bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of REM Sleep Behavior Disorder by Magnetic Resonance Imaging and Machine Learning
Authors: Mei Jie , Rahayel Shady , Desrosiers Christian , Postuma Ronald B. , Montplaisir Jacques , Carrier Julie , Monchi Oury , Frasnelli Johannes , Gagnon Jean-François
Published: September 2021

Background

Idiopathic rapid eye movement sleep behavior disorder (iRBD) is a major risk factor for synucleinopathies, and patients often present with clinical signs and morphological brain changes. However, there is a heterogeneity in the presentation and progression of these alterations, and brain regions that are more vulnerable to neurodegeneration remain to be determined.

Objectives

To assess the feasibility of morphology-based machine learning in the identification and subtyping of iRBD.

Methods

For the classification tasks [iRBD (n=48) vs controls (n=41); iRBD vs Parkinson’s disease (n=29); iRBD with mild cognitive impairment (n=16) vs without mild cognitive impairment (n=32)], machine learning models were trained with morphometric measurements (thickness, surface area, volume, and deformation) extracted from T1-weighted structural magnetic resonance imaging. Model performance and the most discriminative brain regions were analyzed and identified.

Results

A high accuracy was reported for iRBD vs controls (79.6%, deformation of the caudal middle frontal gyrus and putamen, thinning of the superior frontal gyrus, and reduced volume of the inferior parietal cortex and insula), iRBD vs Parkinson’s disease (82%, smaller volume and surface area of the insula, lower thinning of the entorhinal cortex and lingual gyrus, and greater volume of the fusiform gyrus), and iRBD with vs without mild cognitive impairment (84.8%, thinning of the pars triangularis, superior temporal gyrus, transverse temporal cortex, larger surface area of the superior temporal gyrus, and deformation of isthmus of the cingulate gyrus).

Conclusions

Morphology-based machine learning approaches may allow for detection and subtyping of iRBD, potentially enabling efficient preclinical identification of synucleinopathies.
Novel protein-altering variants associated with serum apolipoprotein and lipid levels
Authors: Sandholm Niina , Hotakainen Ronja , Haukka Jani K , Sigfrids Fanny Jansson , Dahlström Emma H , Antikainen Anni , Valo Erkka , Syreeni Anna , Kilpeläinen Elina , Kytölä Anastasia , Palotie Aarno , Harjutsalo Valma , Forsblom Carol , Groop Per-Henrik
Published: September 2021

Dyslipidemia is a major risk factor for cardiovascular disease. While common genetic variants are known to modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesteremia and other genetic disorders of lipid metabolism. Aiming to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits, we analyzed whole-exome and whole-genome sequencing data of 481 and 573 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 97 serum lipid, apolipoprotein, or other metabolic phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance (NMR) technology. Single variant analysis identified a novel association between LIPC p.Thr405Met (rs113298164) and serum apolipoprotein-A1 levels (p=7.8×10−8). In the APOB gene, we identified novel associations at two protein-truncating variants (PTVs) resulting in lower serum apolipoprotein B levels (p=5.6×10−4). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5, and GTF3C5 (p<2.9×10−6). The RBM47 gene is required for apolipoprotein-B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III levels was led by a rare 21 base pair Ala496-Ala502 deletion; as replication, the burden of rare deleterious variants in RBM47 was associated with TG-to-HDLC ratio in WES of 20,917 individuals (p=0.0093). Two PAVs in GTF3C5 were highly Finnish-enriched and associated with cardiovascular phenotypes in external data, whereby the TRMT5 p.Ser185Cys lead variant was associated with stroke phenotypes. Altogether, we identified both novel variant associations in known lipid genes, as well as novel genes implicated in lipoprotein metabolism.
RNA-extraction-free diagnostic method to detect SARS-CoV-2: an assessment from two States, India
Authors: Jayaprakasam Madhumathi , Aggarwal Sumit , Mane Arati , Saxena Vandana , Rao Amrita , Bandopadhyay Bhaswati , Chakraborty Banya , Guha Subhasish Kamal , Taraphdar Mekhala , Acharya Alisha , Gupta Bishal , Deb Sonia , Chowdhury Aparna , Singh Kh Jitenkumar , Tapase Prashant , Pandey Ravindra M , Bhargava Balram , Panda Samiran
Published: September 2021

With increasing demand for large numbers of testing during COVID-19 pandemic, came alternative protocols with shortened turn-around time. We evaluated the performance of such an approach wherein 1138 consecutive clinic attendees were enrolled; 584 and 554 respectively from two independent study sites in the cities of Pune and Kolkata. Paired nasopharyngeal and oropharyngeal swabs were tested by using both reference and index methods in blinded fashion. Prior to conducting RT-PCR, swabs collected in viral transport medium (VTM) were processed for RNA extraction (reference method) and swabs collected in dry tube without VTM were incubated in Tris-EDTA-Proteinase K buffer for 30 minutes and heat inactivated at 98°C for 6 minutes (index method). Overall sensitivity and specificity of the index method were 78.9% (95% CI 71% to 86%) and 99 % (95% CI 98% to 99.6%) respectively. Agreement between the index and reference method was 96.8 % (k = 0.83, SE=0.030). The reference method exhibited enhanced detection of viral genes (E, N and RdRP) with lower Ct values compared to the index method. The index method can be used for detecting SARS-CoV-2 infection with appropriately chosen primer-probe set and heat treatment approach in pressing time; low sensitivity constrains its potential wider use.
Role of Lateral Inhibition on Visual Number Sense
Authors: Zhou Yiwei , Chen Huanwen , Wang Yijun
Published: September 2021

Lateral inhibition is a basic principle of information processing and widely exists in the human and animal nervous systems. Lateral inhibition is also involved in processing visual information because it travels through the retina, primary visual cortex, and visual nervous system. This finding suggests that lateral inhibition is associated with visual number sense in humans and animals. Here, we show a number-sensing neural network model based on lateral inhibition. The model can reproduce the size and distance effects of the output response of human and animal number-sensing neurons when the network connection weights are set randomly without adjustment. The number sense of the model disappears when lateral inhibition is removed. Our study shows that the first effect of lateral inhibition is to strengthen the linear correlation between the total response intensity of the input layer and the number of objects. The second one is to allow the output cells to prefer different numbers. Results indicate that lateral inhibition plays an indispensable role in untrained spontaneous number sense.
Genomic Heritability: A Ragged Diagonal Between Bias and Variance
Authors: Feldmann Mitchell J. , Piepho Hans-Peter , Knapp Steven J.
Published: September 2021

Many important traits in plants, animals, and microbes are polygenic and are therefore difficult to improve through traditional marker-assisted selection. Genomic prediction addresses this by enabling the inclusion of all genetic data in a mixed model framework. The main method for predicting breeding values is genomic best linear unbiased prediction (GBLUP), which uses the realized genomic relationship or kinship matrix (K) to connect genotype to phenotype. The use of relationship matrices allows information to be shared for estimating the genetic values for observed entries and predicting genetic values for unobserved entries. One of the key parameters of such models is genomic heritability, or the variance of a trait associated with a genome-wide sample of DNA polymorphisms. Here we discuss the relationship between several common methods for calculating the genomic relationship matrix and propose a new matrix based on the average semivariance that yields accurate estimates of genomic variance in the observed population regardless of the focal population quality as well as accurate breeding value predictions in unobserved samples. Notably, our proposed method is highly similar to the approach presented by Legarra (2016) despite different mathematical derivations and statistical perspectives and only deviates from the classic approach presented in VanRaden (2008) by a scaling factor. With current approaches, we found that the genomic heritability tends to be either over- or underestimated depending on the scaling and centering applied to the marker matrix (Z), the value of the average diagonal element ofK, and the assortment of alleles and heterozygosity (H) in the observed population and that, unlike its predecessors, our newly proposed kinship matrixKASVyields accurate estimates ofin the observed population, generalizes to larger populations, and produces BLUPs equivalent to common methods in plants and animals.
Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT
Authors: Moksnes Marta R , Hansen Ailin Falkmo , Graham Sarah E , Gagliano Taliun Sarah A , Wu Kuan-Han , Zhou Wei , Thorstensen Ketil , Fritsche Lars G , Gill Dipender , Mason Amy , Cucca Francesco , Schlessinger David , Abecasis Gonçalo R. , Burgess Stephen , Åsvold Bjørn Olav , Nielsen Jonas B , Hveem Kristian , Willer Cristen J , Brumpton Ben M
Published: September 2021

Iron is essential for many biological processes, but iron levels must be tightly regulated to avoid harmful effects of both iron deficiency and overload. Here, we perform genome-wide association studies on four iron related biomarkers (serum iron, serum ferritin, transferrin saturation, total iron binding capacity) in the Trøndelag Health Study (HUNT), the Michigan Genomics Initiative (MGI) and the SardiNIA study, followed by their meta-analysis with publicly available summary statistics, analyzing up to 257 953 individuals. We identify 127 genetic loci associated with iron traits. Among 19 novel protein-altering variants, we observe a rare missense variant (rs367731784) in HUNT, which suggests a role for DNAJC13 in transferrin recycling. We further validate the latest genetic risk scores for each biomarker in HUNT (6% variance in serum iron explained) and present linear and non-linear Mendelian randomization analyses of the traits on all-cause mortality. We find evidence of a harmful effect of increased serum iron and transferrin saturation in linear analyses that estimate population-averaged effects. However, there was weak evidence of a protective effect of increasing serum iron at the very low end of its distribution. Our findings contribute to our understanding of the genes affecting iron status and its consequences on human health.
Effects of myopia and glaucoma in the prelaminar neural canal and anterior lamina cribrosa using 1060-nm swept-source optical coherence tomography
Authors: Lee Sieun , Heisler Morgan , Ratra Dhanashree , Ratra Vineet , Mackenzie Paul J , Sarunic Marinko V , Beg Mirza Faisal
Published: September 2021

Purpose

Investigate the effects of myopia and glaucoma in the prelaminar neural canal and anterior lamina cribrosa using 1060-nm swept-source optical coherence tomography

Design

Retrospective, cross-sectional study

Methods

Setting

Clinical practice

Patient or study population

19 controls (38 eyes); 38 glaucomatous subjects (63 eyes). Inclusion criteria for glaucomatous subjects: i) optic disc neural rim loss; ii) peripapillary nerve fibre layer (NFL) loss on spectral domain optical coherence tomography (SD-OCT); iii) glaucomatous visual field defect with an abnormal pattern standard deviation (P<.05); iv) stable SD-OCT, visual field, and optic disc clinical examination for 6 or more months. Inclusion criteria for control subjects: no evidence of retinal or optic nerve pathology. Exclusion criteria: i) retinal diseases or optic neuropathy other than primary open-angle glaucoma; ii) intraocular pressure less than 10 mmHg or higher than 20 mmHg; iii) ocular media opacities; iv) any surgery-related complication deemed inappropriate for the study.

Intervention or observation procedures

Swept-source optical coherence tomography

Main Outcome Measure(s)

Bruchs membrane opening (BMO) and anterior laminar insertion (ALI) dimension, prelaminar neural canal dimension, anterior lamina cribrosa surface (ALCS) depth

Results

Glaucomatous eyes had more bowed and nasally rotated BMO and ALI, more horizontally skewed prelaminar neural canal, and deeper ALCS than the control eyes. Increased axial length was associated with a wider, longer, and more horizontally skewed neural canal, and decrease in the ALCS depth and curvature.

Conclusion

Our findings suggest that glaucomatous posterior bowing or cupping of lamina cribrosa can be significantly confounded by the myopic expansion of the neural canal. This may be related to higher glaucoma risk associated with myopia from decreased compliance and increased susceptibility to IOP-related damage of LC being pulled taut.
Anti-Bat Ultrasound Production in Moths is Globally and Phylogenetically Widespread
Authors: Barber JR , Plotkin D , Rubin JJ , Homziak NT , Leavell BC , Houlihan P , Miner KA , Breinholt JW , Quirk-Royal B , Padrón PS , Nunez M , Kawahara AY
Published: September 2021

Warning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and outline anti-bat ultrasound production in 52 genera, with eight new subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are theraison d’etrefor sound production in most moths. However, some moths use high-density ultrasound capable of jamming bat sonar. In fact, we find preliminary evidence of independent origins of sonar jamming in at least six subfamilies. Palatability data indicates that jamming and warning are not mutually exclusive strategies. To explore the possible organization of anti-bat warning sounds into acoustic mimicry rings, we intensively studied a community of moths in Ecuador and found five distinct acoustic clusters using machine learning algorithms. While these data represent an early understanding of acoustic aposematism and mimicry across this megadiverse insect order, it is likely that ultrasonically-signaling moths comprise one of the largest mimicry complexes on earth.
Human primitive mesenchymal stem cell-derived retinal progenitor cells promoted neuroprotection and neurogenesis in rd12 mice
Authors: Brown Christina , Agosta Patrina , McKee Christina , Walker Keegan , Mazzella Matteo , Svinarich David , Chaudhry G. Rasul
Published: September 2021

Retinal degenerative diseases (RDD) such as retinitis pigmentosa (RP) have no treatment. Stem cell-based therapies could provide promising opportunities to repair the damaged retina and restore vision. We investigated a novel approach in which human retinal progenitor cells (RPCs) derived from primitive mesenchymal stem cells (pMSCs) were examined to treat retinal degeneration in an rd12 mouse model of RP. Intravitreally transplanted cells improved retinal function and significantly increased retinal thickness. Transplanted cells homed, survived, and integrated to various retinal layers. They also induced anti-inflammatory and neuroprotective responses and upregulated neurogenesis genes. We found that RPCs were more efficacious than pMSCs in improving the retinal structure and function. RNA analyses suggest that RPCs promote neuroprotection and neuronal differentiation by activating JAK/STAT and MAPK, and inhibiting BMP signaling pathways. These promising results provide the basis for clinical studies to treat RDD using RPCs derived from pMSCs.
Lung epithelial CYP1 activity regulates aryl hydrocarbon receptor dependent allergic airway inflammation
Authors: Alessandrini Francesca , de Jong Renske , Wimmer Maria , Maier Ann-Marie , Fernandez Isis , Hils Miriam , Buters Jeroen T. , Biedermann Tilo , Zissler Ulrich , Hoffmann Christian , Esser-von-Bieren Julia , Schmidt-Weber Carsten B. , Ohnmacht Caspar
Published: September 2021

The lung epithelial barrier serves as a guardian towards environmental insults and responds to allergen encounter with a cascade of immune reactions that can possibly lead to inflammation. Whether the environmental sensor aryl hydrocarbon receptor (AhR) together with its downstream targets cytochrome P450 (CYP1) family members contribute to the regulation of allergic airway inflammation remains unexplored. By employing knockout mice for AhR and for single CYP1 family members, we found that AhR-/- and CYP1B1-/- but not CYP1A1-/- or CYP1A2-/- animals display enhanced allergic airway inflammation compared to WT. Expression analysis, immunofluorescence staining of murine and human lung sections and bone marrow chimeras suggest an important role of CYP1B1 in non-hematopoietic lung epithelial cells to prevent exacerbation of allergic airway inflammation. Transcriptional analysis of murine and human lung epithelial cells indicates a functional link of AhR to barrier protection/inflammatory mediator signaling upon allergen challenge. In contrast, CYP1B1 deficiency leads to enhanced expression and activity of CYP1A1 in lung epithelial cells and to an increased availability of the AhR ligand kynurenic acid following allergen challenge. Thus, differential CYP1 family member expression and signaling via the AhR in epithelial cells represents an immunoregulatory layer protecting the lung from exacerbation of allergic airway inflammation.
The anterior paired lateral neuron normalizes odour-evoked activity at the mushroom body calyx
Authors: Prisco Luigi , Deimel Stephan Hubertus , Yeliseyeva Hanna , Fiala André , Tavosanis Gaia
Published: September 2021

To identify and memorize discrete but similar environmental inputs, the brain needs to distinguish between subtle differences of activity patterns in defined neuronal populations. The Kenyon cells of the Drosophila adult mushroom body (MB) respond sparsely to complex olfactory input, a property that is thought to support stimuli discrimination in the MB. To understand how this property emerges, we investigated the role of the inhibitory anterior paired lateral neuron (APL) in the input circuit of the MB, the calyx. Within the calyx, presynaptic boutons of projection neurons (PNs) form large synaptic microglomeruli (MGs) with dendrites of postsynaptic Kenyon cells (KCs). Combining EM data analysis and in vivo calcium imaging, we show that APL, via inhibitory and reciprocal synapses targeting both PN boutons and KC dendrites, normalizes odour-evoked representations in MGs of the calyx. APL response scales with the PN input strength and is regionalized around PN input distribution. Our data indicate that the formation of a sparse code by the Kenyon cells requires APL-driven normalization of their MG postsynaptic responses. This work provides experimental insights on how inhibition shapes sensory information representation in a higher brain centre, thereby supporting stimuli discrimination and allowing for efficient associative memory formation.
DeNovoCNN: A deep learning approach to de novo variant calling in next generation sequencing data
Authors: Khazeeva Gelana , Sablauskas Karolis , van der Sanden Bart , Steyaert Wouter , Kwint Michael , Rots Dmitrijs , Hinne Max , van Gerven Marcel , Yntema Helger , Vissers Lisenka , Gilissen Christian
Published: September 2021

De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major challenge due to sequence errors, uneven coverage, and mapping artifacts. Here, we developed a deep convolutional neural network (CNN) DNM caller (DeNovoCNN), that encodes the alignment of sequence reads for a trio as 160×164 resolution images. DeNovoCNN was trained on DNMs of 5,616 whole exome sequencing (WES) trios achieving total 96.74% recall and 96.55% precision on the test dataset. We find that DeNovoCNN has increased recall/sensitivity and precision compared to existing DNM calling approaches (GATK, DeNovoGear, DeepTrio, Samtools) based on the Genome in a Bottle reference dataset and independent WES and WGS trios. Validations of DNMs based on Sanger and PacBio HiFi sequencing confirm that DeNovoCNN outperforms existing methods. Most importantly, our results suggest that DeNovoCNN is likely robust against different exome sequencing and analyses approaches, thereby allowing the application on other datasets. DeNovoCNN is freely available as a Docker container and can be run on existing alignment (BAM/CRAM) and variant calling (VCF) files from WES and WGS without a need for variant recalling.
Single-cell genetic heterogeneity linked to immune infiltration in glioblastoma
Authors: Walentynowicz Kacper A. , Engelhardt Dalit , Yadav Shreya , Onubogu Ugoma , Salatino Roberto , Vincentelli Cristina , McDonald Thomas O. , Michor Franziska , Janiszewska Michalina
Published: September 2021

Glioblastoma (GBM) is the most aggressive brain tumor with a median survival of ~15 months. Targeted approaches have not been successful in this tumor type due to the large extent of intratumor heterogeneity. Mosaic amplification of oncogenes suggests that multiple genetically distinct clones are present in each tumor. To uncover the relationships between genetically diverse subpopulations of GBM cells and their native tumor microenvironment, we employed highly multiplexed spatial protein profiling, coupled with single-cell spatial mapping of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA. Single-cell FISH analysis of a total of 35,843 single nuclei (~2,100 per tumor) revealed that tumors in which amplifications of EGFR and CDK4 more frequently co-occur in the same cell exhibit higher infiltration of CD163+ immunosuppressive macrophages. Our results suggest that high throughput assessment of genomic alterations at the single cell level could provide a measure for predicting the immune state of GBM.
Bayesian hierarchical models can infer interpretable predictions of leaf area index from heterogeneous datasets
Authors: Stojanović Olivera , Siegmann Bastian , Jarmer Thomas , Pipa Gordon , Leugering Johannes
Published: September 2021

Environmental scientists often have to predict a complex phenomenon from a heterogeneous collection of datasets. This is particularly challenging if there are systematic differences between them, as is often the case. Accounting for these differences requires a larger number of parameters and thus increases the risk of overfitting. We investigate how Bayesian hierarchical models can help mitigate this problem by allowing the practitioner to explicitly incorporate information about the dataset structure and general domain knowledge. To this end, we look at a typical application in remote sensing: the estimation of leaf area index (of white winter wheat), an important indicator for agronomical modeling, from measurements of reflectance spectra collected at different locations and growth stages. Since the insights gained from such a model could be used to inform policy or business decisions, the interpretability of the model is a primary concern. We, therefore, focus on models that capture the association between leaf area index and the spectral reflectance at various wavelengths by spline-based kernel functions, which can be visually inspected and analyzed. We compare models with three different levels of hierarchy: a non-hierarchical baseline model, a model with hierarchical bias parameter, and a model in which bias and kernel parameters are hierarchically structured. We analyze them using Markov Chain Monte Carlo sampling diagnostics and an intervention-based measure of feature importance. The improved robustness and interpretability of this approach lead us to recommend Bayesian hierarchical models as a versatile tool for environmental sciences and beyond, particularly in scenarios where the available data sources are heterogeneous.
Characteristics and mechanism of reciprocal ST-segment depression in acute ST segment elevation myocardial infarction
Authors: Gao Qijun , Bie Fangfang , Hu Yinfu , Chen Yafeng , Yang Bo
Published: September 2021

Background

At present, the mechanism of reciprocal ST-segment depression(RSTD) is still not clear.

Methods

The electrocardiogram and angiography of 85 STEMI patients were retrospectively analyzed to summarize the characteristics of ST segment changes and explore the mechanism of RSTD.

Results

A total of 85 patients were included, of which 75 were patients with RSTD (10 patients with anterior myocardial infarction had no RSTD), all 45 patients with inferior myocardial infarction had limb leads RSTD, and 37 of them had anterior lead ST segment depression.Thirty patients with anterior myocardial infarction were accompanied by mild ST segment changes in the limb leads. According to the characteristics of RSTD, it is speculated that the mechanism of RSTD is that the action potential of infarct area decreased, which could not offset the action potential in non-infarct area.

Conclusion

the mechanism of RSTD in acute myocardial infarction maybe that the negative electrode action potential of the lead was weakened or disappeared, and the positive electrode action potential could not be completely offset, resulting in ST segment depression.
A Purkinje cell to parabrachial nucleus pathway enables broad cerebellar influence over the forebrain
Authors: Chen Christopher H. , Newman Leannah N. , Stark Amanda P. , Bond Katherine E. , Zhang Dawei , Nardone Stefano , Vanderburg Charles R. , Nadaf Naeem M. , Yao Zhiyi , Mutume Kefiloe , Flaquer Isabella , Lowell Bradford B. , Macosko Evan Z. , Regehr Wade G.
Published: September 2021

In addition to its well-known contributions to motor function, the cerebellum is involved in emotional regulation, anxiety, and affect1-4. We found that suppressing the firing of cerebellar Purkinje cells (PCs) rapidly excites forebrain areas that could contribute to such functions (including the amygdala, basal forebrain, and septum), but that the classic cerebellar outputs, the deep cerebellar nuclei (DCN), do not project to these forebrain regions. Here we show that PCs directly inhibit parabrachial nuclei (PBN) neurons that project to and influence numerous forebrain regions in a manner distinct from the DCN pathway. We also found that the PBN and DCN output pathways differentially influence behavior: suppressing the PC to PBN pathway is aversive and does not affect the speed of movement, whereas suppressing the PC to DCN pathway is not aversive and reduces speed. Molecular profiling shows that PCs inhibit numerous types of PBN neurons that control diverse nonmotor behaviors5-9. Therefore, the PBN pathway allows the cerebellum to regulate activity in many forebrain regions and may be an important substrate for nonmotor disorders related to cerebellar dysfunction.
Ion currents through Kir potassium channels are gated by anionic lipids
Authors: Jin Ruitao , He Sitong , Black Katrina A. , Clarke Oliver B. , Wu Di , Bolla Jani R. , Johnson Paul , Periasamy Agalya , Wardak Ahmad , Czabotar Peter , Colman Peter M. , Robinson Carol V. , Laver Derek , Smith Brian J. , Gulbis Jacqueline M.
Published: September 2021

Ion currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook ‘gate’ of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present the first evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this ‘gate’ is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.
Unidirectional ion transport mechanism of a light-driven chloride pump revealed using X-ray free electron lasers
Authors: Hosaka Toshiaki , Nomura Takashi , Kubo Minoru , Nakane Takanori , Fangjia Luo , Sekine Shun-ichi , Ito Takuhiro , Murayama Kazutaka , Ihara Kentaro , Ehara Haruhiko , Kashiwagi Kazuhiro , Katsura Kazushige , Akasaka Ryogo , Hisano Tamao , Tanaka Tomoyuki , Tanaka Rie , Arima Toshi , Yamashita Ayumi , Sugahara Michihiro , Naitow Hisashi , Matsuura Yoshinori , Yoshizawa Susumu , Tono Kensuke , Owada Shigeki , Nureki Osamu , Kimura-Someya Tomomi , Iwata So , Nango Eriko , Shirouzu Mikako
Published: September 2021

Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data ofNonlabens marinusrhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10 μs and 1 ms time-points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied with a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.

Significance

Light-driven chloride pumps have been identified in various species, including archaea and marine flavobacteria. The function of ion transportation controllable by light is utilized for optogenetics tools in neuroscience. Chloride pumps differ among species, in terms of amino acid homology and structural similarity. Our time-resolved crystallographic studies using X-ray free electron lasers reveal the molecular mechanism of halide ion transfer in a light-driven chloride pump from a marine flavobacterium. Our data indicate a common mechanism in chloride pumping rhodopsins, as compared to previous low temperature trapping studies of chloride pumps. These findings are significant not only for further improvements of optogenetic tools but also for a general understanding of the ion pumping mechanisms of microbial rhodopsins.
High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma
Authors: Callahan S. Carson , Kochat Veena , Liu Zhiyi , Raman Ayush T , Schulz Jonathan , Terranova Christopher , Divenko Margarita , Ghosh Archit , Tang Ming , Pickering Curtis , Myers Jeffrey N. , Rai Kunal
Published: September 2021

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant morbidity and mortality and frequent recurrence. Pre-NGS efforts to transcriptionally classify HNSCC into groups of varying prognosis have identified four accepted molecular subtypes of disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigated the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identified samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to atypical subtype were more resistant to bromodomain inhibitors (BETi). PRO-Seq experiments that both TCGA tumors and AT cell lines showed higher eRNA transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, HiChIP experiments suggested higher enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways were upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with high enhancer activity, resistance to BET inhibition, and signaling pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.
KMT2D Loss Promotes Head and Neck Squamous Carcinoma Through Enhancer Reprogramming and Modulation of Immune Microenvironment
Authors: Callahan S. Carson , Divenko Margarita , Barrodia Praveen , Singh Anand K , Arslan Emre , Liu Zhiyi , Yang Jiah , Anvar Nazanin , Amit Moran , Xie Tongxin , Jiang Shan , Schulz Jonathan , Tang Ming , Myers Jeffrey N , Rai Kunal
Published: September 2021

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with 5-year survival of ∼50%. Genomic profiling studies have identified important somatic mutations in this disease which presents an opportunity for precision medicine. We demonstrate that KMT2D, a histone methyltransferase harbors somatic mutations in ∼17% of HNSCC and is associated with 2-year recurrence in TCGA data. Consistent with algorithmic prediction of bring a driver tumor-suppressor event, its loss results in larger oral tumors in immune-proficient orthotopic models. Mechanistically, we find that KMT2D knockdown or KMT2D mutation causes loss of H3K4me1-marked enhancers harboring IRF7/9 binding sites, which is known to regulate interferon signaling. Indeed, KMT2D loss in human and murine cell lines deregulated transcriptional levels of cytokine expression and impacted numerous immune signaling pathways, including interferon signaling. Consistently, Kmt2d knockdown in murine tumors exhibited decrease in IFNγ-producing effector T cells and an increase in T-cells with an exhausted phenotype. Epistasis experiments showed that exogenous treatment with IFNγ abrogated the increased tumor growth in Kmt2d-deficient oral tumors. Together, these results support the role of KMT2D as a tumor suppressor in HNSCC that regulates the tumor microenvironment by modulating H3K4me1-marked enhancers controlling interferon signaling.
Stimulant Use Interventions May Strengthen ‘Getting to Zero’ Initiatives in Illinois: Insights from a Modeling Study
Authors: Lee Francis , Sheeler Daniel , Hotton Anna , Del Vecchio Natascha , Flores Rey , Fujimoto Kayo , Harawa Nina , Schneider John A. , Khanna Aditya S.
Published: September 2021

Objective(s)

Young Black men who have sex with men (YBMSM) are a key population identified in the Illinois Getting to Zero (GTZ) initiative who have experienced disproportionate HIV incidence. Rising stimulant use has been determined to impede the effectiveness of ART and pre-exposure prophylaxis for suppressing HIV transmission in populations. This modeling study explores the impact of stimulant use on HIV incidence among YBMSM – given the limited development of dedicated or culturally appropriate interventions for this population – and assesses the impact of these interventions on downstream HIV transmission in the context of achieving GTZ goals.

Methods

A previously developed agent-based network model (ABNM), calibrated using data for YBMSM in Illinois, was extended to incorporate the impact of stimulant use (methamphetamines, crack/cocaine, and ecstasy) on sexual networks and engagement in HIV treatment and prevention continua. The model simulated the impact of a residential behavioral intervention (BI) for reducing stimulant dependency and an outpatient biomedical intervention (mirtazapine) for treating methamphetamine dependence on improved engagement in the HIV treatment and prevention continua. The downstream impact of these interventions on population-level HIV incidence was the primary intervention outcome.

Results

Baseline simulated annual HIV incidence in the ABNM was 6.9(95% CI: 6.83,7.04) per 100 person years (py) and 453 (95% CI: 445.9,461.2) new infections annually. A residential targeted to 25% of stimulant users yielded a 27.1% decline in the annual number of new infections. Initiating about 50% of methamphetamine users on mirtazapine reduced the overall HIV incidence by about 11%. A 25% increase in antiretroviral treatment (ART) and preexposure prophylaxis (PrEP) uptake in the non-stimulant using YBMSM population combined with a 25% uptake of BI for stimulant users produces an HIV incidence consistent with HIV elimination targets (about 200 infections/year) identified in the GTZ initiative.

Conclusions

Targeted behavioral and biomedical interventions to treat stimulant dependency are likely to provide additive benefits to expanding ART and PrEP uptake for everyone in accomplishing GTZ initiatives for HIV elimination.
Human papillomavirus type 16 circular RNA is barely detectable for the claimed transformation activity
Authors: Yu Lulu , Zheng Zhi-Ming
Published: September 2021

The human papillomavirus type 16 (HPV16) E7 oncoprotein plays an essential role in cervical carcinogenesis and is encoded predominantly by a viral E6*I mRNA through alternative RNA splicing of a p97 promoter-transcribed bicistronic E6E7 pre-mRNA. Recently, Zhao et al. detected the HPV16 circular RNA circE7, which is generated aberrantly through backsplicing of the E6E7 pre-mRNA from two HPV16-positive cervical cancer cell lines, CaSki and SiHa. Based on their findings that HPV16 E7 was translated from circE7 and knockdown of circE7 in CaSki cells led to reduction of E7 oncoprotein, cell proliferation, and xenograft tumor formation, the authors claimed that circE7 is functionally important in cell transformation. We believe, however, that the reported circE7 function is overstated. We found that circE7 in CaSki cells is only 0.4 copy per cell and determine that the claimed circE7 function in the published report was resulted from off-targeting viral E7 linear mRNAs by their circE7 small interfering RNAs.
Lowland ecotype Cyperus rotundus L. affects growth and yield of rice under flooded conditions in the Philippines
Authors: Donayre Dindo King M. , Jimenez Jessica Joyce L. , Latonio Anna Maria Lourdes S. , Martin Edwin C. , Chauhan Bhagirath S.
Published: September 2021

Lowland ecotype Cyperus rotundus L. has been reported infesting irrigated lowland ricefields in the Philippines. Its effects on growth and yield of rice under flooded conditions are unknown. Two experimental runs were conducted in a screenhouse to determine the growth of lowland ecotype C. rotundus with transplanted rice and wet direct-seeded rice at a sowing density of 0, 22, 44, 66, and 88 tubers m-2; and its effect on growth and yield of rice. Except for height, growth variables of lowland ecotype C. rotundus were increased with the increase in its initial tuber densities. Compared with 22 tubers m-2, its number of off-shoots and tubers, and shoot and root biomass at 44 to 88 tubers m-2 increased by up to 3x. Growth variables of rice were reduced by the weed. Grain yield of transplanted rice was reduced by 14 to 38%; wet direct-seeded rice by 11 to 28%. Results suggest that lowland ecotype C. rotundus can grow well and reduce growth and yield of rice under flooded conditions. It also imply the need of developing a holistic weed control strategy against the weed.
Rumen Sampling Methods Bias Bacterial Communities Observed
Authors: Hagey Jill V. , Laabs Maia , Maga Elizabeth A. , DePeters Edward J.
Published: September 2021

The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey shifts in the microbial community in response to feed additives and dietary changes. Oral stomach tubing a cow for a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method, as well as type of sample collected (liquid vs solid), bias the microbial populations observed. The abundance of major archaeal populations was not different at the family level in samples acquired via rumen cannula or stomach tube. Liquid samples were enriched for the order WCHB1-41 (phylum Kiritimatiellaeota) as well as the family Prevotellaceae and had significantly lower abundance of Lachnospiraceae compared with grab samples from the rumen cannula. Solid samples most closely resembled the grab samples; therefore, inclusion of particulate matter is important for an accurate representation of the rumen microbes. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with samples from the rumen.
Functional study ofLeishmania braziliensisprotein arginine methyltransferases (PRMTs) reveals that PRMT1 and PRMT5 are required for macrophage infection
Authors: Lorenzon Lucas , Quilles Junior José C. , Campagnaro Gustavo Daniel , Almeida Leticia , Veras Flavio Protasio , Magalhães Rubens D. M. , Diniz Juliana Alcoforado , Ferreira Tiago R. , Cruz Angela K.
Published: September 2021

In trypanosomatids, regulation of gene expression occurs mainly at the posttranscriptional level, and RNA-binding proteins (RBPs) are key players in determining the fates of transcripts. RBPs are major targets of protein arginine methyltransferases (PRMTs), which posttranslationally regulate the RNA-binding capacity and other macromolecular interactions of RBPs by transferring methyl groups to protein arginine residues. Herein, we present the results of a study that functionally characterized the five predicted PRMTs inLeishmania braziliensisby gene knockout and endogenous protein HA tagging using CRISPR/Cas9 gene editing. We report that arginine methylation profiles vary amongLeishmaniaspecies and that target protein methylation changes across differentL. braziliensislife cycle stages, with higher PRMT expression in the promastigote stages than in the axenic amastigote stage. Knockout of some of theL. braziliensisPRMTs led to significant changes in global arginine methylation patterns without affecting promastigote axenic growth. Deletion of either PRMT1 or PRMT3 disrupted most type I PRMT activity, resulting in a global increase in monomethyl arginine (MMA) levels, which is mainly catalyzed by PRMT7. Putative targets and/or PRMT-interacting proteins were identified by coimmunoprecipitation using HA-tagged PRMTs, revealing a network of target RBPs and suggesting functional interactions between them and a relevant participation in epigenetic control of gene expression. Finally, we demonstrate thatL. braziliensisPRMT1 and PRMT5 are required for efficient macrophage infectionin vitro, and that in the absence of PRMT1 and PRMT5, axenic amastigote proliferation is impaired. The results indicate that arginine methylation is modulated across life cycle stages inL. braziliensisand show possible functional overlap and cooperation among the different PRMTs in targeting proteins. Overall, our data suggest important regulatory roles of these proteins throughout theL. braziliensislife cycle, showing that arginine methylation is important for parasite-host cell interactions.
Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades
Authors: Klitting Raphaëlle , Kafetzopoulou Liana E. , Thiery Wim , Dudas Gytis , Gryseels Sophie , Kotamarthi Anjali , Vrancken Bram , Gangavarapu Karthik , Momoh Mambu , Sandi John Demby , Goba Augustine , Alhasan Foday , Grant Donald S. , Garry Robert F. , Smither Allison R. , Zeller Mark , Pauthner Matthias G. , McGraw Michelle , Hughes Laura D. , Duraffour Sophie , Günther Stephan , Suchard Marc A. , Lemey Philippe , Andersen Kristian G. , Dellicour Simon
Published: September 2021

Lassa fever is listed among the diseases that pose the greatest risks to public health by the World Health Organization. This severe viral hemorrhagic fever is caused by Lassa virus, a zoonotic pathogen that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate change, transformations in land use, and human population growth could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. We project that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in areas suitable for Lassa virus may grow from about 100 million to 700 million by 2070. By analysing geotagged viral genomes, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades. Our results highlight how the endemic area of Lassa virus may expand well beyond West Africa in the next decades due to human impact on the environment, putting hundreds of million more people at risk of infection.
A novel view on the mechanism of biological activity of antifreeze proteins
Authors: Melnik Bogdan S. , Glukhova Ksenia A. , Sokolova Evgeniya A. , Balalaeva Irina V. , Finkelstein Alexei V.
Published: September 2021

The adaptation of organisms to sub-zero temperatures is an intriguing problem in biology and biotechnology. The ice-binding antifreeze proteins are known to be responsible for the adaptation, but the mechanism of their action is still far from being clear. Here we show that: (i) in contrast to common belief, ice-binding proteins do not reduce the water freezing temperature and even raise (1) the ice melting point; (ii) at sub-zero temperatures (to ≈ -30°C), ice can be formed only on ice-binding surfaces, but, for kinetic reasons, not in bulk water; (iii) living cells have some large surfaces, which can bind the antifreeze proteins. These facts allow suggesting that the task of antifreeze proteins is not to bind to the ice crystals already formed in the cell and stop their growth or rearrangement, but to bind to those cell surfaces where the ice nuclei can form, and thus to prevent ice formation completely.