to that ofC. neoformans. The genes responsible for the biosynthesis of chitosan are highly conserved in the R265 genome; the roles of the three chitin deacetylases (CDA) have however, been modified. To deduce their roles, single, double and a tripleCDAdeletion strains were constructed in a R265 background and were subjected to mammalian infection studies. UnlikeC. neoformanswhere Cda1 has a discernible role in fungal pathogenesis, in R265 Cda3 is critical for virulence. Deletion of eitherCDA3alone (cda3Δ) or in combination with eitherCDA1(cda1Δ3Δ) orCDA2(cda2Δ3Δ) or both (cda1Δ2Δ3Δ) rendered the yeast cells avirulent and were cleared from the infected host. Moreover, thecda1Δ2Δ3Δstrain of R265 induced a protective response to a subsequent infection with R265. These studies shed more light into the regulation of chitosan biosynthesis ofC. gattiiand its subsequent effect on fungal virulence.

Importance

The fungal cell wall is an essential organelle whose components provide the first line of defense against host-induced antifungal activity. Chitosan is one of the carbohydrate polymers in the cell wall that significantly affects the outcome of host-pathogen interaction. Chitosan-deficient strains are avirulent, implicating chitosan as a critical virulence factor.C. gattiiR265 is an important fungal pathogen of concern due to its ability to cause infections in individuals with no apparent immune dysfunction and an increasing geographical distribution. Characterization of the fungal cell wall and understanding the contribution of individual molecules of the cell wall matrix to fungal pathogenesis offers new therapeutic avenues for intervention. In this report, we show that theC. gattiiR265 strain has evolved alternate regulation of chitosan biosynthesis under both laboratory growth conditions and during mammalian infection compared to that ofC. neoformans.