bluuebunny/crossref_metadata_2025 huggingface dataset:
BatchServer: a web server for batch effect evaluation, visualization and correction
Authors: Zhu Tiansheng , Chen Guo-Bo , Yuan Chunhui , Sun Rui , Zhang Fangfei , Yi Xiao , Zhou Shuigen , Guo Tiannan
Published: March 2020

Batch effects are unwanted data variations that may obscure biological signals, leading to bias or errors in subsequent data analyses. Effective evaluation and elimination of batch effects are necessary for omics data analysis. In order to facilitate the evaluation and correction of batch effects, here we present BatchSever, an open-source R/Shiny based user-friendly interactive graphical web platform for batch effects analysis. In BatchServer we introduced autoComBat, a modified version of ComBat, which is the most widely adopted tool for batch effect correction. BatchServer uses PVCA (Principal Variance Component Analysis) and UMAP (Manifold Approximation and Projection) for evaluation and visualizion of batch effects. We demonstate its application in multiple proteomics and transcriptomic data sets. BatchServer is provided athttps://lifeinfo.shinyapps.io/batchserver/as a web server. The source codes are freely available athttps://github.com/guomics-lab/batch_server.
The role of UCP3 in brown adipose tissue mitochondrial bioenergetics is complementary to that of UCP1
Authors: Riley Christopher L. , Mills Edward M.
Published: March 2020

Mitochondrial uncoupling protein 3 (UCP3) plays a complementary role in uncoupling protein 1 (UCP1)-dependent uncoupling in mammalian thermogenesis. Using mouse strains that lack UCP1 or UCP3, plus a UCP1/UCP3 double knockout, we have previously demonstrated that UCP3 is necessary for sustained heat production. However, how and where UCP3 is essential for heat production remains unknown. Here we use brown adipocyte mitochondria from mice lacking UCP1, UCP3, or UCP1 plus UCP3 (double knockout) we found that in the absence of UCP1, UCP3 does not act as a free fatty acid-inducible uncoupling protein; however, UCP3 is necessary for maximal GDP-sensitive respiration. We additionally confirm that the loss of UCP1 is a dominant regulator of mitochondrial respiratory chain activity, assembly, and composition in brown adipose tissue. Our data suggest without UCP1, brown adipose tissue is not a significant source of heat production, and that UCP3-dependent heat generation serves a regulatory function outside of adipose tissues. Together these findings suggest that in brown adipose tissue, UCP3’s thermogenic function is independent of its role as abona fideuncoupling protein.
Ab-Ligity: Identifying sequence-dissimilar antibodies that bind to the same epitope
Authors: Wong Wing Ki , Robinson Sarah A. , Bujotzek Alexander , Georges Guy , Lewis Alan P. , Shi Jiye , Snowden James , Taddese Bruck , Deane Charlotte M.
Published: March 2020

Solving the structure of an antibody-antigen complex gives atomic level information of the interactions between an antibody and its antigen, but such structures are expensive and hard to obtain. Alternative experimental sources include epitope mapping and binning experiments which can be used as a surrogate to identify key interacting residues. However, their resolution is usually not sufficient to identify if two antibodies have identical interactions. Computational approaches to this problem have so far been based on the premise that antibodies with similar sequences behave similarly. Such approaches will fail to identify sequence-distant antibodies that target the same epitope.

We present Ab-Ligity, a structure-based similarity measure tailored to antibody-antigen interfaces. Using predicted paratopes on model antibody structures, we assessed its ability to identify those antibodies that target highly similar epitopes. Most antibodies adopting similar binding modes can be identified from sequence similarity alone, using methods such as clonotyping. In the challenging subset of antibodies whose sequences differ significantly, Ab-Ligity is still able to predict antibodies that would bind to highly similar epitopes (precision of 0.95 and recall of 0.69). We compared Ab-Ligity’s performance to an existing tool for comparing general protein interfaces, InterComp, and showed improved performance on antibody cases alongside a significant speed-up. These results suggest that Ab-Ligity will allow the identification of diverse (sequence-dissimilar) antibodies that bind to the same epitopes from large datasets such as immune repertoires. The tool is available athttp://opig.stats.ox.ac.uk/resources.
Channel Embedding for Informative Protein Identification from Highly Multiplexed Images
Authors: Magid Salma Abdel , Jang Won-Dong , Schapiro Denis , Wei Donglai , Tompkin James , Sorger Peter K. , Pfister Hanspeter
Published: March 2020

Interest is growing rapidly in using deep learning to classify biomedical images, and interpreting these deep-learned models is necessary for life-critical decisions and scientific discovery. Effective interpretation techniques accelerate biomarker discovery and provide new insights into the etiology, diagnosis, and treatment of disease. Most interpretation techniques aim to discover spatially-salient regions within images, but few techniques consider imagery with multiple channels of information. For instance, highly multiplexed tumor and tissue images have 30-100 channels and require interpretation methods that work across many channels to provide deep molecular insights. We propose a novel channel embedding method that extracts features from each channel. We then use these features to train a classifier for prediction. Using this channel embedding, we apply an interpretation method to rank the most discriminative channels. To validate our approach, we conduct an ablation study on a synthetic dataset. Moreover, we demonstrate that our method aligns with biological findings on highly multiplexed images of breast cancer cells while outperforming baseline pipelines.
Autocatalytic–Protection for an Unknown Locus CRISPR–Cas Countermeasure for Undesired Mutagenic Chain Reactions
Authors: Schonfeld Ethan , Schonfeld Elan , Schonfeld Dan
Published: March 2020

The mutagenic chain reaction (MCR) is a genetic tool to use a CRISPR–Cas construct to introduce a homing endonuclease, allowing gene drive to influence whole populations in a minimal number of generations1,2,3. The question arises: if an active genetic terror event is released into a population, could we prevent the total spread of the undesired allele4? Thus far, MCR protection methods require knowledge of the terror locus5. Here we introduce a novel approach, anautocatalytic-Protection for an Unknown Locus(a-PUL), whose aim is to spread through a population and arrest and decrease an active terror event’s spread without any prior knowledge of the terror-modified locus, thus allowing later natural selection and ERACR drives to restore the normal locus6. a-PUL, using a mutagenic chain reaction, includes (i) a segment encoding a non-Cas9 endonuclease capable of homology-directed repair suggested as Type II endonuclease Cpf1 (Cas12a), (ii) a ubiquitously-expressed gene encoding a gRNA (gRNA1) with a U4AU4 3′-overhang specific to Cpf1 and with crRNA specific to some desired genomic sequence of non-coding DNA, (iii) a ubiquitously-expressed gene encoding two gRNAs (gRNA2/gRNA3) both with tracrRNA specific to Cas9 and crRNA specific to two distinct sites of the Cas9 locus, and (iv) homology arms flanking the Cpf1/gRNA1/gRNA2/gRNA3 cassette that are identical to the region surrounding the target cut directed by gRNA17. We demonstrate the proof-of-concept and efficacy of our protection construct through a Graphical Markov model and computer simulation.
SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems
Authors: Blanco-Melo Daniel , Nilsson-Payant Benjamin E. , Liu Wen-Chun , Møller Rasmus , Panis Maryline , Sachs David , Albrecht Randy A. , tenOever Benjamin R.
Published: March 2020

One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections throughin vitro, ex vivo, andin vivomodel systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.
Virus infection is controlled by cell type-specific sensing of murine cytomegalovirus through MyD88 and STING
Authors: Piersma Sytse J. , Poursine-Laurent Jennifer , Yang Liping , Barber Glen N. , Parikh Bijal A. , Yokoyama Wayne M.
Published: March 2020

Recognition of DNA viruses, such as cytomegaloviruses (CMVs), through patternrecognition receptor (PRR) pathways involving MyD88 or STING constitute a first-line defense against infections mainly through production of type I interferon (IFN-I). However, the role of these pathways in different tissues is incompletely understood, an issue particularly relevant to the CMVs which have broad tissue tropisms. Herein, we investigated anti-viral effects of MyD88 and STING in distinct cell types that are infected with murine CMV (MCMV). Bone marrow chimeras revealed STING-mediated MCMV control in hematological cells, similar to MyD88. However, unlike MyD88, STING also contributed to viral control in non-hematological, stromal cells. Infected splenic stromal cells produced IFN-I in a cGAS-STING-dependent and MyD88-independent manner, while plasmacytoid dendritic cell IFN-I had inverse requirements. MCMV-induced natural killer (NK) cytotoxicity was dependent on MyD88 and STING. Thus, MyD88 and STING contribute to MCMV control in distinct cell types that initiate downstream immune responses.
Holistic assessment of large old trees: a framework and its application for Romania
Authors: Arghius Viorel , Malos Cristian , Macicasan Vlad , Hartel Tibor
Published: March 2020

Large old trees are keystone ecological structures and have exceptional sociocultural values. Still, holistic approaches to national assessments of large old trees are scarse in the scientific literature. Here we propose and apply a holistic framework to understand the distribution of large old trees, the formal regulations targeting the conservation of large old trees and the ways large old trees are present in the popular news in Romania. There were 4032 large old tree records in Romania most of the records being concentrated in the Central and North-Western part of Romania. The number of tree records decreases with the decreasing terrain accessibility. Almost 50% of the large old tree records are in areas not covered by nature conservation regulations and 2/3 of the terrestrial protected areas have no open access large old tree records, so far. We identified five formal regulations which could be relevant for large old tree conservation in Romania, however, only two of these explicitly targets large old trees. The lack of knowledge and interest, the lack of expertize, institutional capacity, vested interests (corruption) and inconsistencies within the regulations are the major barriers in the formal protection of large old trees. We also identified several opportunities for the local initiatives to protect large old trees, based on the current legislative frameworks. We identified 259 internet news targeting large old trees in Romania which reveals a wide range of values and concerns associated to large old trees at the level of the local communities. While discussing our results we highlight the benefits of a wider adoption of our approach for science, decision making and local initiatives to save large old trees.
Persistence of aWolbachia-driven sex ratio bias in an island population ofEuremabutterflies
Authors: Kageyama Daisuke , Narita Satoko , Konagaya Tatsuro , Miyata Mai N. , Abe Jun , Mitsuhashi Wataru , Nomura Masashi
Published: March 2020

It is generally believed that when maternally inherited sex ratio distorters become predominant, either the host population goes extinct or nuclear suppressors evolve in the host. Here, we show an empirical case where all-female-producingWolbachiais likely to be stably maintained at a high frequency. On an island population of the butterflyEurema mandarina, aWolbachiastrainwFem, which makes female hosts produce all-female offspring without sibling lethality (female drive), is highly prevalent. We found that, with some fluctuations,wFem appeared to be stably maintained for at least 12 years at a high frequency, resulting in the existence of an abnormally high number of virgin females. Interestingly, comparison between sex ratios of captive individuals and sex ratios deduced fromwFem frequencies suggested a plastic behavioral change of males and females in response to the shift of sex ratios.wFem presence does not affect brood size but has a slightly negative effect on body size. Stable coexistence ofwFem-positive and -negative females in the population may be explained via mate choice by males, which keepswFem in check. Taken together, this butterfly population is an attractive model for future studies on the population dynamics of sex ratios and mating behavior.
Prevalence and trend of malaria with anaemia among under-five children in Jasikan District, Ghana
Authors: Domechele William , Wak George Pokoanti , Zotor Francis Bruno
Published: March 2020

Background

Malaria still remains a major killer of children under-five, claiming the life of one child every two minutes globally. More than 78% of deaths among children under-five in Africa are as a result of malaria infection. Despite the several interventions to reduce malaria and anaemia, the disease remains a global public concern as more children continue to die. This study assessed the prevalence and trend of malaria and anaemia in children under-five years from 2012 to 2016.

Methods

We conducted a descriptive cross-sectional study among children under-five with malaria and anaemia who received care at the hospital in Jasikan town, Ghana from 2012 to 2016. Data were extracted from the children’s ward admission and discharge registers. We computed descriptive statistics to describe the data. STATA version 14 was used to carry out the analyses.

Results

Out of 30082 malaria cases, 835 were with anaemia from 2012 to 2016. This study demonstrated an overall proportion of malaria with anaemia as 0.028 (28 per 1000 malaria cases). Year 2014 recorded the highest proportion (38 per 1,000 malaria cases) of malaria with anaemia cases in the district. Overall, prevalence rate of malaria and anaemia cases separately was found as 61.5% and 4.4% respectively from 2012-2016. Children within 24-35 months’ age group contributed the highest (28.3%) and 0-11 months accounted for the lowest (12.9%) malaria with anaemia cases. Majority of malaria with anaemia cases 531 (63.6%) occurred in the rainy season from June to July.

Conclusion

There is a high prevalence of malaria with anaemia cases among children under-five from 2012-2016. Age and seasonal variation were found to be predictors of an increase in the prevalence of malaria with anaemia.
A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis
Authors: Snijder Eric J. , Limpens Ronald W.A.L. , de Wilde Adriaan H. , de Jong Anja W. M. , Zevenhoven-Dobbe Jessika C. , Maier Helena J. , Faas Frank F.G.A. , Koster Abraham J. , Bárcena Montserrat
Published: March 2020

Zoonotic coronavirus (CoV) infections, like those responsible for the current SARS-CoV-2 epidemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). While double-membrane vesicles (DMVs) appear to be apan-coronavirus RO element, studies to date describe an assortment of additional coronavirus-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in coronavirus infection.
De NovoPhosphoinositide Synthesis in Zebrafish Is Required for Triad Formation but Not Essential for Myogenesis
Authors: Smith Lindsay , Fabian Lacramioara , Al-Maawali Almundher , Noche Ramil R. , Dowling James J.
Published: March 2020

Phosphoinositides (PIPs) and their regulatory enzymes are key players in many cellular processes and are required for aspects of vertebrate development. Dysregulated PIP metabolism has been implicated in several human diseases, including a subset of skeletal myopathies that feature structural defects in the triad. The role of PIPs in skeletal muscle formation, and particularly triad biogenesis, has yet to be determined. CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) catalyzes the formation of phosphatidylinositol, which is the base of all PIP species. Loss of CDIPT should, in theory, result in the failure to produce PIPs, and thus provide a strategy for establishing the requirement for PIPs during embryogenesis. In this study, we generatedcdiptmutant zebrafish and determined the impact on skeletal myogenesis. Analysis ofcdiptmutant muscle revealed no apparent global effect on early muscle development. However, small but significant defects were observed in triad size, with T-tubule area, inter terminal cisternae distance and gap width being smaller incdiptmutants. This was associated with a decrease in motor performance. Overall, these data suggest that myogenesis in zebrafish does not requirede novoPIP synthesis but does implicate a role for CDIPT in triad formation.
Unilateral vocal nerve resection alters neurogenesis in the avian song system in a region-specific manner
Authors: Aronowitz Jake V. , Perez Alice , O’Brien Christopher , Aziz Siaresh , Rodriguez Erica , Wasner Kobi , Ribeiro Sissi , Green Dovounnae , Faruk Farhana , Pytte Carolyn L.
Published: March 2020

New neurons undergo a critical period soon after migration during which the behavior of the animal may result in the survival or culling of these cells. In the songbird song system, new neurons may be maintained in the song motor pathway with respect to motor progression toward a target song--during juvenile song learning, seasonal song restructuring, and experimentally manipulated song variability. However, it is not known whether the quality of song per se, without progressive improvement, may also influence new neuron survival. To test this idea, we experimentally altered song acoustic structure by unilateral denervation of the syrinx. We found no effect of aberrant song on numbers of new neurons in the HVC of the song motor pathway, a loss of left-side dominance in new neurons in the auditory region caudomedial nidopallium (NCM), and a bilateral decrease in new neurons in the basal ganglia nucleus Area X. We propose new neuron survival may be determined in response to behavioral feedback in accordance with the function of new neurons within a given brain region. Studying the effects of singing behaviors on new neurons across multiple brain regions that subserve singing may give rise to general rules underlying the regulation of new neuron survival across taxa and brain regions more broadly.
From a biological template model to gait assistance with an exosuit
Authors: Firouzi Vahid , Davoodi Ayoob , Bahrami Fariba , Sharbafi Maziar A.
Published: March 2020

By invention of soft wearable assistive devices, known as exosuits, a new aspect in assisting unimpaired subjects is introduced. In this study, we designed and developed an exosuit with compliant biarticular thigh actuators, called BAExo. Unlike common method of using rigid actuators in exosuits, the BAExo is made of serial elastic actuators (SEA) resembling artificial muscles (AM). This bioinsipred design is complemented by the novel control concept of using the ground reaction force to adjust these AMs’ stiffness in the stance phase. By locking the motors in the swing phase the SEAs will be simplified to passive biarticular springs, which is sufficient for leg swinging. The key concept in our design and control approach is synthesizing human locomotion to develop assistive device, instead of copying the outputs of human motor control. Analysing human walking assistance using an experiment-based OpenSim model demonstrates the advantages of the proposed design and control of BAExo, regarding metabolic cost reduction and efficiency of the system. In addition, pilot experiments with the recently developed BAExo hardware support the applicability of the introduced method.

Author summary

Aging and mobility of elderly people are of crucial concern in developed countries. The U.S. Census Bureau reports that by the middle of the 21st century, about 80 million Americans will be 65 or older. According to the group’s research, medical costs resulting from falls by the elderly are expected to approach $32.4 billion by 2020. Therefore, assistance of elderly people and making the assistive devices more intelligent is a need in near future. However, this is not the only application of assistive devices. Exosuits, as soft wearable robots, introduced a new aspect in assisting a large range of population, even healthy young people. We introduce a novel design and control method for a new exosuit. As the research in the field of wearable assistive devices is growing in recent years and its application in daily life becomes more evident for the society, such studies with a unique view in design and control could have a significant impact. Our proposed biologically inspired approach could be potentially applied to other exosuits.
Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives
Authors: Bohutínská Magdalena , Vlček Jakub , Yair Sivan , Laenen Benjamin , Konečná Veronika , Fracassetti Marco , Slotte Tanja , Kolář Filip
Published: March 2020

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of twoArabidopsisspecies which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ~ 0.02 to 18 million years of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over theArabidopsiscandidate genes and showed that a decreasing probability of repeated selection of the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

Significance statement

Repeated evolution tends to be more predictable. The impressive spectrum of recent reports on genomic parallelism, however, revealed that the fraction of the genome that evolves in parallel largely varies, possibly reflecting different evolutionary scales investigated. Here, we demonstrate divergence-dependent parallelism using a comprehensive genome-wide dataset comprising 12 cases of parallel alpine adaptation and identify decreasing probability of adaptive re-use of genetic variation as the major underlying cause. This finding empirically demonstrates that evolutionary predictability is scale dependent and suggests that availability of pre-existing variation drives parallelism within and among populations and species. Altogether, our results inform the ongoing discussion about the (un)predictability of evolution, relevant for applications in pest control, nature conservation, or the evolution of pathogen resistance.
Harvestman: A framework for hierarchical feature learning and selection from whole genome sequencing data
Authors: Frisby Trevor S. , Baker Shawn James , Marçais Guillaume , Hoang Quang Minh , Kingsford Carl , Langmead Christopher James
Published: March 2020

We present Harvestman, a method that takes advantage of hierarchical relationships among the possible biological interpretations and representations of genomic variants to perform automatic feature learning, feature selection, and model building. We demonstrate that Harvestmanscales to thousands of genomes comprising more than 84 million variants by processing phase 3 data from the 1000 Genomes Project, the largest publicly available collection of whole genome sequences. Next, using breast cancer data from The Cancer Genome Atlas, we show that Harvestmanselects a rich combination of representations that are adapted to the learning task, and performs better than a binary representation of SNPs alone. Finally, we compare Harvestmanto existing feature selection methods and demonstrate that our method selects smaller and less redundant feature subsets, while maintaining accuracy of the resulting classifier. The data used is available through either the 1000 Genomes Project or The Cancer Genome Atlas. Access to TCGA data requires the completion of a Data Access Request through the Database of Genotypes and Phenotypes (dbGaP). Binary releases of Harvestmancompatible with Linux, Windows, and Mac are available for download athttps://github.com/cmlh-gp/Harvestman-public/releases
Profiling anti-apoptotic protein BCL-xL expression in U-87 MG glioblastoma cells and patient-derived tumorspheres
Authors: Fanfone D. , Gabut M. , Ichim G.
Published: March 2020

Glioblastoma is one of the cancers with the worst prognosis, despite huge efforts to understand its unusual heterogeneity and aggressiveness. These are mainly attributable to glioblastoma stem cells, which are also responsible for the frequent tumour recurrence following surgery or chemo/radiotherapy. We report here that tumorspheres derived from the U-87 MG glioblastoma cells have an increased expression of the anti-apoptotic protein BCL-xL. Modulation of this expression in tumorspheres enlightened us on the potential role of apoptosis and BCL-2 proteins might play in the survival of glioblastoma stem cells. Moreover, increased BCL-xL expression appears to sensitise glioblastoma cells to the newly developed BH3 mimetics, opening new therapeutic perspectives for treating glioblastoma patients.
Towards CNN Representations for Small Mass Spectrometry Data Classification: From Transfer Learning to Cumulative Learning
Authors: Seddiki Khawla , Saudemont Philippe , Precioso Frédéric , Ogrinc Nina , Wisztorski Maxence , Salzet Michel , Fournier Isabelle , Droit Arnaud
Published: March 2020

Rapid and accurate clinical diagnosis of pathological conditions remains highly challenging. A very important component of diagnosis tool development is the design of effective classification models with Mass spectrometry (MS) data. Some popular Machine Learning (ML) approaches have been investigated for this purpose but these ML models require time-consuming preprocessing steps such as baseline correction, denoising, and spectrum alignment to remove non-sample-related data artifacts. They also depend on the tedious extraction of handcrafted features, making them unsuitable for rapid analysis. Convolutional Neural Networks (CNNs) have been found to perform well under such circumstances since they can learn efficient representations from raw data without the need for costly preprocessing. However, their effectiveness drastically decreases when the number of available training samples is small, which is a common situation in medical applications. Transfer learning strategies extend an accurate representation model learnt usually on a large dataset containing many categories, to a smaller dataset with far fewer categories. In this study, we first investigate transfer learning on a 1D-CNN we have designed to classify MS data, then we develop a new representation learning method when transfer learning is not powerful enough, as in cases of low-resolution or data heterogeneity. What we propose is to train the same model through several classification tasks over various small datasets in order to accumulate generic knowledge of what MS data are, in the resulting representation. By using rat brain data as the initial training dataset, a representation learning approach can have a classification accuracy exceeding 98% for canine sarcoma cancer cells, human ovarian cancer serums, and pathogenic microorganism biotypes in 1D clinical datasets. We show for the first time the use of cumulative representation learning using datasets generated in different biological contexts, on different organisms, in different mass ranges, with different MS ionization sources, and acquired by different instruments at different resolutions. Our approach thus proposes a promising strategy for improving MS data classification accuracy when only small numbers of samples are available as a prospective cohort. The principles demonstrated in this work could even be beneficial to other domains (astronomy, archaeology…) where training samples are scarce.
Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter
Authors: Pittis Alexandros A. , Goh Valerie , Cebrian-Serrano Alberto , Wettmarshausen Jennifer , Perocchi Fabiana , Gabaldón Toni
Published: March 2020

Mitochondrial calcium (mt-Ca2+) uptake is central for the regulation of numerous cellular processes in eukaryotes1. This occurs through a highly selective Ca2+uniporter located at the inner mitochondrial membrane and driven by the membrane potential2–4. While the physiological role of the uniporter was extensively studied for decades, its genetic identity was only recently determined, with MCU5,6, MICU17and EMRE8constituting pore-forming and regulatory subunits. Preliminary evolutionary analyses suggested an ancient eukaryotic origin of mt-Ca2+uptake, but also pinpointed inconsistent phylogenetic distributions of MCU, MICU1, and EMRE within fungi, where homologs of MCU were present in the absence of the supposedly essential regulators, MICU1 and EMRE9,10. Here, we perform the most comprehensive phylogenomic analysis of the mt-Ca2+uptake system and trace its evolution across 1,156 fully-sequenced eukaryotes. In contrast to earlier assumptions9–11we find compelling evidence that previously identified animal and fungal MCUs, the targets of several structural and functional efforts11–16, represent two distinct paralogous subfamilies originating from an ancestral duplication. We further uncover a complete “animal-like” uniporter complex within chytrid fungi, including bona-fide orthologs of MCU, MICU1, and EMRE. This first identification of EMRE outside Holozoa (animals and their unicellular relatives) and its strong coevolution with “animal-like” MICU1 and MCU indicates that these three components formed the core of the ancestral opisthokont uniporter. We confirm this finding experimentally, by showing that chytrid EMRE orthologs in combination with either human or “animal-like” MCUs, but not with “fungal-specific” MCUs, can reconstitute mt-Ca2+uptakein vivoin the yeastSaccharomyces cerevisiae. Hence, we here solve a purported evolutionary paradox: the presence of MCU homologs in fungal species devoid of other uniporter components and with no detectable mt-Ca2+uptake. Altogether, our study clarifies the evolution of the mt-Ca2+uniporter and identifies new important targets for comparative structural and functional studies.
Landscape of oncoviral genotype and co-infection via Human papilloma and Hepatitis B viral tumor in-situ profiling
Authors: Bubie Adrian , Zoulim Fabien , Testoni Barbara , Miles Brett , Posner Marshall , Villanueva Augusto , Losic Bojan
Published: March 2020

Hepatitis B virus (HBV) and human papillomavirus (HPV) infection are known risk factors for developing several cancers. However, the effect of viral genotype and co-infection in actually driving oncogenesis remains unclear. We have developed and deployed a new scalable, high throughput tool (ViralMine) for sensitive and precise oncoviral genotype deconvolution using tumor RNA sequencing data from 537 virally infected liver, cervical, and head and neck tumors. We provide the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor onco-viral genotype. We find that HBV and HPV genotype, and surprisingly high rates of multi-genotype co-infection, serve as significant predictors of patient survival, tumor immune responsiveness, andAPOBECactivity modulation. Finally, we demonstrate that HPV genotype strongly associates with viral onco-gene expression over cancer type, implying expression may be similar across episomal and stochastic integration-based infections.

Significance Statement

We demonstrate that scalable, high-accuracy oncoviral genotyping, gene expression, and co-infection estimation is feasible from legacy tumor RNA-seq data. While HBV and HPV genotype are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections.
Wavelet Screening: a novel approach to analysing GWAS data
Authors: Denault William , Gjessing Håkon K. , Juodakis Julius , Jacobsson Bo , Jugessur Astanand
Published: March 2020

We present here an alternative method for genome-wide association study (GWAS) that is more powerful than traditional GWAS methods for locus detection. Single-variant GWAS methods incur a substantial multiple-testing burden because of the vast number of single nucleotide polymorphisms (SNPs) being tested simultaneously. Furthermore, these methods do not consider the functional genetic effect on the outcome because they ignore more complex joint effects of nearby SNPs within a region. By contrast, our method reduces the number of tests to be performed by screening the entire genome for associations using a sliding-window approach based on wavelets. In this context, a sequence of SNPs represents a genetic signal, and for each screened region, we transform the genetic signal into the wavelet space. The null and alternative hypotheses are modelled using the posterior distribution of the wavelet coefficients. We enhance our decision procedure by using additional information from the regression coefficients and by taking advantage of the pyramidal structure of wavelets. When faced with more complex signals than single-SNP associations, we show through simulations that Wavelet Screening provides a substantial gain in power compared to both the traditional GWAS modelling as well as another popular regional-based association test called ‘SNP-set (Sequence) Kernel Association Test’ (SKAT). To demonstrate feasibility, we re-analysed data from the large Norwegian HARVEST cohort.
High-Throughput 5’ UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies
Authors: Cao Jicong , Novoa Eva Maria , Zhang Zhizhuo , Chen William C.W. , Liu Dianbo , Choi Gigi C G , Wong Alan S L , Wehrspaun Claudia , Kellis Manolis , Lu Timothy K
Published: March 2020

Despite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major challenge. One approach to increase protein expression is by optimizing translation through the engineering of 5’ untranslated regions (5’ UTRs). Here, we developed a high-throughput strategy to design, screen, and optimize novel 5’UTRs that enhance protein expression from a strong human cytomegalovirus (CMV) promoter. We first identified naturally occurring 5’ UTRs with high translation efficiencies and used this information within silicogenetic algorithms to generate synthetic 5’ UTRs. A total of ∼12,000 5’ UTRs were then screened using a recombinase-mediated integration strategy that greatly enhances the sensitivity of high-throughput screens by eliminating copy number and position effects that limit lentiviral approaches. Using this approach, we identified three synthetic 5’ UTRs that outperformed commonly used non-viral gene therapy plasmids in expressing protein payloads. Furthermore, combinatorial assembly of these 5’ UTRs enabled even higher protein expression than obtained with each individual 5’ UTR. In summary, we demonstrate that high-throughput screening of 5’ UTR libraries with recombinase-mediated integration can identify genetic elements that enhance protein expression, which should have numerous applications for engineered cell and gene therapies.
Sub-3 Å resolution structure of apoferritin using a multi-purpose TEM with a side-entry cryo-holder
Authors: Kayama Yoko , Burton-Smith Raymond N. , Song Chihong , Terahara Naoya , Kato Takayuki , Murata Kazuyoshi
Published: March 2020

The structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method in recent years. Many results of cryo-EM SPA are based on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment. Here, we used a multi-purpose TEM with a side entry cryo-holder at our facility to evaluate the potential of high-resolution SPA. We report a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. The map clearly showed two positions of an aromatic side chain. We also verified the optimal imaging conditions depending on different electron microscope and camera combinations. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA.
Human microglia upregulate cytokine signatures and accelerate maturation of neural networks
Authors: Schmunk Galina , Kim Chang N. , Soliman Sarah S. , Keefe Matthew G. , Bogdanoff Derek , Tejera Dario , Ziffra Ryan S. , Shin David , Allen Denise E. , Chhun Bryant B. , McGinnis Christopher S. , Winkler Ethan A. , Abla Adib A. , Chang Edward F. , Gartner Zev J. , Mehta Shalin B. , Piao Xianhua , Hengen Keith B. , Nowakowski Tomasz J.
Published: March 2020

Microglia are the resident macrophages of the brain that emerge in early development and play vital role disease states, as well as in normal development. Many fundamental questions about microglia diversity and function during human brain development remain unanswered, as we currently lack cellular-resolution datasets focusing on microglia in developing primary tissue, or experimental strategies for interrogating their function. Here, we report an integrative analysis of microglia throughout human brain development, which reveals molecular signatures of stepwise maturation, as well as human-specific cytokine-associated subtype that emerges around the onset of neurogenesis. To demonstrate the utility of this atlas, we have compared microglia across several culture models, including cultured primary microglia, pluripotent stem cell-derived microglia. We identify gene expression signatures differentially recruited and attenuated across experimental models, which will accelerate functional characterization of microglia across perturbations, species, and disease conditions. Finally, we identify a role for human microglia in development of synchronized network activity using a xenotransplantation model of human microglia into cerebral organoids.
Genetically Encoded, Multivalent Liquid Glycan Array (LiGA)
Authors: Sojitra Mirat , Sarkar Susmita , Maghera Jasmine , Rodrigues Emily , Carpenter Eric , Seth Shaurya , Vinals Daniel Ferrer , Bennett Nicholas , Reddy Revathi , Khalil Amira , Xue Xiaochao , Bell Michael , Zheng Ruixiang Blake , Zhang Ping , Nycholat Corwin , Ling Chang-Chun , Lowary Todd L. , Paulson James C. , Macauley Matthew S. , Derda Ratmir
Published: March 2020

The Central Dogma of Biology does not allow for the study of glycans using DNA sequencing. We report a “Liquid Glycan Array” (LiGA) platform comprising a library of DNA ‘barcoded’ M13 virions that display 30-1500 copies of glycans per phage. A LiGA is synthesized by acylation of phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins such as CD22 on cellsin vitroand immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identifies the glycoconjugates with optimal avidity necessary for binding to lectins on living cellsin vitroandin vivo; measurements that cannot be performed with canonical glass slide-based glycan arrays.

Dedication

The paper is dedicated to Laura L. Kiessling on the occasion of her 60thbirthday.
Alternative splicing switches STIM1 targeting to specialized membrane contact sites and modifies SOCE
Authors: Knapp Mona L. , Förderer Kathrin , Alansary Dalia , Jung Martin , Schwarz Yvonne , Lis Annette , Niemeyer Barbara A.
Published: March 2020

Alternative splicing is a potent modifier of protein function. Stromal interaction molecule 1 (Stim1) is the essential activator molecule of store-operated Ca2+entry (SOCE) and a sorting regulator of certain ER proteins such as Stimulator of interferon genes (STING). Here, we characterize a conserved new variant, Stim1A, where splice-insertion translates into an additional C-terminal domain. We find prominent expression ofexonAmRNA in testes, astrocytes, kidney and heart and confirm Stim1A protein in Western blot of testes. In situ, endogenous Stim1 with domain A, but not Stim1 without domain A localizes to unique adhesion junctions and to specialized membrane retrieval sites (tubulobulbar complexes) in testes. Functionally, using Ca2+imaging and patch-clamp analysis, Stim1A shows a dominant-negative effect on SOCE and ICRAC, despite normal clustering and interaction with Orai1 investigated by combined TIRF and FRET analyses and as confirmed by an increased SOCE upon knock-down of endogenous Stim1A in astrocytes. Mutational analyses in conjunction with imaging and patch-clamp analyses of residues either in domain A or within the N-terminal region of Orai1 demonstrate a specific defect in stabilized channel gating. Our findings demonstrate that cell-type specific splicing of STIM1 adds both an intracellular targeting switch and adapts SOCE to meet the Ca2+requirements of specific subcellular contact sites.
The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity
Authors: Yu Jia , Yuso Permeen Akhtar Bt Mohamed , Goh Pamela , Harmston Nathan , Epstein David M. , Virshup David M. , Madan Babita
Published: March 2020

A subset of Wnt-addicted cancers are sensitive to targeted therapies that block Wnt secretion or receptor engagement. RNF43 loss-of-function mutations that increase cell surface Wnt receptor abundance cause sensitivity to Wnt inhibitors. However, it is not clear which of the clinically identified RNF43 mutations affect its functionin vivo. We assayed 90 missense and 45 truncating RNF43 mutations found in human cancers, using a combination of cell-based reporter assays, genome editing, flow cytometry and immunofluorescence microscopy. Patent-derived xenograft (PDX) models with C-terminal truncating RNF43 mutations were tested for Wnt inhibitor sensitivity. We find that five common germline variants of RNF43 have wild-type activity. The majority of cancer-associated missense mutations in the RING and PA domains are either loss of function or hyperactivating. Hyperactivating mutants appear to function through formation of inactive dimers with endogenous RNF43 and/or ZNRF3. C-terminal truncation mutants including the common G659fs mutant, have discordant behavior inin vitroversusin vivoassays. PDXs and cell lines with C-terminal truncations show increased cell surface FZD, Wnt/β-catenin signaling and are responsive to PORCN inhibitionin vivo, providing clear evidence of RNF43 loss of function. In conclusion, RNF43 nonsense and frameshift mutations, including those in the C-terminal domain, and specific missense mutations in RING and PA are loss of function and predict response to upstream Wnt inhibitors in microsatellite stable cancers. This study expands the landscape of actionable RNF43 mutations, potentially extending the benefit of these therapies to additional patients.

Statement of Significance

Loss of function RNF43 mutations, first described in pancreatic cancers, drive progression of multiple cancers by increasing cellular sensitivity to Wnt ligands. These cancers are therefore uniquely sensitive to agents such as PORCN inhibitors that block Wnt production. As the PORCN inhibitors and other upstream inhibitors advance into clinical trials it is important to identify the right patients to treat with these upstream Wnt inhibitors. Hence a detailed map of mutations that are actionable is required.

Here we systematically examined a spectrum of 135 patient-derived RNF43 mutations from multiple cancers. Using cell-based reporter assays, genome editing and patient-derived xenografts, we identify rules to guide patient selection. MSS cancers with either truncating mutations anywhere in the gene, including C-terminal truncations around the G659 position, or point mutations in well-defined functional domains, are likely to have RNF43 loss of function and hence a response to therapy.