bluuebunny/crossref_metadata_2025 huggingface dataset:
Post-traumatic osteoarthritis development is not modified by postnatal chondrocyte deletion of CCN2
Authors: Keenan Craig M , Ramos-Mucci Lorenzo , Kanakis Ioannis , Milner Peter I , Leask Andrew , Abraham David , Bou-Gharios George , Poulet Blandine
Published: February 2020

CCN2 is a matricellular protein involved in several critical biological processes. In particular, CCN2 is involved in cartilage development and in osteoarthritis. CCN2 null mice exhibit a range of skeletal dysmorphisms, highlighting its importance in regulating matrix formation during development, however its role in adult cartilage remains unclear. The aim of this study was to determine the role of CCN2 in postnatal chondrocytes in models of post-traumatic osteoarthritis (PTOA). CCN2 deletion was induced in articular chondrocytes of male transgenic mice at 8 weeks of age. PTOA was induced in knees either surgically or non-invasively by repetitive mechanical loading at 10 weeks of age. Knee joints were harvested, scanned with micro-CT, and processed for histology. Sections were stained with toluidine blue and scored using the OARSI grading system. In the non-invasive model cartilage lesions were present in the lateral femur but no significant differences were observed between wildtype (WT) and CCN2 knockout (KO) mice 6 weeks post-loading. In the surgical model, severe cartilage degeneration was observed in the medial compartments but no significant differences were observed between WT and CCN2 KO mice at 2, 4, and 8 weeks post-surgery. We conclude that CCN2 deletion in chondrocytes did not modify the development of PTOA in mice, suggesting that chondrocyte expression of CCN2 in adults is not a critical player in protecting cartilage from the degeneration associated with PTOA.

Summary Statement

Post-natal deletion of CCN2 in chondrocytes does not affect the development of post-traumatic osteoarthritis in mice.
Downward Gazing for Steadiness
Authors: Koren Yogev , Mairon Rotem , Sofer Ilay , Parmet Yisrael , Ben-Shahar Ohad , Bar-Haim Simona
Published: February 2020

When walking on an uneven surface or complex terrain, humans tend to gaze downward. Previous investigations indicate that visual information can be used for online control of stepping. Behavioral investigations suggest that, during walking, the availability of visual information increases stepping accuracy, but probably through a feedforward control mechanism. Consequently, downward gazing (DWG) is usually interpreted as a strategy used to acquire useful information for online and/or feedforward control of stepping.

Visual information is not exclusively used for guiding locomotion; a wealth of literature has been published on the usefulness of visual information for feedback postural control. Critically, postural control has been shown to be sensitive to the visual flow arising from the respective motion of the individual and the 3D environment.

To investigate whether DWG can be used to enhance feedback control of posture, rather than feedforward/online control of gait, we conducted a series of experiments that explore this possible interplay. Through these experiments we were able to show that DWG, just a few steps ahead, results in a steadier standing and walking posture, without the need for accuracy. Moreover, we were able to demonstrate that humans resort to DWG when walking stability is compromised, even when destabilizing features were visually unpredictable.

This series of experiments provides sufficient evidence of the possible interplay between visual information used for guiding locomotion and that used for postural control. Moreover, this evidence raises concerns regarding the way we interpret gaze behavior without the knowledge of the type and use of the information gathered.
Two particle picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER
Authors: Wagner Thorsten , Lusnig Luca , Pospich Sabrina , Stabrin Markus , Schönfeld Fabian , Raunser Stefan
Published: February 2020

Structure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here we present two approaches for selecting filamentous complexes: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, the other one, called SPHIRE-STRIPER, is based on a classical line detection approach. The advantage of the crYOLO based procedure is that it accurately performs on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. We evaluate the performance of both procedures on tobacco mosaic virus and filamentous F-actin data sets to demonstrate the robustness of each method.
Crystallography of lamin A facilitated by chimeric fusions
Authors: Stalmans Giel , Lilina Anastasia V. , Strelkov Sergei V.
Published: February 2020

All proteins of the intermediate filament (IF) family contain the signature central α-helical domain which forms a coiled-coil dimer. Because of its length, past structural studies relied on a ‘divide-and-conquer’ strategy whereby fragments of this domain were recombinantly produced, crystallized and analysed using X-rays. Here we describe a further development of this approach towards structural studies of nuclear IF protein lamin. To this end, we have fused lamin A fragments to short N- and C-terminal capping motifs which provide for the correct formation of parallel, in-register coiled-coil dimers. As the result, a chimeric construct containing lamin A residues 17-70 C-terminally capped by the Eb1 domain was solved to 1.83 Å resolution. Another chimera containing lamin A residues 327-403 N-terminally capped by the Gp7 domain was solved to 2.9 Å. In the latter case the capping motif was additionally modified to include a disulphide bridge at the dimer interface. We discuss multiple benefits of fusing coiled-coil dimers with such capping motifs, including a convenient crystallographic phasing by either molecular replacement or sulphur single-wavelength anomalous dispersion (S-SAD) measurements.
SULF1 suppresses Wnt3A-driven growth of bone metastatic prostate cancer in perlecan-modified 3D cancer-stroma-macrophage triculture models
Authors: da Costa Fabio Henrique Brasil , Lewis Michael , Truong Anna , Carson Daniel , Farach-Carson Mary
Published: February 2020

Bone marrow stroma influences metastatic prostate cancer (PCa) progression, latency, and recurrence. At sites of PCa bone metastasis, cancer-associated fibroblasts and tumor-associated macrophages interact to establish a perlecan-rich desmoplastic stroma. As a heparan sulfate proteoglycan, perlecan (HSPG2) stores and stabilizes growth factors, including heparin-binding Wnt3A, a positive regulator of PCa cell growth. Because PCa cells alone do not induce CAF production of perlecan in the desmoplastic stroma, we sought to discover the sources of perlecan and its growth factor-releasing modifiers SULF1, SULF2, and heparanase in PCa cells and xenografts, bone marrow fibroblasts, and macrophages. SULF1, produced primarily by bone marrow fibroblasts, was the main glycosaminoglycanase present, a finding validated with primary tissue specimens of PCa metastases with desmoplastic bone stroma. Expression of bothHSPG2andSULF1was concentrated inαSMA-rich stroma near PCa tumor nests, where infiltrating pro-tumor TAMs also were present. To decipher SULF1’s role in the reactive bone stroma, we created a bone marrow biomimetic hydrogel incorporating perlecan, PCa cells, macrophages, and fibroblastic bone marrow stromal cells. Finding that M2-like macrophages increased levels ofSULF1andHSPG2produced by fibroblasts, we examined SULF1 function in Wnt3A-mediated PCa tumoroid growth in tricultures. Comparing control orSULF1knockout fibroblastic cells, we showed that SULF1 reduces Wnt3A-driven growth, cellularity, and cluster number of PCa cells in our 3D model. We conclude that SULF1 can suppress Wnt3A-driven growth signals in the desmoplastic stroma of PCa bone metastases, andSULF1loss favors PCa progression, even in the presence of pro-tumorigenic TAMs.
New Radiological Classification of Glioma and validation with the survival analysis
Authors: Kamble Akshaykumar Nana , Agrawal Nidhi K , Koundal Surabhi , Bhargava Salil , Kamble Abhaykumar Nana
Published: February 2020

Radiology based classification of glioma independent of histological or genetic markers predicting survival of patients is an unmet need. Until now radiology is chasing these markers rather than focussing directly on the clinical outcome. Our study is first of its kind to come up with the independent new radiological classification of gliomas encompassing both low-and high-grade gliomas under single classification system.

TCGA-LGG and REMBRANDT public domain dataset of glioma were analyzed as training and testing dataset respectively. Based on MRI images, gliomas were classified into six types in detailed classification & three types in simplified classification system. Survival analysis using Kaplan Meier and Cox regression was done. Secondary objective was to evaluate the sensitivity and specificity of novel signs with existing histological and genetic markers.

The study predicted survival in both training and testing dataset independent of genetic or histological information. Novel signs, “Ball on Christmas tree” sign(highly specific), Type-4 lineage sign(highly sensitive) identifies IDH-wild and high-grade gliomas (grade-III and IV) while Type-2 lineage sign showed good specificity in identifying 1p19q non co-deleted IDH-mutated, ATRX del/mutated, Grade-II gliomas. There is a substantial interobserver agreement for the classification and novel signs. New radiological classification of glioma predicts the survival of patients independent of genetic or histological information. This can act as a scaffolding to formulate and streamline the treatment guidelines for glioma patients. This classification has potential of improving the quality of care of glioma patients by predicting the survival without the need of invasive biopsy.
The low complexity regions in the C-terminus are essential for the subcellular localisation of Leishmania casein kinase 1 but not for its activity
Authors: Martel Daniel , Pine Stewart , Bartsch Katharina , Clos Joachim , Späth Gerald F. , Rachidi Najma
Published: February 2020

Casein Kinase 1 (CK1) family members are serine/threonine protein kinases ubiquitously expressed in eukaryotic organisms. They are involved in a wide range of important cellular processes, such as membrane trafficking, or vesicular transport in organisms from yeast to humans. Due to its broad spectrum of action, CK1 activity and expression is tightly regulated by a number of mechanisms, including subcellular sequestration. Defects in CK1 regulation, localisation or the introduction of mutations in the CK1 coding sequence are often associated with important diseases such as cancer. Increasing evidence suggest that the manipulation of host cell CK1 signalling pathways by intracellular pathogens, either by exploiting the host CK1 or by exporting the CK1 of the pathogen into the host cell may play an important role in infectious diseases. Leishmania CK1.2 is essential for parasite survival and released into the host cell, playing an important role in host pathogen interactions. Although Leishmania CK1.2 has dual role in the parasite and in the host cell, nothing is known about its parasitic localisation and organelle-specific functions. In this study, we show that CK1.2 is a ubiquitous kinase, which is present in the cytoplasm, associated to the cytoskeleton and localised to various organelles, indicating potential roles in kinetoplast and nuclear segregation, as well as ribosomal processing and motility. Furthermore, using truncated mutants, we show for the first time that the two low complexity regions (LCR) present in the C-terminus of CK1.2 are essential for the subcellular localisation of CK1.2 but not for its kinase activity, whereas the deletion of the N-terminus leads to a dramatic decrease in CK1.2 abundance. In conclusion, our data on the localisation and regulation of Leishmania CK1.2 contribute to increase the knowledge on this essential kinase and get insights into its role in the parasite.
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Authors: Maynard Kristen R. , Collado-Torres Leonardo , Weber Lukas M. , Uytingco Cedric , Barry Brianna K. , Williams Stephen R. , Catallini Joseph L. , Tran Matthew N. , Besich Zachary , Tippani Madhavi , Chew Jennifer , Yin Yifeng , Kleinman Joel E. , Hyde Thomas M. , Rao Nikhil , Hicks Stephanie C. , Martinowich Keri , Jaffe Andrew E.
Published: February 2020

We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex (DLPFC). We identified extensive layer-enriched expression signatures, and refined associations to previous laminar markers. We overlaid our laminar expression signatures onto large-scale single nuclei RNA sequencing data, enhancing spatial annotation of expression-driven clusters. By integrating neuropsychiatric disorder gene sets, we showed differential layer-enriched expression of genes associated with schizophrenia and autism spectrum disorder, highlighting the clinical relevance of spatially-defined expression. We then developed a data-driven framework to define unsupervised clusters in spatial transcriptomics data, which can be applied to other tissues or brain regions where morphological architecture is not as well-defined as cortical laminae. We lastly created a web application for the scientific community to explore these raw and summarized data to augment ongoing neuroscience and spatial transcriptomics research (http://research.libd.org/spatialLIBD).
A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities
Authors: Barlow Jacob T. , Bogatyrev Said R. , Ismagilov Rustem F.
Published: February 2020

A fundamental goal in microbiome studies is to determine which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative microbial abundances, which cannot capture absolute changes. Moreover, studies often focus on a single site (usually stool), although microbial demographics differ substantially among gastrointestinal (GI) locations. Here, we developed a quantitative framework to accurately measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compared microbial loads in lumenal and mucosal samples at several sites along the GI tract. Measurements of absolute (but not relative) abundances revealed decreases in total microbial loads on the ketogenic diet and enabled us to accurately determine the effect of the diet on each taxon at each GI location. Quantitative measurements also revealed different patterns in how the ketogenic diet affected each taxon’s abundance in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework applied to samples from relevant GI locations will enable mapping microbial biogeography of the mammalian GI tract and more accurately capture the changes of microbial taxa in experimental microbiome studies.
Unique structural features of mammalian NEIL2 DNA glycosylase prime its activity for diverse DNA substrates and environments
Authors: Eckenroth Brian E. , Cao Vy , Averill April M. , Dragon Julie A. , Doublié Sylvie
Published: February 2020

Oxidative damage on DNA arising from both endogenous and exogenous sources can result in base modifications that promote errors in replication as well as generate sites of base loss (abasic sites) that present unique challenges to maintaining genomic integrity. These lesions are excised by DNA glycosylases in the first step of the base excision repair pathway. Here we present the first crystal structure of a NEIL2 glycosylase, an enzyme active on cytosine oxidation products and abasic sites. The structure reveals an unusual “open” conformation not seen in NEIL1 or NEIL3 orthologs. NEIL2 is predicted to adopt a “closed” conformation when bound to its substrate. Combined crystallographic and solution scattering studies show the enzyme to be conformationally dynamic in a manner distinct among the NEIL glycosylases and provide insight into the unique substrate preference of the enzyme. Additionally, we characterized three cancer variants of human NEIL2, namely S140N, G230W, and G303R.
The Effect of a Virtual No-Step Zone on Balance Control in Walking
Authors: Fettrow Tyler , DiBianca Stephen , dos Santos Fernando Vanderlinde , Reimann Hendrik , Jeka John
Published: February 2020

Humans need to actively control their upright posture during walking to avoid loss of balance. We do not have a comprehensive theory for how humans regulate balance during walking, especially in complex environments. Balance must be maintained in a variety of contexts including crowded city side-walks, rocky nature trails, walks on the beach, or fast-paced sporting events. The nervous system must process many aspects of the environment to produce an appropriate motor output in order to maintain balance on two legs. We have previously identified three balance mechanisms that young healthy adults use to maintain balance while walking: 1) The ankle roll mechanism, a modulation of ankle inversion/eversion; 2) The foot placement mechanism, a shift of the swing foot placement; and 3) The push-off mechanism, a modulation of the ankle plantarflexion angle during double stance. We know that these mechanisms are interdependent and can be influenced by internal factors such as the phase of the gait cycle and walking cadence. Here we seek to determine whether there are changes in neural control of balance when walking in the presence of environmental constraints. Subjects walked on a selfpaced treadmill while immersed in a virtual environment that provides three different colored pathways. Subjects were instructed not to step in theNo-Step Zone, which appeared either on the right or left side of the subject. While walking, subjects received balance perturbations in the form of galvanic vestibular stimulation, providing the sensation of falling sideways, either toward theNo-Stepzone or toward theNeutralzone on the other side. The results indicate that the use of the balance mechanisms are subtly altered depending on whether the perceived fall is toward theNo-Stepor theNeutralzone. This experiment provides further evidence that the balance control system during walking is extremely flexible, recruiting multiple mechanisms at different times in the gait cycle to adapt to environmental constraints.
Parkin coordinates mitochondrial lipid remodeling to execute mitophagy
Authors: Lin Chao-Chieh , Yan Jin , Kapur Meghan D. , Norris Kristi L. , Hsieh Cheng-Wei , Lai Chun-Hsiang , Vitale Nicolas , Lim Kah-Leong , Guan Ziqiang , Chi Jen-Tsan , Yang Wei-Yuan , Yao Tso-Pang
Published: February 2020

Mitochondrial failure caused by Parkin mutations contributes to Parkinson’s disease. Parkin binds, ubiquitinates, and targets impaired mitochondria for autophagic destruction. Robust mitophagy involves peri-nuclear concentration of Parkin-tagged mitochondria, followed by dissemination of juxtanuclear mitochondrial aggregates, and efficient sequestration of individualized mitochondria by autophagosomes. Here, we report that the execution of complex mitophagic events requires active mitochondrial lipid remodeling. Parkin recruits phospholipase D2 to the depolarized mitochondria and generate phosphatidic acid (PA). Mitochondrial PA is subsequently converted to diacylglycerol (DAG) by Lipin-1 phosphatase-a process that further requires mitochondrial ubiquitination and ubiquitin-binding autophagic receptors, NDP52 and Optineurin. We show that Optineurin transports, via Golgi-derived vesicles, a PA-binding factor EndoB1 to ubiquitinated mitochondria, thereby facilitating DAG production. Mitochondrial DAG activates both F-actin assembly to drive mitochondrial individualization, and autophagosome biogenesis to efficiently restrict impaired mitochondria. Thus Parkin, autophagic receptors and the Golgi complex orchestrate mitochondrial lipid remodeling to execute robust mitophagy.
Core and Matrix Thalamic Sub-Populations Relate to Spatio-Temporal Cortical Connectivity Gradients
Authors: Müller Eli , Munn Brandon , Hearne Luke J. , Smith Jared B. , Fulcher Ben , Cocchi Luca , Shine James M.
Published: February 2020

Recent neuroimaging experiments have defined low-dimensional gradients of functional connectivity in the cerebral cortex that subserve a spectrum of capacities that span from sensation to cognition. Despite well-known anatomical connections to the cortex, the subcortical areas that support cortical functional organization have been relatively overlooked. One such structure is the thalamus, which maintains extensive anatomical and functional connections with the cerebral cortex across the cortical mantle. The thalamus has a heterogeneous cytoarchitecture, with at least two distinct cell classes that send differential projections to the cortex: granular-projecting ‘Core’ cells and supragranular-projecting ‘Matrix’ cells. Here we use high-resolution 7T resting-state fMRI data and the relative amount of two calcium-binding proteins, parvalbumin and calbindin, to infer the relative distribution of these two cell-types (Core and Matrix, respectively) in the thalamus. First, we demonstrate that thalamocortical connectivity recapitulates large-scale, low-dimensional connectivity gradients within the cerebral cortex. Next, we show that diffusely-projecting Matrix regions preferentially correlate with cortical regions with longer intrinsic fMRI timescales. We then show that the Core–Matrix architecture of the thalamus is important for understanding network topology in a manner that supports dynamic integration of signals distributed across the brain. Finally, we replicate our main results in a distinct 3T resting-state fMRI dataset. Linking molecular and functional neuroimaging data, our findings highlight the importance of the thalamic organization for understanding low-dimensional gradients of cortical connectivity.
Gene Networks and Pathways for Plasma Lipid Traits via Multi-tissue Multi-omics Systems Analysis
Authors: Blencowe Montgomery , Ahn In Sook , Saleem Zara , Luk Helen , Cely Ingrid , Mäkinen Ville-Petteri , Zhao Yuqi , Yang Xia
Published: February 2020

Genome-wide association studies (GWAS) have implicated ∼380 genetic loci for plasma lipid regulation. However, these loci only explain 17-27% of the trait variance and a comprehensive understanding of the molecular mechanisms has not been achieved. In this study, we utilized an integrative genomics approach leveraging diverse genomic data from human populations to investigate whether genetic variants associated with various plasma lipid traits, namely total cholesterol (TC), high and low density lipoprotein cholesterol (HDL and LDL), and triglycerides (TG), from GWAS were concentrated on specific parts of tissue-specific gene regulatory networks. In addition to the expected lipid metabolism pathways, gene subnetworks involved in ‘interferon signaling’, ‘autoimmune/immune activation’, ‘visual transduction’, and ‘protein catabolism’ were significantly associated with all lipid traits. Additionally, we detected trait-specific subnetworks, including cadherin-associated subnetworks for LDL, glutathione metabolism for HDL, valine, leucine and isoleucine biosynthesis for TC, and insulin signaling and complement pathways for TG. Finally, utilizing gene-gene relations revealed by tissue-specific gene regulatory networks, we detected both known (e.g.APOH, APOA4, andABCA1) and novel (e.g.F2in adipose tissue) key regulator genes in these lipid-associated subnetworks. Knockdown of theF2gene (Coagulation Factor II, Thrombin) in 3T3-L1 and C3H10T1/2 adipocytes reduced gene expression ofAbcb11, Apoa5, Apof, Fabp1, Lipc, andCd36, reduced intracellular adipocyte lipid content, and increased extracellular lipid content, supporting a link between adipose thrombin and lipid regulation. Our results shed light on the complex mechanisms underlying lipid metabolism and highlight potential novel targets for lipid regulation and lipid-associated diseases.
An original model of brain infection identifies the hijacking of host lipoprotein import as a bacterial strategy for blood-brain barrier crossing
Authors: Benmimoun Billel , Papastefanaki Florentia , Périchon Bruno , Segklia Katerina , Roby Nicolas , Miriagou Vivi , Schmitt Christine , Dramsi Shaynoor , Matsas Rebecca , Spéder Pauline
Published: February 2020

Pathogens able to cross the blood-brain barrier (BBB) induce long-term neurological sequelae and death. Understanding how neurotropic pathogens bypass this strong physiological barrier is a prerequisite to devise therapeutic strategies. Here we propose an innovative model of infection in the developing Drosophila brain, combining whole brain explants within vivosystemic infection. We identified several mammalian pathogens able to cross the Drosophila BBB, including Group B Streptococcus (GBS). Amongst GBS surface components, lipoproteins, and in particular the B leucin-rich Blr, were important for BBB crossing and virulence in Drosophila. Further, we identified (V)LDL receptor LpR2, expressed in the BBB, as a host receptor for Blr, allowing GBS translocation through endocytosis. Finally, we demonstrated that Blr is required for BBB crossing and pathogenicity in a murine model of infection. Our results support the relevance of Drosophila for studying host-pathogen interactions and identify a new mechanism by which pathogens exploit host barriers to generate brain infection.
Genomic and phenotypic heterogeneity of clinical isolates of the human pathogensAspergillus fumigatus, Aspergillus lentulusandAspergillus fumigatiaffinis
Authors: dos Santos Renato Augusto Corrêa , Steenwyk Jacob L. , Rivero-Menendez Olga , Mead Matthew E. , Silva Lilian Pereira , Bastos Rafael Wesley , Alastruey-Izquierdo Ana , Goldman Gustavo Henrique , Rokas Antonis
Published: February 2020

Fungal pathogens are a global threat to human health. For example, fungi from the genusAspergilluscause a spectrum of diseases collectively known as aspergillosis. Most of the >200,000 life-threatening aspergillosis infections per year worldwide are caused byAspergillus fumigatus. Recently, molecular typing techniques have revealed that aspergillosis can also be caused by organisms that are phenotypically similar toA. fumigatusbut genetically distinct, such asAspergillus lentulusandAspergillus fumigatiaffinis. Importantly, some of these so-called cryptic species exhibit different virulence and drug susceptibility profiles thanA. fumigatus, however, our understanding of their biology and pathogenic potential has been stymied by the lack of genome sequences and phenotypic profiling. To fill this gap, we phenotypically characterized the virulence and drug susceptibility of 15 clinical strains ofA. fumigatus, A. lentulus, andA. fumigatiaffinisfrom Spain and sequenced their genomes. We found heterogeneity in virulence and drug susceptibility across species and strains. Genes known to influence drug susceptibility (cyp51Aandfks1) vary in paralog number and sequence among these species and strains and correlate with differences in drug susceptibility. Similarly, genes known to be important for virulence inA. fumigatusshowed variability in number of paralogs across strains and across species. Characterization of the genomic similarities and differences of clinical strains ofA. lentulus, A. fumigatiaffinis, and A. fumigatusthat vary in disease-relevant traits will advance our understanding of the variance in pathogenicity betweenAspergillusspecies and strains that are collectively responsible for the vast majority of aspergillosis infections in humans.
Modeling cannabinoids from a large-scale sample ofCannabis sativachemotypes
Authors: Vergara Daniela , Gaudino Reggie , Blank Thomas , Keegan Brian
Published: February 2020

The accelerating legalization ofCannabishas opened the industry to using contemporary analytical techniques. The gene regulation and pharmacokinetics of dozens of cannabinoids remain poorly understood. Because retailers in many medical and recreational jurisdictions are required to report chemical concentrations of cannabinoids, commercial laboratories have growing chemotype datasets of diverseCannabiscultivars. Using a data set of 17,600 cultivars tested by Steep Hill Inc., we apply machine learning techniques to interpolate missing chemotype observations and cluster cultivars together based on similarity. Our results show that cultivars cluster based on their chemotype, and that some imputation methods work better than others at grouping these cultivars based on chemotypic identity. However, due to the missing data for some of the cannabinoids their behavior could not be accurately predicted. These findings have implications for characterizing complex interactions in cannabinoid biosynthesis and improving phenotypical classification ofCannabiscultivars.
In vivodiscovery of RNA proximal proteins in human cells via proximity-dependent biotinylation
Authors: Lin Xianzhi , Fonseca Marcos A. S. , Corona Rosario I. , Lawrenson Kate
Published: February 2020

RNA molecules function as messengers or noncoding adaptor molecules, structural components, and regulators of genome organization and gene expression. Their roles and regulation are mediated by other molecules they interact with, especially RNA binding proteins (RBPs). Here we report RNA proximity labeling (RPL), an RNA-centric method based on fusion of an endonuclease-deficient Type VI CRISPR-Cas protein (dCas13b) and engineered ascorbate peroxidase (APEX2) to discoverin vivotarget RNA proximal proteins (RPPs) through proximity-based biotinylation.U1RPPs enriched by proximity-based biotinylation included bothU1snRNA canonical and noncanonical functions-related proteins. In addition, profiling of poly(A) tail proximal proteins uncovered expected categories of RBPs for poly(A) tails and also provided novel evidence for poly(A)+ RNA 5’-3’ proximity and expanded subcellular localizations. Our results suggest that RPL is a rapid approach for identifying both interacting and neighboring proteins associated with target RNA molecules in their native cellular contexts.
Induced mutagenesis by the DNA cytosine deaminase APOBEC3H Haplotype I protects against lung cancer
Authors: Hix Mark A. , Wong Lai , Flath Ben , Chelico Linda , Cisneros G. Andrés
Published: February 2020

The DNA cytosine deaminases APOBEC3A, APOBEC3B, and APOBEC3H Haplotype I can induce mutations in cells that lead to cancer evolution. The database of cancer biomarkers in DNA repair genes (DNArCdb) identified a single nucleotide polymorphism (rs139298) of APOBEC3H Haplotype I that is involved in lung cancer1. Here, we show that this single nucleotide polymorphism causes the destabilization of APOBEC3H Haplotype I. Computational analysis suggests that the resulting K121E change affects the structure of APOBEC3H leading to active site disruption and destabilization of the RNA-mediated dimer interface. A K117E mutation in a K121E background stabilized the APOBEC3H Haplotype I, enabled biochemical study, and showed that the K121E affected catalytic activity, single-stranded DNA binding, and oligomerization on single-stranded DNA. That the destabilization of a DNA mutator would be associated with lung cancer suggests that too much mutation could result in immune recognition or death of tumor cells, suggesting that multiple APOBEC3s would not be expressed in the same tumor cells. In support of this hypothesis, stably expressed APOBEC3H Haplotype I caused a high amount of double-stranded DNA breaks in a lung cancer cell line that endogenously expressed APOBEC3B. Altogether, the data support the model that high APOBEC3 mutations in tumors are protective.
Video Recording Can Conveniently Assay Mosquito Locomotor Activity
Authors: da Silva Araujo Maisa , Guo Fang , Rosbash Michael
Published: February 2020

Anopheles gambiaeandAedes aegyptiare perhaps the best studied mosquito species and important carriers of human malaria and arbovirus, respectively. Mosquitoes have daily rhythms in behaviors and show a wide range of activity patterns. AlthoughAnophelesis known to be principally nocturnal andAedesprincipally diurnal, details of mosquito activity are not easily assayed in the laboratory. We recently described FlyBox, a simple tracking system for assayingDrosophilalocomotor activity rhythms and thought that it might also be applicable to monitoring mosquito activity. Indeed, we show here that FlyBox can easily, conveniently, affordably and accurately measure the activity ofAnophelesas well asAedesover several days. The resulting profiles under light-dark as well as constant darkness conditions are compatible with results in the literature, indicating that this or similar systems will be useful in the future for more detailed studies on a range of insect species and under more diverse laboratory conditions.
Host genotype and colonist arrival order jointly govern plant microbiome composition and function
Authors: Leopold Devin R. , Busby Posy E.
Published: February 2020

The composition of host-associated microbiomes can have important consequences for host health and fitness [1–3]. Yet, we still lack understanding of many fundamental processes that determine microbiome composition [4,5]. There is mounting evidence that historical contingency during microbiome assembly may overshadow more deterministic processes, such as the selective filters imposed by host traits [6–8]. More specifically, species arrival order has been frequently shown to affect microbiome composition [9–12], a phenomenon known as priority effects [13–15]. However, it is less clear whether priority effects during microbiome assembly are consequential for the host [16], or whether intraspecific variation in host traits can alter the trajectory of microbiome assembly under priority effects. In a greenhouse inoculation experiment using the black cottonwood (Populus trichocarpa) foliar microbiome, we manipulated host genotype and the colonization order of common foliar fungi. We quantified microbiome assembly outcomes using fungal marker-gene sequencing and measured susceptibility of the colonized host to a leaf rust pathogen, Melampsora × columbiana. We found that the effect of species arrival order on microbiome composition, and subsequent disease susceptibility, depended on the host genotype. Additionally, we found that microbiome assembly history can affect host disease susceptibility independent of microbiome composition at the time of pathogen exposure, suggesting that the interactive effects of species arrival order and host genotype can decouple community composition and function. Overall, these results highlight the importance of a key process underlying stochasticity in microbiome assembly while also revealing which hosts are most likely to experience these effects.
Bacterial infections in the early period after liver transplantation in adults: A prospective single‐center cohort study
Authors: Jafarpour Zahra , Pouladfar Gholamreza , Malek Hosseini Seyed Ali , Firoozifar Mohammad , Jafari Peyman
Published: February 2020

Liver transplantation (LT) is a potentially curative treatment for terminal stage hepatic diseases. Bacterial infections are the main causes of mortality and morbidity in the early period after LT. Identifying the risk factors could help in minimizing their development. We prospectively investigated the incidence, characteristics, and risk factors of bacterial infections among the recipients during hospitalization after LT and assigned a predictive score. All 389 consecutive adults who underwent LT at the main referral hospital of LT in Iran during 1 year were enrolled prospectively in a cohort study. Infection group consisted of 143 recipients (36.8%). Urinary tract and surgical site infections were the most frequent ones. Gram‐negative bacteria were more prevalent than Gram‐positive ones. Independent risk factors were female sex (relative risks = 2.13), age ≤ 43.5 years (3.70), hospital stay ≥ 9.5 days (5.22), abdominal reoperation (3.03), vancomycin‐resistant Enterococci colonization (5.52), hospitalization 3 months prior to LT (3.25), mechanical ventilation ≥48 hr (4.93), and renal replacement therapies (13.40). We developed a risk score for the prediction of bacterial infections with an area under the receiver operating characteristic curve of 0.85 (95% CI, 0.81–0.89) with sensitivity of 88% and specificity of 64%. In the infection group, mortality was higher than in controls (18.9% vs. 2.0%) with longer hospitalization (16 vs. 10 days; P < 0.001). We detected a high rate of bacterial infections leading to longer hospital stay and higher mortality rate. The formulated risk score can help predict bacterial infections; however, it requires clinical validation in further studies.
Palms and trees resist extreme drought in Amazon forests with shallow water tables
Authors: Sousa Thaiane R. , Schietti Juliana , Coelho de Souza Fernanda , Esquivel‐Muelbert Adriane , Ribeiro Igor O. , Emílio Thaise , Pequeno Pedro A. C. L. , Phillips Oliver , Costa Flavia R. C.
Published: February 2020

The intensity and frequency of severe droughts in the Amazon region have increased in the recent decades. These extreme events are associated with changes in forest dynamics, biomass and floristic composition. However, most studies of drought response have focused on upland forests with deep water tables, which may be especially sensitive to drought. Palms, which tend to dominate the less well‐drained soils, have also been neglected. The relative neglect of shallow water tables and palms is a significant concern for our understanding of tropical drought impacts, especially as one‐third of Amazon forests grow on shallow water tables (<5 m deep).

We evaluated the drought response of palms and trees in forests distributed over a 600 km transect in central‐southern Amazonia, where the landscape is dominated by shallow water table forests (SWTF). We compared vegetation dynamics before and following the 2015–2016 El Nino drought, the hottest and driest on record for the region (−214 mm of cumulative water deficit).

We observed no change in stand mortality rates and no biomass loss in response to drought in these forests. Instead, we observed an increase in recruitment rates, which doubled to 6.78% year‐1 ± 4.40 (M ± SD) during 2015–2016 for palms and increased by half for trees (to 2.92% year‐1 ± 1.21), compared to rates in the pre‐El‐Nino interval. Within these SWTF, mortality and recruitment rates varied as a function of climatic drought intensity and water table depth for both palms and trees, with mortality being greatest in climatically and hydrologically wetter environments and recruitment greatest in drier environments. Across our transect, there was a significant increase over time in tree biomass.

Synthesis. Our results indicate that forests growing over shallow water tables—relatively under‐studied vegetation that nonetheless occupies one‐third of Amazon forests—are remarkably resistant to drought. These findings are consistent with the hypothesis that local hydrology and its interactions with climate strongly constrain forest drought effects, and has implications for climate change feedbacks. This work enhances our understanding of integrated drought effects on tropical forest dynamics and highlights the importance of incorporating neglected forest types into both the modelling of forest climate responses and into public decisions about priorities for conservation.
Back to Stormont: The New Decade, New Approach Agreement and What it Means for Northern Ireland
Authors: Haughey Sean
Published: February 2020

The decision of the Democratic Unionist Party and Sinn Féin to once again share power in Northern Ireland has ended a three‐year hiatus in the region’s devolved government. The deal which resurrects the devolved institutions—New Decade, New Approach—is not short of ambition. It introduces significant institutional reforms which place the institutions on a more sustainable footing and limit the potential for abuse of the Assembly’s infamous Petition of Concern. Nettles have been grasped on issues to do with language, culture, and identity that have long vexed political parties in Northern Ireland. Tucked away in the deal’s appendices are commitments to implement outstanding pledges made in previous agreements, plus ambitious plans for the new Northern Ireland Executive. However, as parties in the region were quick to discover, aspects of this deal are easier said than done. This article considers what New Decade, New Approach promises and, if fully implemented, what its implications are for politics and governance in Northern Ireland.
Making Plans for Michael: providing for a student with moderate learning difficulties in a secondary academy
Authors: Mays Dennis
Published: February 2020

The profile of a student with learning difficulties is described and also the learning context in 2017. Previous models of provision are then described in terms of their aetiology with discussion of strengths and shortcomings. Some influential features of curriculum planning and delivery are identified. A model of provision involving specific literacy teaching and differentiation is advocated.
New insights in cerebral findings associated with fetal myelomeningocele: a retrospective cohort study in a single tertiary centre
Authors: Maurice P , Garel J , Garel C , Dhombres F , Friszer S , Guilbaud L , Maisonneuve E , Ducou Le Pointe H , Blondiaux E , Jouannic J‐M
Published: February 2020

Objective

To investigate cerebral anomalies other than Chiari type 2 malformation in fetuses with myelomeningocele (MMC).

Design

A retrospective cohort study in a single tertiary centre.

Setting

A review of associated cerebral anomalies in cases with prenatal diagnosis of myelomeningocele.

Population

Seventy cases of fetal myelomeningocele.

Methods

Ultrasound and MRI images were blindly reviewed. Postnatal imaging and results of the postmortem results were also reviewed. The association between cerebral anomalies and the following ultrasound findings was measured: level of the defect, ventriculomegaly, microcephaly and fetal talipes.

Main outcome measures

A microcephaly was observed in 32/70 cases (46%) and a ventriculomegaly was observed in 39/70 cases (56%). Other cerebral anomalies were diagnosed in 47/70 (67%).

Results

Other cerebral anomalies were represented by 42/70 cases with abnormal CC (60%), 8/70 cases with perinodular heterotopia (PNH; 11%), 2/70 cases with abnormal gyration (3%). MRI performed only in fetal surgery cases confirmed the ulltrasound findings in all cases and provided additional findings in two cases (PNH). Risk ratios of fetal cerebral anomalies associated with MMC did not reach significance for microcephaly, ventriculomegaly, talipes or the level of the defect There was an overall good correlation between pre‐ and postnatal findings with a Kappa value of 0.79 [95% CI 0.57–1] and 82% agreement.

Conclusion

Fetal brain anomalies other than Chiari type 2 malformation are frequently observed in fetuses with myelomeningocele, predominantly represented by CC anomalies. Whether these associated cerebral anomalies have an impact on selecting cases eligible for fetal surgery needs further evaluation.

Tweetable abstract

Fetal cerebral anomalies other than Chiari type 2 malformation, microcephaly, and ventriculomegaly may be associated with MMC in up to 67% of the cases.
Ultrasonic pretreatment improved the antioxidant potential of enzymatic protein hydrolysates from highland barley brewer's spent grain (BSG)
Authors: Ikram Sana , Zhang Huijuan , Ahmed Muhammad Saad , Wang Jing
Published: February 2020

Highland barley brewer's spent grain (BSG), being China's brewing industry's major by‐product is the focus of current research. The aim of the present study was to scrutinize the effects of ultrasound and heat pretreatments on enzymatic hydrolysis of highland barley BSG protein hydrolysates (HBSGPH) and evaluate the effect of enzymatic hydrolysis time on the antioxidant activity of hydrolysates by Alcalase. Different ultrasonic waves (40 and 50 kHz) and heat pretreatment temperatures (50 and 100 °C) were chosen and the pretreatment time was 15, 30, and 60 min. The obtained results revealed that the ultrasound pretreatment of highland barley BSG protein at 40 and 50 kHz has significantly (P < 0.05) enhanced about 57 and 67% of oxygen radical absorption capacity of obtained hydrolysate over the untreated substrate. The 1,1‐diphenyl‐2‐picrylhdrazl (DPPH) radical scavenging activity (DRSA) 28%, metal chelating activity (MCA) 54%, superoxide radical scavenging activity (SRSA) 18%, and hydroxyl radical scavenging activity (HRSA) 25% of HBSGPH at 50 kHz were also improved (P < 0.05) significantly. HBSGPH from heat treatment at 100 °C showed no SRSA and HRSA scavenging activities but improved significantly (P < 0.05) about 27% ferric reducing antioxidant power (FRAP) assay values. In the present work, the resultant HBSGPH had stronger antioxidant properties with ultrasound pretreatment at 50 kHz and the enzymatic hydrolysis after 4 hr was facilitating the enzymatic release of antioxidant peptides from HBSGPH.

Practical Application

Highland barley BSG is attracting toward natural food products due to its potent natural antioxidants to overcome the risk of diseases and are beneficial for human health.
Lifespan of long‐lived growth hormone receptor knockout mice was not normalized by housing at 30°C since weaning
Authors: Fang Yimin , McFadden Samuel , Darcy Justin , Hascup Erin R. , Hascup Kevin N. , Bartke Andrzej
Published: February 2020

Growth hormone receptor knockout (GHRKO) mice are remarkably long‐lived and have improved glucose homeostasis along with altered energy metabolism which manifests through decreased respiratory quotient (RQ) and increased oxygen consumption (VO2). Short‐term exposure of these animals to increased environmental temperature (eT) at 30°C can normalize their VO2 and RQ. We hypothesized that increased heat loss in the diminutive GHRKO mice housed at 23°C and the consequent metabolic adjustments to meet the increased energy demand for thermogenesis may promote extension of longevity, and preventing these adjustments by chronic exposure to increased eT will reduce or eliminate their longevity advantage. To test these hypotheses, GHRKO mice were housed at increased eT (30°C) since weaning. Here, we report that contrasting with the effects of short‐term exposure of adult GHRKO mice to 30°C, transferring juvenile GHRKO mice to chronic housing at 30°C did not normalize the examined parameters of energy metabolism and glucose homeostasis. Moreover, despite decreased expression levels of thermogenic genes in brown adipose tissue (BAT) and elevated core body temperature, the lifespan of male GHRKO mice was not reduced, while the lifespan of female GHRKO mice was increased, along with improved glucose homeostasis. The results indicate that GHRKO mice have intrinsic features that help maintain their delayed, healthy aging, and extended longevity at both 23°C and 30°C.
Can multitasking influence professional scepticism?
Authors: Fehrenbacher Dennis D. , Triki Anis , Weisner Martin Michael
Published: February 2020

Motivated by concerns about the adverse effects of multitasking in audit practice and research that highlights the effects of mindset orientation on professional scepticism, we investigate how the performance of tasks consistent with different mindset orientations affects auditors’ professional scepticism in a subsequent, unrelated task. Results show that auditors who first complete a task that requires concrete (abstract) thinking display greater professional scepticism during a subsequent, unrelated task that involves evaluating a narrow and complete set of evidence (a broad and incomplete set of evidence). We discuss the implications for professional scepticism in multitasking environments.