bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial community dynamics of surface water in British Columbia, Canada
Authors: Uyaguari-Diaz Miguel I. , Croxen Matthew A. , Cronin Kirby , Luo Zhiyao , Isaac-Renton Judith , Prystajecky Natalie A. , Tang Patrick
Published: August 2019

Traditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such asEscherichia coli, often tested as a weekly grab sample. To understand the stability ofE.coliconcentrations over time, we evaluated three approaches to measuringE. colilevels in water: microbial culture using Colilert, quantitative PCR foruidAand next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period.Enterobacteriaceaecomprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities ofE. colicompared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such asPrevotellaandBacteroidesshowed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.
Reference intervals of spot urine copper excretion in preschool children and potential application in pre-symptomatic screening of Wilson’s disease
Authors: Tang Nelson Leung-sang , Hui Joannie , Huang Dan , Tang Man Fung , Wang Xingyan , Wu Junyi , Chan Iris HS , Leung Ting Fan
Published: August 2019

Background

With spot urine collected from a large control sample of preschool children (aged 3-7 years), reference range of spot urine copper excretion indexes and their biological variation were defined.

Methods

In order to investigate their test performance in screening of Wilson disease in this age group, multiple spot urine samples from 6 WD patients diagnosed at presymptomatic stage were analysed. Cut-off values for spot urine copper concentration, copper to creatinine ratio and copper to osmolality ratio at 0.5 µmol/L, 0.1 µmol/mmol and 0.00085 µmol/mOsmol (32 µg/L, 56 µg/g creatinine and 0.054 µg/mOsmol, respectively, in conventional units) have potential application in differentiation of WD patients.

Results

The data provides a new insight that the inter-individual variation of spot urine copper indexes (CVg) were moderate with figures around 60% which was similar to other clinically useful urine tests, such as urine albumin excretion ratio. Spot urine copper excretion strongly correlated with both urine creatinine and osmolality. And more than 95% of data points in health preschool children fell within prediction regions by linear regression suggesting a good utility of normalisation by these 2 analytes. Receiver operator curve (ROC) showed that copper to osmolality ratio was the best index with an area under curve (AUC) greater than 0.98.

Conclusions

Based on the data, a new WD screening time window targeting preschool children is proposed. Application of a bivariate screening strategy using spot urine copper concentration and urine osmolality may be useful in a population screening program for preschool children.
Antagonism between regular and atypical Cxcr3 receptors regulates macrophage migration during infection and injury in zebrafish
Authors: Sommer Frida , Torraca Vincenzo , Kamel Sarah , Lombardi Amber , Meijer Annemarie H.
Published: August 2019

The CXCR3-CXCL11 chemokine-signaling axis plays an essential role in infection and inflammation by orchestrating leukocyte trafficking in human and animal models, including zebrafish. Atypical chemokine receptors (ACKRs) play a fundamental regulatory function in signaling networks by shaping chemokine gradients through their ligand scavenging function, while being unable to signal in the classic G-protein-dependent manner. Two copies of the CXCR3 gene in zebrafish, cxcr3.2 and cxcr3.3, are expressed on macrophages and share a highly conserved ligand-binding site. However, Cxcr3.3 has structural characteristics of ACKRs indicative of a ligand-scavenging role. In contrast, we previously showed that Cxcr3.2 is an active CXCR3 receptor since it is required for macrophage motility and recruitment to sites of mycobacterial infection. In this study, we generated a cxcr3.3 CRISPR-mutant to functionally dissect the antagonistic interplay between the cxcr3 paralogs in the immune response. We observed that cxcr3.3 mutants are more susceptible to mycobacterial infection, while cxcr3.2 mutants are more resistant. Furthermore, macrophages in the cxcr3.3 mutant are more motile, show higher activation status, and are recruited more efficiently to sites of infection or injury. Our results suggest that Cxcr3.3 is an ACKR that regulates the activity of Cxcr3.2 by scavenging common ligands and that silencing the scavenging function of Cxcr3.3 results in an exacerbated Cxcr3.2 signaling. In human, splice variants of CXCR3 have antagonistic functions and CXCR3 ligands also interact with ACKRs. Therefore, in zebrafish, an analogous regulatory mechanism appears to have evolved after the cxcr3 gene duplication event, through diversification of conventional and atypical receptor variants.

Summary sentence

CXCR3 paralogue with structural characteristics of atypical chemokine receptors regulates the activity of a conventional receptor involved in macrophage motility by scavenging shared ligands.
The paternal and maternal genetic history of Vietnamese populations
Authors: Macholdt Enrico , Arias Leonardo , Duong Nguyen Thuy , Ton Nguyen Dang , Phong Nguyen Van , Schröder Roland , Pakendorf Brigitte , Hai Nong Van , Stoneking Mark
Published: August 2019

Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and 2.34 mB sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with some limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.
Causal relationship of cerebrospinal fluid biomarkers with the risk of Alzheimer’s disease: A two-sample Mendelian randomization study
Authors: Kim Soyeon , Kim Kiwon , Nho Kwangsik , Myung Woojae , Won Hong-Hee
Published: August 2019

Whether the epidemiological association of amyloid beta (Aβ) and tau pathology with Alzheimer’s disease (AD) is causal remains unclear. The recent failures to demonstrate the efficacy of several amyloid beta-modifying drugs may indicate the possibility that the observed association is not causal. These failures also led to efforts to develop tau-directed treatments whose efficacy is still tentative. Herein, we conducted a two-sample Mendelian randomization analysis to determine whether the relationship between the cerebrospinal fluid (CSF) biomarkers for amyloid and tau pathology and the risk of AD is causal. We used the summary statistics of a genome-wide association study (GWAS) for CSF biomarkers (Aβ1-42, phosphorylated tau181[p-tau], and total tau [t-tau]) in 3,146 individuals and for late-onset AD (LOAD) in 21,982 LOAD cases and 41,944 cognitively normal controls. We tested the association between the change in the genetically predicted CSF biomarkers and LOAD risk. We found a modest decrease in the LOAD risk per one standard deviation (SD) increase in the genetically predicted CSF Aβ (odds ratio [OR], 0.63 for AD; 95% confidence interval [CI], 0.38-0.87;P= 0.02). In contrast, we observed a significant increase in the LOAD risk per one SD increase in the genetically predicted CSF p-tau (OR, 2.37; 95% CI, 1.46-3.28;P= 1.09×10−5). However, no causal association was observed of the CSF t-tau with the LOAD risk (OR, 1.15; 95% CI, 0.85-1.45;P= 0.29). Our findings need to be validated in future studies with more genetic variants identified in larger GWASs for CSF biomarkers.
Extraction of active RhoGTPases by RhoGDI regulates spatiotemporal patterning of RhoGTPases
Authors: Golding Adriana , Visco Ilaria , Bieling Peter , Bement William
Published: August 2019

The RhoGTPases are characterized as membrane-associated molecular switches cycling between active, GTP-bound and inactive, GDP-bound states. However, 90-95% of RhoGTPases are maintained in a soluble form by RhoGDI, which is generally viewed as a passive shuttle for inactive RhoGTPases. Our current understanding of RhoGTPase:RhoGDI dynamics has been limited by two experimental challenges: direct visualization of the RhoGTPasesin vivoand reconstitution of the cyclein vitro. We developed methods to directly image vertebrate RhoGTPasesin vivoor on lipid bilayersin vitro. Using these tools, we identified pools of active and inactive RhoGTPase associated with the membrane, showed that RhoGDI can actively extract both inactive and active RhoGTPases, and that the extraction of active RhoGTPase contributes to their spatial regulation around wounds. In contrast to the textbook model of the RhoGTPase cycle, these results indicate that RhoGDI actively contributes to spatiotemporal patterning by removing active RhoGTPases from the plasma membrane.
Age-related changes to macrophages are detrimental to fracture healing
Authors: Clark Daniel , Brazina Sloane , Yang Frank , Hu Diane , Niemi Erene , Miclau Ted , Nakamura Mary , Marcucio Ralph
Published: August 2019

The elderly population suffers from higher rates of complications during fracture healing that result in increased morbidity and mortality. Inflammatory dysregulation is associated with increased age and is a contributing factor to the myriad of age-related diseases. Therefore, we investigated age-related changes to an important cellular regulator of inflammation, the macrophage, and the impact on fracture healing outcomes. We demonstrated that old mice (24 months) have delayed fracture healing with significantly less bone and more cartilage compared to young mice (3 months). The quantity of infiltrating macrophages into the fracture callus was similar in old and young mice. However, RNA-seq analysis demonstrated distinct differences in the transcriptomes of macrophages derived from the fracture callus of old and young mice, with an upregulation of M1/pro-inflammatory genes in macrophages from old mice as well as dysregulation of other immune-related genes. Preventing infiltration of the fracture site by macrophages in old mice improved healing outcomes, with significantly more bone in the calluses of treated mice compared to age-matched controls. After preventing infiltration by macrophages, the macrophages within the fracture callus were collected and examined via RNA-seq analysis, and their transcriptome resembled macrophages from young calluses. Taken together, infiltrating macrophages from old mice demonstrate detrimental age-related changes, and depleting infiltrating macrophages can improve fracture healing in old mice.
A putative ER-PM contact site complex relocalizes in response to Rare Earth Elements –induced endocytosis
Authors: Lee EunKyoung , Vila Nova Santana Brenda , Samuels Elizabeth , Benitez-Fuente Francisco , Corsi Erica , Botella Miguel A. , Perez-Sancho Jessica , Vanneste Steffen , Friml Jiří , Macho Alberto , Azevedo Aristea Alves , Rosado Abel
Published: August 2019

In plant cells, environmental stressors induce changes in the cytosolic concentration of calcium ([Ca2+]cyt) that are transduced by Ca2+-sensing proteins. To confer specificity to the stress signaling response, [Ca2+]cytsensing must be tightly regulated in space and time; the molecular mechanisms that restrict the localization and dynamics of Ca2+sensors in plants, however, are largely unknown. In this report, we identify a putative Ca2+-sensitive complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+-dependent lipid binding protein (CLB1), which is enriched at ER-PM contact sites (EPCS) and relocalizes in response to Rare Earth Elements (REEs)-induced endocytosis. Our results show that endocytosed REEs influence cytosolic Ca2+signaling, as indicated by the activation of the Ca2+/Calmodulin-based ratiometric sensor GCaMP3, and promote the cytoskeleton-dependent accumulation of ER-PM contact sites at the cell cortex. Based on these results, we propose that the EPCS-localized SYT1/SYT5/CLB1 complex is part of an evolutionarily conserved and spatially regulated Ca2+-responsive mechanism that control cER-PM communication during stress episodes.
The Habenular Receptor GPR151 Regulates Addiction Vulnerability Across Drug Classes
Authors: Antolin-Fontes Beatriz , Li Kun , Ables Jessica L. , Riad Michael H. , Görlich Andreas , Williams Maya , Wang Cuidong , Lipford Sylvia M. , Dao Maria , Molina Henrik , Liu Jianxi , Kenny Paul J. , Ibañez-Tallon Ines
Published: August 2019

The habenula controls the addictive properties of nicotine but also densely expresses opioid and cannabinoid receptors. As such, identification of strategies to manipulate habenular activity may yield new approaches to treat substance use disorders. Here we show that GPR151, an orphan G protein-coupled receptor (GPCR) highly enriched in the habenula of humans and rodents plays a critical role in regulating habenular function and behavioral responses to addictive drugs. We show that GPR151 is expressed on axonal and presynaptic membranes and synaptic vesicles, and regulates synaptic fidelity and plasticity. We find that GPR151 associates with synaptic components controlling vesicle release and ion transport and couples to the G-alpha inhibitory protein Gαo1to reduce cAMP levels. Stable cell lines expressing GPR151 confirm that it signals via Gi/o and are amenable to ligand screens.Gpr151null mice show diminished behavioral responses to nicotine, and self-administer greater quantities of the drug, phenotypes rescued by viral re-expression ofGpr151in the habenula.Gpr151null mice are also insensitive to the behavioral actions of morphine and cannabinoids. These data identify GPR151 as a critical modulator of habenular function that controls addiction vulnerability across different drug classes.

Highlights

Habenula neurons are enriched in nicotinic, opioid, cannabinoid and GPR151 receptors

GPR151 modulates synaptic fidelity and release probability at habenular terminals.

Habenular GPR151 plays a role in drug abuse and food intake/weight control

GPR151 couples to the G-alpha inhibitory protein Gαo1to reduce cAMP levels.

eTOC Blurb

Antolin-Fontes at al. identify a G protein-coupled receptor, GPR151, which is highly enriched in human habenular neurons. These neurons are primarily enriched with nicotinic, opioid and cannabinoid receptors. We find that GPR151 modulates habenular synaptic vesicle release probability and behavioral responses to these drugs of abuse.
The Acute Myeloid Leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme
Authors: Norvil Allison B. , AlAbdi Lama , Liu Bigang , Forstoffer Nicole E. , Michie Amie R. , Chen Taiping , Gowher Humaira
Published: August 2019

Mutations in DNMT3A, particularly the Arg882His substitution is highly prevalent in acute myeloid leukemia. Although the reduced activity of DNMT3A Arg882His variant alters DNA methylation, the underlying cause of its oncogenic effect is not fully understood. Our data show that DNMT3A Arg882His variant acquires CpG flanking sequence preference highly similar to that of DNMT3B. Interestingly, a similar substrate preference was observed in DNMT3A WT enzyme upon the loss of cooperative kinetic mechanism. We tested if DNMT3A Arg882His could preferably methylate DNMT3B-specific target sites. Rescue experiments in Dnmt3a/3b double knockout mouse embryonic stem cells show that the corresponding Arg878His mutation in mouse DNMT3A severely impairs its ability to methylate major satellite DNA, a DNMT3A-preferred target, but has no overt effect on the ability to methylate minor satellite DNA, a DNMT3B-preferred target. Our data suggest that methylation of DNMT3B target sites by DNMT3A Arg882His variant could contribute to its oncogenic potential.
Parallel Tempering with Lasso for Model Reduction in Systems Biology
Authors: Gupta Sanjana , Lee Robin E.C. , Faeder James R.
Published: August 2019

Systems Biology models reveal relationships between signaling inputs and observable molecular or cellular behaviors. The complexity of these models, however, often obscures key elements that regulate emergent properties. We use a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization to identify minimal subsets of reactions in a signaling network that are sufficient to reproduce experimentally observed data. The Bayesian approach finds distinct reduced models that fit data equivalently. A variant of this approach based on Group Lasso is applied to the NF-κB signaling network to test the necessity of feedback loops for responses to pulsatile and continuous pathway stimulation. Taken together, our results demonstrate that Bayesian parameter estimation combined with regularization can isolate and reveal core motifs sufficient to explain data from complex signaling systems.
LRP5-deficiency in OsxCreERT2 mice models intervertebral disc degeneration by aging and compression
Authors: Silva Matthew J. , Holguin Nilsson
Published: August 2019

Osterix is a critical transcription factor of mesenchymal stem cell fate, where its loss or loss of WNT signaling diverts differentiation to a chondrocytic lineage. Intervertebral disc (IVD) degeneration activates differentiation of prehypertrophic chondrocyte-like cells and inactivates WNT signaling, but its interacting role with osterix is unclear. First, compared to young-adult (5mo), mechanical compression of old (18mo) IVD induced greater IVD degeneration. Aging (5 vs 12mo) and/or compression reduced the transcription of osterix and notochordal marker T by 40-75%. Compression elevated transcription of hypertrophic chondrocyte marker MMP13 and pre-osterix transcription factor RUNX2, but less so in 12mo IVD. Next, using an Ai9/td reporter and immunohistochemistry, annulus fibrosus and nucleus pulposus cells of 5mo IVD expressed osterix, but aging and compression reduced its expression. Lastly, in vivo LRP5-deficiency in osterix-expressing cells degenerated the IVD, inactivated WNT signaling, reduced the biomechanical properties by 45-70%, and reduced transcription of osterix, notochordal markers and chondrocytic markers by 60-80%. Overall, these data indicate that age-related inactivation of WNT signaling in osterix-expressing cells may limit regeneration by depleting progenitors and attenuating the expansion of chondrocyte-like cells.
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Authors: Low Wai Yee , Tearle Rick , Liu Ruijie , Koren Sergey , Rhie Arang , Bickhart Derek M. , Rosen Benjamin D. , Kronenberg Zev N. , Kingan Sarah B. , Tseng Elizabeth , Thibaud-Nissen Françoise , Martin Fergal J. , Billis Konstantinos , Ghurye Jay , Hastie Alex R. , Lee Joyce , Pang Andy W.C. , Heaton Michael P. , Phillippy Adam M. , Hiendleder Stefan , Smith Timothy P.L. , Williams John L.
Published: August 2019

We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants
Authors: Xiang Jiale , Peng Jiguang , Peng Zhiyu
Published: August 2019

Null variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGen’s SVI Working Group and achieved an interpretation concordance of 95% (53/56). A further analysis of 28,586 putative loss-of-function variants by AutoPVS1 demonstrated that at least 27.6% of them do not reach a very strong strength level, with 17.4% based on variant-specific issues and 10.2% on disease mechanism considerations. Moreover, 40.7% (1,918/4,717) of splicing variants were assigned a decreased PVS1 strength level, significantly higher than frameshift and nonsense variants. Our results reinforce the necessity of considering variant-specific issues and disease mechanisms in variant interpretation, and demonstrate that AutoPVS1 is an accurate, reproducible, and reliable tool which facilitates PVS1 interpretation and will thus be of great importance to curators.
Out of the blue: Phototropins of the leaf vascular bundle sheath mediate the regulation of leaf hydraulic conductance by blue light
Authors: Grunwald Yael , Gosa Sanbon Chaka , Srivastava Tanmayee Torne , Moran Nava , Moshelion Menachem
Published: August 2019

The Arabidopsis leaf veins bundle sheath cells (BSCs) – a selective barrier to water and solutes entering the mesophyll – increase the leaf radial hydraulic conductance (Kleaf) by acidifying the xylem sap by their plasma membrane H+-ATPase, AHA2. Based on this and on the BSCs’ expression of PHOT1 and PHOT2, and the known blue-light (BL)-induced Kleaf increase, we hypothesized that, resembling the guard cells, BL perception by the BSCs’ phots activates its H+-ATPase, which, consequently, upregulates Kleaf. Indeed, under BL, the Kleaf of the knockout mutant lines phot1-5, phot2-1, phot1-5phot2-1, and aha2-4 was lower than that of the WT. BSC-only-directed complementation of phot1-5 or aha2-4 by PHOT1 or AHA2, respectively, restored the BL-induced Kleaf increase. BSC-specific silencing of PHOT1 or PHOT2 prevented such Kleaf increase. A xylem-fed kinase inhibitor (tyrphostin 9) replicated this also in WT plants. White light – ineffective in the phot1-5 mutant – acidified the xylem sap (relative to darkness) in WT and in the PHOT1-complemented phot1-5. These results, supported by BL increase of BSC protoplasts’ water permeability and cytosolic pH and their hyperpolarization by BL, identify the BSCs as a second phot-controlled water conductance element in leaves, in series with stomatal conductance. Through both, BL regulates the leaf water balance.

One-Sentence summary

Blue light regulates the leaf hydraulic conductance via the bundle-sheath cells’ blue light PHOT receptors which, via an autonomous signaling pathway, activate the BSCs’ AHA2 H+-pump.
The genome ofPeronospora belbahriireveals high heterozygosity, a low number of canonical effectors and CT-rich promoters
Authors: Thines Marco , Sharma Rahul , Rodenburg Sander Y. A. , Gogleva Anna , Judelson Howard S. , Xia Xiaojuan , van den Hoogen Johan , Kitner Miloslav , Klein Joël , Neilen Manon , de Ridder Dick , Seidl Michael F. , Van den Ackerveken Guido , Govers Francine , Schornack Sebastian , Studholme David J.
Published: August 2019

Along withPlasmopara destructor, Peronosopora belbahriihas arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies ofPe. belbahrii. Peronospora belbahriihas undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity inPeronosporaspecies. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
LXR alters CD4+ T cell function through direct regulation of glycosphingolipid synthesis
Authors: Waddington Kirsty E , Robinson George A , Rubio-Cuesta Beatriz , Chrifi-Alaoui Eden , Andreone Sara , Poon Kok-Siong , Ivanova Iveta , Martin-Gutierrez Lucia , Owen Dylan M , Jury Elizabeth C , Pineda-Torra Inés
Published: August 2019

The liver X receptor (LXR) is a key transcriptional regulator of cholesterol, fatty acid, and phospholipid metabolism. Dynamic remodeling of immunometabolic pathways, including lipid metabolism, is a crucial step in T cell activation. Here we explored the role of LXR-regulated metabolic processes in primary human CD4+ T cells, and their role in controlling plasma membrane lipids (glycosphingolipids and cholesterol) which strongly influence T cell immune signaling and function. Crucially, we identified the glycosphingolipid biosynthesis enzyme glucosylceramide synthase (UGCG) as a direct transcriptional LXR target. LXR activation by agonist GW3965 or endogenous oxysterol ligands significantly altered the glycosphingolipid:cholesterol balance in the plasma membrane by increasing glycosphingolipid levels and reducing cholesterol. Consequently, LXR activation lowered plasma membrane lipid order (stability), and an LXR antagonist could block this effect. LXR stimulation also reduced lipid order at the immune synapse and accelerated activation of proximal T cell signaling molecules. Ultimately, LXR activation dampened pro-inflammatory T cell function. Finally, compared to responder T cells, regulatory T cells had a distinct pattern of LXR-target gene expression corresponding to reduced lipid order. This suggests LXR-driven lipid metabolism could contribute to functional specialization of these T cell subsets. Overall, we report a novel mode of action for LXR in T cells involving the regulation of glycosphingolipid and cholesterol metabolism, and demonstrate its relevance in modulating T cell function.
The polyQ expansion modulates the configuration and phosphorylation of huntingtin
Authors: Jung Taeyang , Shin Baehyun , Tamo Giorgio , Kim Hyeongju , Vijayvargia Ravi , Leitner Alexander , Marcaida Maria Jose , Astorga-Wells Juan , Jung Roy , Aebersold Ruedi , Peraro Matteo Dal , Hebert Hans , Seong Ihn Sik , Song Ji-Joon
Published: August 2019

The polyQ-expansion at the N-terminus of huntingtin (HTT) is the prime cause of Huntington’s disease. The recent cryo-EM structure of HTT with HAP40 provides information on the protein’s prominent HEAT-repeats. Here, we present analyses of the impact of polyQ-length on the conformation of HTT by cryo-EM, the domain-interactions by cross-linking mass spectrometry and the phosphorylation of HTT. The cryo-EM analysis of normal (Q23-) and disease (Q78-) type HTTs in their apo forms shows that the structures of apo HTTs significantly differ from the structure of HTT-HAP40, and that the polyQ expansion induces global structural changes consisting of significant domain movements of the C-HEAT domain relative to the N-HEAT domain. In addition, we show that the polyQ-expansion alters the phosphorylation pattern across the full-length HTT and that the specific phosphorylation (Ser2116p) in turn affects the global structure of HTT, which influences the activity of polyQ-expanded HTT. These results provide a molecular basis for the effect of the N-terminal polyQ segment on HTT structure and activity, that may be important for the cell-selective toxicity of mutant HTT.
Shifting roles ofDrosophilapair-rule gene orthologs: segmental expression and function in the milkweed bugOncopeltus fasciatus
Authors: Reding Katie , Chen Mengyao , Lu Yong , Jarvela Alys M. Cheatle , Pick Leslie
Published: August 2019

The discovery of pair-rule genes (PRGs) inDrosophilarevealed the existence of an underlying two-segment-wide prepattern directing embryogenesis. The milkweed bugOncopeltus, a hemimetabolous insect, is a more representative arthropod: most of its segments form sequentially after gastrulation. Here we report the expression and function of orthologs of the complete set of nineDrosophilaPRGs inOncopeltus. SevenOf-PRG-orthologs are expressed in stripes in the primordia of every segment, rather than every-other segment,Of-runtis PR-like, and several are also expressed in the segment addition zone. RNAi-mediated knockdown ofOf-odd-skipped,pairedandsloppy-pairedimpacted all segments, with no indication of PR-like register. We confirm thatOf-E75Ais expressed in PR-like stripes, although it is not PR inDrosophila, demonstrating the existence of an underlying PR-like prepattern inOncopeltus. These findings reveal that a switch occurred in regulatory circuits leading to segment formation: while several holometabolous insects are “Drosophila-like,” utilizing PRG-orthologs for PR-patterning, mostOf-PRGs are expressed segmentally inOncopeltus, a more basally-branching insect. Thus, an evolutionarily stable phenotype – segment formation – is directed by alternate regulatory pathways in diverse species.

Summary Statement

Despite the broad of conservation of segmentation in insects, the regulatory genes underlying this process inDrosophilahave different roles in the hemipteran,Oncopeltus fasciatus.
Structural Basis of the Transmembrane Domain Dimerization in the Activation Mechanism of TrkA by NGF
Authors: Franco María L. , Nadezhdin Kirill D. , Goncharuk Sergey A. , Mineev Konstantin S , Arseniev Alexander S. , Vilar Marçal
Published: August 2019

Trk receptors are essential for the nervous system development. The molecular mechanism of TrkA activation by its ligand NGF is still unsolved. Recent data indicates that at endogenous levels most of TrkA is in an equilibrium monomer-dimer and the binding of NGF induces an increase of the dimer and oligomer forms of the receptor. An unsolved issue is the role of the transmembrane domain (TMD) in the dimerization of TrkA and the structural details of the TMD in the active dimer receptor. We found that TrkA-TMD can form dimers, identified the structural determinants of the dimer interface in the active receptor and validated this interface using site-directed mutagenesis together with functional and cell differentiation studies. Usingin vivocrosslinking we identified a reordering of the extracellular juxtamembrane (JTM) region after ligand binding. Replacement of some residues in the JTM region with cysteine form ligand-independent active dimers and reveal a preferred dimer interface. In addition to that, insertion of leucine residues into the TMD helix induces a ligand-independent TrkA activation suggesting that a rotation of the TMD dimers could be behind TrkA activation by NGF. Altogether our data indicates that the transmembrane and juxtamembrane regions of the receptor play a key role in the dimerization and activation of TrkA by NGF.
Post-acute administration of the GABAA α5 antagonist S44819 promotes recovery of peripheral limb fine motor skills after permanent distal middle cerebral artery occlusion in rats
Authors: Pace Marta , Falappa Matteo , Machado Patricia , Facchin Laura , Hermann Dirk M. , Bassetti Claudio L.
Published: August 2019

Background

Ischemic stroke induces hypoexcitability of the peri-infarct cortex by increased tonic GABA activity, which impairs stroke recovery. The GABAA α5 antagonist S44819 has recently been shown to promote post-ischemic motor-coordination recovery after transient proximal middle cerebral artery occlusion (MCAO) in mice. The effects of S44819 on post-ischemic skilled limb movement recovery have so far not yet been assessed in rats.

Methods

Male Sprague-Dawley rats were subjected to permanent distal MCAO. Starting 3 days post-stroke, vehicle or S44819 (3 or 10 mg/kg) were delivered orally twice a day for 28 days. A single pellet reaching test was performed at baseline, before treatment onset and at weekly intervals thereafter. Animals were sacrificed at 45 days post-stroke (that is, at 42 days post-treatment onset) after 14 days of drug washout. Body weight was monitored, and infarct size was determined by histology.

Results

S44819, administered at 10 mg/kg but not 3 mg/kg significantly improved single pellet reaching performance over 45 days (F(2,96)=22.43, p<0.001). Body weight was not altered. S44819 had no effect on infarct size.

Conclusion

Our data indicate that post-acute administration of S44819 at 10 mg/kg promotes skilled forelimb movements. The effect was maintained after S44819 wash out.
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
Authors: Dong Kangning , Zhang Shihua
Published: August 2019

The rapid accumulation of single-cell chromatin accessibility data offers a unique opportunity to investigate common and specific regulatory mechanisms across different cell types. However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing ~80,000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory network shows strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue related TFs, and many of them reveal novel regulatory mechanisms (e.g., a kidney-specific promoter-enhancer loop of clock-controlled gene Gys2).
Variants of intrinsic disorder: structural characterization
Authors: Forcelloni Sergio , Deiana Antonio , Giansanti Andrea
Published: August 2019

In a recent study, we have introduced an operational classification of the human proteome in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), intrinsically disordered proteins (IDPs). That classification was useful in functionally separating IDPRs from IDPs, which up until now have been generally considered as a whole. In this study, we corroborate this distinction by considering different physical-chemical and structural properties. Both ORDPs and IDPRs are enriched in order-promoting amino acids, whereas only IDPs show an enrichment in disordered-promoting amino acids. Consistently, ORDPs and IDPRs are preferentially located in the ordered phase of the charge-hydropathy plot, whereas IDPs are widespread over the disordered phase. We introduce the mean packing - mean pairwise energy (MP-MPE) plane to structurally characterize these variants even in the absence of a structural model. As expected for well-packed proteins, a negative linear correlation is observed between MP and MPE for ORDPs and IDPRs, whereas IDPs break this linear dependence. Finally, we find that IDPs have a more extended conformation as measured by the scaling law between the radius of gyration and the length of these proteins, and accordingly they have higher solubility and accessible surface area than ORDPs and IDPRs. Overall, our results confirm the relevance of our operational separation of IDPRs from IDPs and provide further validation of our criteria to separate IDPs from the rest of human proteome.
LUZP1, a novel regulator of primary cilia and the actin cytoskeleton, is altered in Townes-Brocks Syndrome
Authors: Bozal-Basterra Laura , Gonzalez-Santamarta María , Bermejo-Arteagabeitia Aitor , Da Fonseca Carolina , Pampliega Olatz , Andrade Ricardo , Martín-Martín Natalia , Branon Tess C , Ting Alice Y , Carracedo Arkaitz , Rodríguez Jose A. , Elortza Felix , Sutherland James D. , Barrio Rosa
Published: August 2019

Primary cilia are sensory organelles that are crucial for cell signaling during development and organ homeostasis. Cilia arise from the centrosome and their formation is governed by numerous regulatory factors. We show that the leucine-zipper protein LUZP1 localizes to the pericentriolar material and actin cytoskeleton. Using TurboID proximity labeling and pulldowns, LUZP1 associates with factors linked to centrosome and actin filaments. Loss of LUZP1 reduces F-actin levels, facilitating ciliogenesis and altering Sonic Hedgehog signaling, pointing to a key role in the cytoskeleton-cilia interdependency. Moreover, we show that LUZP1 interacts with a truncated form of the transcription factor SALL1 that causes Townes-Brocks Syndrome. TBS is characterized by digit, heart and kidney malformations and is linked in part to defective cilia. Truncated SALL1 increases the ubiquitin proteasome-mediated degradation of LUZP1. Alteration of LUZP1 levels may be a contributing factor to TBS, suggesting possible therapies using modulators of cilia and cytoskeletal function.
Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation
Authors: Christodoulaki Eirini , Barghi Neda , Schlötterer Christian
Published: August 2019

Polygenic adaptation is frequently associated with small allele frequency changes of many loci. Recent works suggest, that large allele frequency changes can be also expected. Laboratory natural selection (LNS) experiments provide an excellent experimental framework to study the adaptive architecture under controlled laboratory conditions: time series data in replicate populations evolving independently to the same trait optimum can be used to identify selected loci. Nevertheless, the choice of the new trait optimum in the laboratory is typically an ad hoc decision without consideration of the distance of the starting population to the new optimum. Here, we used forward-simulations to study the selection signatures of polygenic adaptation in populations evolving to different trait optima. Mimicking LNS experiments we analyzed allele frequencies of the selected alleles and population fitness at multiple time points. We demonstrate that the inferred adaptive architecture strongly depends on the choice of the new trait optimum in the laboratory and the significance cut-off used for identification of selected loci. Our results not only have a major impact on the design of future Evolve and Resequence (E&R) studies, but also on the interpretation of current E&R data sets.
The association between mineralised tissue formation and the mechanical local in vivo environment: Time-lapsed quantification of a mouse defect healing model
Authors: Tourolle né Betts Duncan C , Wehrle Esther , Paul Graeme R , Kuhn Gisela A , Christen Patrik , Hofmann Sandra , Müller Ralph
Published: August 2019

An improved understanding of how local mechanical stimuli guide the fracture healing process has the potential to enhance clinical treatment of bone injury. Recent preclinical studies of bone defect in animal models have used cross-sectional data to examine this phenomenon indirectly. In this study, a direct time-lapsed imaging approach was used to investigate the local mechanical strains that precede the formation of mineralised tissue at the tissue scale. The goal was to test two hypotheses: 1) the local mechanical signal that precedes the onset of tissue mineralisation is higher in areas which mineralise, and 2) this local mechanical signal is independent of the magnitude of global mechanical loading of the tissue in the defect. Two groups of mice with femoral defects of length 0.85 mm (n=10) and 1.45 mm (n=9) were studied, allowing for distinct distributions of tissue scale strains in the defects. The regeneration and (re)modelling of mineralised tissue was observed weekly using in vivo micro-computed tomography (micro-CT), which served as a ground truth for resolving areas of mineralised tissue formation. The mechanical environment was determined using micro-finite element analysis (micro-FE) on baseline images. The formation of mineralised tissue showed strong association with areas of higher mechanical strain (area-under-the-curve: 0.91±0.04, true positive rate: 0.85±0.05) while surface based strains could correctly classify 43% of remodelling events. These findings support our hypotheses by showing a direct association between the local mechanical strains and the formation of mineralised tissue.
Adaptive thermogenesis in mice requires adipocyte light-sensing via Opsin 3
Authors: Nayak Gowri , Vemaraju Shruti , Zhang Kevin X. , Odaka Yoshinobu , Buhr Ethan D. , Holt-Jones Amanda , Smith April N. , Upton Brian A. , Zhan Jesse J. , Diaz Nicolás , Murakami Kazutoshi , D’Souza Shane , Nguyen Minh-Thanh , Gordon Shannon A. , Wu Gang , Schmidt Robert , Mei Xue , Petts Nathan T. , Batie Matthew , Rao Sujata , Nakamura Takahisa , Sweeney Alison M. , Hogenesch John B. , Van Gelder Russell N. , Sanchez-Gurmaches Joan , Lang Richard A.
Published: August 2019

Almost all life forms can decode light information for adaptive advantage. Examples include the visual system, where photoreceptor signals are interpreted as images, and the circadian system, where light entrains a physiological clock. Here we describe a local, non-visual light response in mice that employs encephalopsin (OPN3, a 480 nm, blue light responsive opsin) to regulate the function of adipocytes. Germ line null and adipocyte-specific conditional null mice show a deficit in thermogenesis that is phenocopied in mice under blue-light deficient conditions. We show that blue light stimulation of adipocytes activates hormone sensitive lipase, the rate limiting enzyme in the lipolysis pathway, and that this is OPN3-dependent. Opn3 adipocyte conditional null mice also use reduced levels of fat mass when fasted and cold exposed further suggesting a lipolysis deficit. These data suggest the hypothesis that in mice, a local, OPN3-dependent light response in adipocytes is a mechanism for regulation of energy homeostasis.
Bivalent and Broad Chromatin Domains Regulate Pro-metastatic Drivers in Melanoma
Authors: Terranova Christopher , Tang Ming , Maitituoheti Mayinuer , Raman Ayush T. , Schulz Jonathan , Amin Samir B. , Orouji Elias , Tomczak Katarzyna , Sarkar Sharmistha , Oba Junna , Creasy Caitlin , Wu Chang-Jiun , Zhao Dongyu , Chen Kaifu , Haydu Lauren E. , Wang Wei-Lien , Lazar Alexander J. , Woodman Scott E. , Bernatchez Chantale , Rai Kunal
Published: August 2019

Chromatin deregulation is an emerging hallmark of cancer. However, the extent of epigenetic aberrations during tumorigenesis and their relationship with genetic aberrations are poorly understood. Using ChIP-sequencing for enhancers (H3K27ac and H3K4me1), promoters (H3K4me3), active transcription (H3K79me2) and polycomb (H3K27me3) or heterochromatin (H3K9me3) repression we generated chromatin state profiles in metastatic melanoma using 46 tumor samples and cell lines. We identified a strong association of NRAS, but not BRAF mutations, with bivalent states harboring H3K4me3 and H3K27me3 marks. Importantly, the loss and gain of bivalent states occurred on important pro-metastasis regulators including master transcription factor drivers of mesenchymal phenotype including ZEB1, TWIST1, SNAI1 and CDH1. Unexpectedly, a subset of these and additional pro-metastatic drivers (e.g. POU3F2, SOX9 and PDGFRA) as well as melanocyte-specific master regulators (e.g. MITF, ZEB2, and TFAP2A) were regulated by exceptionally wide H3K4me3 domains that can span tens of thousands of kilobases suggesting roles of this new epigenetic element in melanoma metastasis. Overall, we find that BRAF, NRAS and WT melanomas may use bivalent states and broad H3K4me3 domains in a specific manner to regulate pro-metastatic drivers. We propose that specific epigenetic traits – such as bivalent and broad domains – get assimilated in the epigenome of pro-metastatic clones to drive evolution of cancer cells to metastasis.
The uneasy coexistence of predators and pathogens
Authors: Eilersen Andreas , Sneppen Kim
Published: August 2019

Disease and predation are both highly important in ecology, and pathogens with multiple host species have turned out to be common. Nonetheless, the interplay between multi-host epidemics and predation has received relatively little attention. Here, we analyse a model of a predator-prey system with disease in both prey and predator populations and determine reasonable parameter values using allometric mass scaling relations. Our analysis focuses on the possibility of extinction events rather than the linear stability of the model equations. We find that if the predator is a specialist, epidemics frequently drive the predator species to extinction. If the predator has an additional, immune prey species, predators will usually survive. Coexistence of predator and disease is impossible in the single-prey model. We conclude that for the prey species, carrying a pathogen can be an effective weapon against predators, and that being a generalist is a major advantage for a predator.