bluuebunny/crossref_metadata_2025 huggingface dataset:
Somatic copy number variant load in neurons of healthy controls and Alzheimer’s disease patients
Authors: Turan Zeliha Gözde , Richter Vincent , Bochmann Jana , Parvizi Poorya , Yapar Etka , Işıldak Ulaş , Waterholter Sarah-Kristin , Leclere-Turbant Sabrina , Son Çağdaş Devrim , Duyckaerts Charles , Yet İdil , Arendt Thomas , Somel Mehmet , Ueberham Uwe
Published: May 2022

Background

The possible role of somatic copy number variations (CNVs) in Alzheimer’s disease (AD) aetiology has been controversial. Although cytogenetic studies suggested increased CNV loads in AD brains, a recent single-cell whole-genome sequencing (scWGS) experiment, studying frontal cortex brain samples, found no such evidence. Here we readdressed this issue using lowcoverage scWGS on pyramidal neurons dissected using laser capture microdissection (LCM) across five brain regions: entorhinal cortex, temporal cortex, hippocampal CA1, hippocampal CA3, and the cerebellum.

Results

Among reliably detected somatic CNVs identified in 1301 cells obtained from the brains of 13 AD patients and 7 healthy controls, deletions were more frequent compared to duplications. Interestingly, we observed slightly higher frequencies of CNV events in cells from AD compared to similar numbers of cells from controls (4.1% vs. 1.4%, or 0.9% vs. 0.7%, using different filtering approaches), although the differences were not statistically significant. We also observed that LCM-isolated cells show higher within-cell read depth variation compared to cells isolated with fluorescence activated cell sorting (FACS), which we argue may have both biological and technical causes. Furthermore, we found that LCM-isolated neurons in AD harbour slightly more read depth variability than neurons of controls, which might be related to the reported hyperploid profiles of some AD-affected neurons. We also propose a principal component analysis-based denoising approach that significantly reduces within-cell read depth variation in scWGS data.

Conclusions

We find slightly higher somatic CNV frequencies in the brains of AD patients, and higher sequencing coverage variability, although the effects measured do not reach statistical significance. The results call for improved experimental protocols to determine the possible role of CNVs in AD pathogenesis.
Incilius alvarius cell-based synthesis of 5-MeO-DMT
Authors: Lerer Leonard , Reynolds Eric , Varia Jeet , Blakolmer Karin , Lerer Bernard
Published: May 2022

There is growing interest in the therapeutic potential of 5-MeO-DMT (5-methoxy-N,N-dimethyltryptamine) for psychiatric disorders. While 5-MeO-DMT can be chemically synthesized, the parotoid gland secretions of Incilius alvarius (also known as the Colorado River or Sonoran Desert toad) contain 5-MeO-DMT and other molecules including bufotenine, bufagenins, bufotoxins, and indole alkylamines that may have individual clinical utility or act as entourage molecules to enhance the activity of 5-MeO-DMT. Incilius alvarius is currently under severe ecological pressure due to demand for natural 5-MeO-DMT and habitat loss. We established a cell line from tissue obtained by wedge biopsy of the Incilius alvarius parotoid gland and confirmed the cell-based biosynthesis of 5-MeO-DMT by LC-MS/MS. Cell-based biosynthesis of Incilius alvarius parotoid gland secretions is a potentially cruelty-free and sustainable source of naturally derived 5-MeO-DMT for research and drug development.

Graphical Abstract
Unique Effects of Sedatives, Dissociatives, Psychedelics, Stimulants, and Cannabinoids on Episodic Memory: A Review and Reanalysis of Acute Drug Effects on Recollection, Familiarity, and Metamemory
Authors: Doss Manoj K. , Samaha Jason , Barrett Frederick S. , Griffiths Roland R. , de Wit Harriet , Gallo David A. , Koen Joshua D.
Published: May 2022

Despite distinct classes of psychoactive drugs producing putatively unique states of consciousness, there is surprising overlap in terms of their effects on episodic memory and cognition more generally. Episodic memory is supported by multiple subprocesses that have been mostly overlooked in psychopharmacology and could differentiate drug classes. Here, we reanalyzed episodic memory confidence data from 10 previously published datasets (28 drug conditions total) using signal detection models to estimate 2 conscious states involved in episodic memory and 1 consciously-controlled metacognitive process of memory: the retrieval of specific details from one’s past (recollection), noetic recognition in the absence of retrieved details (familiarity), and accurate introspection of memory decisions (metamemory). We observed that sedatives, dissociatives, psychedelics, stimulants, and cannabinoids had unique patterns of effects on these mnemonic processes dependent on which phase of memory (encoding, consolidation, or retrieval) was targeted. All drugs at encoding except stimulants impaired recollection, and sedatives, dissociatives, and cannabinoids at encoding impaired familiarity. The effects of sedatives on metamemory were mixed, whereas dissociatives and cannabinoids at encoding tended to enhance metamemory. Surprisingly, psychedelics at encoding tended to enhance familiarity and did not impact metamemory. Stimulants at encoding and retrieval enhanced metamemory, but at consolidation, they impaired metamemory. Together, these findings may have relevance to mechanisms underlying unique subjective phenomena under different drug classes, such as blackouts from sedatives or déjà vu from psychedelics. This study provides a framework for interrogating drug effects within a domain of cognition beyond the global impairments on task performance typically reported in psychopharmacology.

Public significance statement

This systematic review and reanalysis of several datasets indicate that sedatives (alcohol, zolpidem, triazolam), dissociatives (ketamine, dextromethorphan), psychedelics (psilocybin, MDMA), stimulants (dextroamphetamine, dextromethamphetamine), and cannabinoids (THC) can each have idiosyncratic effects on episodic memory, differentially impairing certain mnemonic processes while sparing or even facilitating others. Such findings inform how different drugs can produce unique subjective phenomena and provide a framework for future work to differentiate the effects of psychoactive drugs within a domain of cognition.
Variant-specific symptoms of COVID-19 among 1,542,510 people in England
Authors: Whitaker Matthew , Elliott Joshua , Bodinier Barbara , Barclay Wendy , Ward Helen , Cooke Graham , Donnelly Christl A. , Chadeau-Hyam Marc , Elliott Paul
Published: May 2022

Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.
The SARS-CoV-2 spike protein binds and modulates estrogen receptors
Authors: Solis Oscar , Beccari Andrea R. , Iaconis Daniela , Talarico Carmine , Ruiz-Bedoya Camilo A. , Nwachukwu Jerome C. , Cimini Annamaria , Castelli Vanessa , Bertini Riccardo , Montopoli Monica , Cocetta Veronica , Borocci Stefano , Prandi Ingrid G. , Flavahan Kelly , Bahr Melissa , Napiorkowski Anna , Chillemi Giovanni , Ooka Masato , Yang Xiaoping , Zhang Shiliang , Xia Menghang , Zheng Wei , Bonaventura Jordi , Pomper Martin G. , Hooper Jody E. , Morales Marisela , Rosenberg Avi Z. , Nettles Kendall W. , Jain Sanjay K. , Allegretti Marcello , Michaelides Michael
Published: May 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 (ACE2) at the cell surface, which constitutes the primary mechanism driving SARS-CoV-2 infection. Molecular interactions between the transduced S and endogenous proteins likely occur post-infection, but such interactions are not well understood. We used an unbiased primary screen to profile the binding of full-length S against >9,000 human proteins and found significant S-host protein interactions, including one between S and human estrogen receptor alpha (ERα). After confirming this interaction in a secondary assay, we used bioinformatics, supercomputing, and experimental assays to identify a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit and an S-ERα binding mode. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects and ACE2 expression. Noninvasive multimodal PET/CT imaging in SARS-CoV-2-infected hamsters using [18F]fluoroestradiol (FES) localized lung pathology with increased ERα lung levels. Postmortem experiments in lung tissues from SARS-CoV-2-infected hamsters and humans confirmed an increase in cytoplasmic ERα expression and its colocalization with S protein in alveolar macrophages. These findings describe the discovery and characterization of a novel S-ERα interaction, imply a role for S as an NRC, and are poised to advance knowledge of SARS-CoV-2 biology, COVID-19 pathology, and mechanisms of sex differences in the pathology of infectious disease.
Intranasal pediatric parainfluenza virus-vectored SARS-CoV-2 vaccine candidate is protective in macaques
Authors: Le Nouën Cyril , Nelson Christine E. , Liu Xueqiao , Park Hong-Su , Matsuoka Yumiko , Luongo Cindy , Santos Celia , Yang Lijuan , Herbert Richard , Castens Ashley , Moore Ian N. , Wilder-Kofie Temeri , Moore Rashida , Walker April , Zhang Peng , Lusso Paolo , Johnson Reed F. , Garza Nicole L. , Via Laura E. , Munir Shirin , Barber Daniel , Buchholz Ursula J.
Published: May 2022

Pediatric SARS-CoV-2 vaccines are needed that elicit immunity directly in the airways, as well as systemically. Building on pediatric parainfluenza virus vaccines in clinical development, we generated a live-attenuated parainfluenza virus-vectored vaccine candidate expressing SARS-CoV-2 prefusion-stabilized spike (S) protein (B/HPIV3/S-6P) and evaluated its immunogenicity and protective efficacy in rhesus macaques. A single intranasal/intratracheal dose of B/HPIV3/S-6P induced strong S-specific airway mucosal IgA and IgG responses. High levels of S-specific antibodies were also induced in serum, which efficiently neutralized SARS-CoV-2 variants of concern. Furthermore, B/HPIV3/S-6P induced robust systemic and pulmonary S-specific CD4+ and CD8+ T-cell responses, including tissue-resident memory cells in lungs. Following challenge, SARS-CoV-2 replication was undetectable in airways and lung tissues of immunized macaques. B/HPIV3/S-6P will be evaluated clinically as pediatric intranasal SARS-CoV-2/parainfluenza virus type 3 vaccine.

One-Sentence Summary

Intranasal parainfluenza virus-vectored COVID-19 vaccine induces anti-S antibodies, T-cell memory and protection in macaques.
Non-equilibrium protein folding and activation by ATP-driven chaperones
Authors: Xu Huafeng
Published: May 2022

Abstract

Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein sub-strates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each breaks a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen’s hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermo-dynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
Enhancing the anti-tumor efficacy of Bispecific T cell engagers via cell surface glycocalyx editing
Authors: Yang Zhuo , Hou Yingqin , Grande Geramie , Wang Chao , Shi Yujie , Zak Jaroslav , Cho Jong Hyun , Liu Dongfang , Teijaro John R. , Lerner Richard A. , Wu Peng
Published: May 2022

Bispecific T-cell engager (BiTE)-based cancer therapies that activate the cytotoxic T cells of a patient’s own immune system have gained momentum with the recent FDA approval of Blinatumomab for treating B cell malignancies. However, this approach has had limited success in targeting solid tumors. Here, we report the development of BiTE-sialidase fusion proteins that enhance tumor cell susceptibility to BiTE-mediated cytolysis by T cells via targeted desialylation at the BiTE-induced T cell-tumor cell interface. Targeted desialylation results in better immunological synapse formation, T-cell activation and effector function. As a result, BiTE-sialidase fusion proteins show remarkably increased efficacy in inducing T-cell-dependent tumor cell cytolysis in response to target antigens compared to the parent BiTE molecules alone. This enhanced function is seen bothin vitroand inin vivoxenograft and syngeneic solid tumor mouse models. Our findings highlight BiTE-sialidase fusion proteins as promising candidates for the development of next-generation bispecific T-cell engaging molecules for cancer immunotherapy.
Estimating chromosome sizes from karyotype images enables validation of de novo assemblies
Authors: Ludwig Arne , Dibrov Alexandr , Myers Gene , Pippel Martin
Published: May 2022

Highly contiguous genome assemblies are essential for genomic research. Chromosome-scale assembly is feasible with the modern sequencing techniques in principle, but in practice, scaffolding errors frequently occur, leading to incorrect number and sizes of chromosomes. Relating the observed chromosome sizes from karyotype images to the generated assembly scaffolds offers a method for detecting these errors.

Here, we present KICS, a semi-automated approach for estimating relative chromosome sizes from karyotype images and their subsequent comparison to the corresponding assembly scaffolds. The method relies on threshold-based image segmentation and uses the computed areas of the chromosome-related connected components as a proxy for the actual chromosome size. We demonstrate the validity and practicality of our approach by applying it to karyotype images of humans and various amphibians, birds, fish, insects, mammals, and plants. We found a strong linear relationship between pixel counts and the DNA content of chromosomes. Averaging estimates from eight human karyotype images, KICS predicts most of the chromosome sizes within an error margin of just 6 Mb.

Our method provides additional means of validating genome assemblies at low costs. An interactive implementation of KICS is available at https://github.com/mpicbg-csbd/napari-kics.
Greater alteration of gut microbiota occurs in childhood obesity than adulthood obesity
Authors: Yu Zhongjia , Yu Xiang-Fang , Zhao Xiu , Ren Pei-Gen
Published: May 2022

The children’s gut microbiota, associated with the development of obesity, is in maturation. The impact of obesity on the gut microbiota in childhood could have a more significant effect than on adulthood and eventually be lifelong lasting, but it has been rarely studied. Aimed to discover the difference in gut microbiota between obese children and adults, we collected and re-analyzed published data from National Center for Biotechnology Information (NCBI). We found that the gut microbiota had a significant difference between children with and without obesity, but this did not happen in adults. Based on the random forest model, childhood obesity is more challenging to predict using gut microbiota than adulthood obesity. Our results suggest that gut microbiota in childhood is more easily affected than in adulthood. Hence, early intervention for childhood obesity is essential to improve children’s health and lifelong gut microbiota-related health.
Turing Test Inspired Method for Analysis of Biases Prevalent in Artificial Intelligence-Based Medical Imaging
Authors: Tripathi Satvik , Augustin Alisha Isabelle , Dako Farouk , Kim Edward
Published: May 2022

Abstract

Background

Because of the growing need to provide better global healthcare, computer-based and robotic healthcare equipment that depend on artificial intelligence have seen an increase in development. In order to evaluate artificial intelligence (AI) in computer technology, the Turing test was created. For evaluating the future generation of medical diagnostics and medical robots, it remains an essential qualitative instrument.

Method

We propose a novel methodology to assess AI-based healthcare technology that provided verifiable diagnostic accuracy and statistical robustness. In order to run our test, we used a State-of-the-art AI model and compared it against radiologist for checking how generalized of the model is and if any biases are prevalent.

Results

We achieved results that can evaluate the performance of our chosen model for this study in a clinical setting and we also applied a quantifiable methods for evaluating our modified turing test results using a meta-analytical evaluation framework.

Conclusion

This test provides a translational standard for upcoming AI modalities. Our modified Turing Test is a notably strong standard to measure the actual performance of the AI model on a variety of edge cases and normal cases and also helps in detecting if the algorithm is biased towards any one type of case. This method extends the flexibility detect any prevalent biases and also classify the type of bias.
gExcite - A start-to-end framework for single-cell gene expression, hashing, and antibody analysis
Authors: Grob Linda , Bertolini Anne , Carrara Matteo , Menzel Ulrike , Tastanova Aizhan , Beisel Christian , Levesque Mitchell P. , Stekhoven Daniel J. , Singer Franziska
Published: May 2022

Single-cell RNA sequencing (scRNA-seq) based gene expression analysis is now an established powerful technique to decipher tissues at a single-cell level. Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single-cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focussed on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitude of samples. To this end, we designed gExcite, a start-to-end workflow that provides both gene expression and CITE-seq analysis, as well as hashing deconvolution. Embedded in the Snakemake workflow manager, gExcite facilitates reproducible and scalable analyses. We showcase the output of gExcite on a study of different dissociation protocols on PBMC samples.

Availability

gExcite is open source available on github at https://github.com/ETH-NEXUS/gExcite_pipeline The software is distributed under the GNU General Public License 3 (GPL3).

Contact

singer@nexus.ethz.ch

Supplementary Information

Supplementary information is available at the journal’s web site.
Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics
Authors: Allen Kelly S. , DeIulio Gregory A. , Pyne Robert , Maman Jacob , Guo Li , Wick Robert L. , Simon James , Gershenson Anne , Ma Li-Jun
Published: May 2022

Sweet basil (Ocimum basilicum L.) production is threatened by the oomycete pathogen Peronospora belbahrii causing basil downy mildew (BDM); BDM resistant cultivar ‘Mrihani’ (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM-susceptible ‘Newton’ (SB22), but the molecular mechanisms conferring resistance in MRI and progeny remained unknown

Comparative transcriptomics was performed to identify candidate resistance genes and potential mechanisms for BDM resistance; RNA samples from BDM-infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to differentiate interactions in resistant and susceptible plants.

Three categories of genes uniquely induced in resistant MRI upon pathogen challenge were identified: nucleotide-binding leucine rich repeat proteins (NLRs), multi-functional receptor-like kinases (RLKs), and secondary metabolic enzymes; validation of the top resistance candidate NLR gene confirmed its unique presence in MRI as well as in two of four resistant MRIxSB22 F2 progeny.

In MRI, pathogen challenge also upregulated transcripts in the salicylic acid synthesis pathway, suggesting its role in BDM resistance, and demonstrating the application of using comparative transcriptomics to identify resistance genes and mechanisms in non-model crops for marker-assisted breeding approaches.
The electric field generated by cationic TiO2 nanoparticles can be their key antimicrobial factor
Authors: Zhukova Lyudmila V.
Published: May 2022

The antimicrobial effect of TiO2 nanoparticles (TiO2 NPs) has been reliably established. However, the mechanism of this action remains unclear. Currently, according to the dominant hypothesis, it is assumed that the key destructive mechanism is the photocatalytic oxidation of cell components, and the key antimicrobial factor is the reactive oxygen species (ROS) formed on the surface of TiO2 NPs as a result of photocatalysis. In this communication, for the first time, the influence of the electric field created by cationic TiO2 NPs is suggested as a key killing factor, and the key antimicrobial mechanism - the electrical breakdown of the cell membranes and the destruction of the DNA molecule under the action of this field. Here, it was shown by mathematical calculation that TiO2 NPs are able to generate an electric field with a strength sufficient for an electrical breakdown of bilayer lipid membranes, which can lead to a violation of the structure and vital functions of the cytoplasmic membrane (CPM) and to collapse of DNA molecule.

GRAPHICAL ABSTRACT
Whole-Genome RNA Sequencing of Femoral Head Impingement Cartilage Identifies FGF18 As A Biomarker in Hip Osteoarthritis Progression
Authors: Kuhns Benjamin D. , Reuter John M. , Hansen Victoria L. , Soles Gillian , Jonason Jennifer H. , Ackert-Bicknell Cheryl , Wu Chia-Lung , Giordano Brian D.
Published: May 2022

Introduction

The natural history of Femoroacetabular Impingement (FAI) has been clinically associated with the development of hip osteoarthritis (OA); however, the pathobiological mechanisms underlying the transition from focal impingement to global joint degeneration remain unclear. The goal of the study was to investigate differences in transcriptomic profiles of the cartilage from FAI and hip OA patients using whole-genome RNA sequencing.

Methods

Thirty-seven patients were included in the study with 20 diagnosed with FAI undergoing arthroscopic treatment and 15 diagnosed with hip OA undergoing total hip arthroplasty (THA). Cartilage samples were obtained intraoperatively over the femoral head-neck junction for both FAI and OA cohorts. Whole-genome RNA sequencing was performed on 10 gender-matched patients in the FAI and OA cohorts with the remaining samples used for histopathologic analysis using the Osteoarthritis Research Society International (OARSI) grading system and qRT-PCR validation. Target validation was further confirmed with immunohistochemical staining for FGF18 on FAI and OA cartilage samples.

Results

We identified a total of 3,531 Differentially Expressed Genes (DEGs) between the FAI and OA cohorts with multiple targets for genes implicated in canonical OA pathways. qRT-PCR validation confirmed increased expression of FGF18 and WNT16 in the FAI samples, while there was increased expression of MMP13 and ADAMTS4 in the OA samples. Expression levels of FGF18 and WNT16 were also higher in FAI samples with mild cartilage damage (OARSI grades 1-2) compared to FAI samples with severe cartilage damage or OA cartilage (OARSI grade 4-6). Immunohistochemical evaluation identified increased FGF18 staining in OARSI grade 1-2 FAI samples compared to OARSI grade 5-6 FAI and OA samples.

Conclusions

RNA sequencing of cartilage of FAI and hip OA patients identified a negative association of FGF18 expression levels with cartilage damage severity, suggesting that FGF18 may be used as a marker for hip OA progression. Future evaluation of FGF18 signaling as well as other markers in early OA may yield further insight into disease prevention and treatment.
Rapid, in-patient adaptations of Legionella pneumophila to the human host
Authors: Leenheer Daniël , Moreno Anaísa B. , Murray Susan , Jarraud Sophie , Ginevra Christophe , Guy Lionel
Published: May 2022

Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires’ disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite these similarities, the hosts are different enough so that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The clinical strain, carrying the mutated OMP homolog, grows faster in macrophages than the wild type strain, and thus appears to be better adapted to the human host. The other is a gene coding for a protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, convergent evolution – here mutations in the same genes observed in independent human infections – could point to adaptations to the accidental human host. These results suggest that despite its ability to infect, replicate, and disperse from amoebae, L. pneumophila is not well adapted to the human host.

Impact statement

Legionella pneumophila is primarily infecting amoeboid protists, but occasionally infects human lung macrophages, causing Legionnaires’ disease, an atypical pneumonia. By comparing 171 isolates from patients to their probable environmental source, we identified 119 mutations that presumably occurred in-patient. Among these, several mutations occurred in the gene. In particular, two genes were mutated thrice, significantly more often than expected by chance alone, and are likely to represent adaptations to the human host. We experimentally show that, for one mutation at least, the mutated strain grows faster in human macrophages than in amoebae. By specifically investigating in-patient mutations, we were able to identify two genes that might be involved in human host-specific adaptations of L. pneumophila. This result suggests that L. pneumophila is not particularly well adapted to the human host, as mutations get fixed in-patient, during the short course of an infection (2-14 days), indicating a very high selective value.

Data Summary

The sequencing data generated in this study are available in the NCBI database under the BioProject accession number: PRJEB52976.
A protocol for the use of cold plasma treatment to inhibit in vitro growth of Fusarium graminearum
Authors: Kaur M. , Hüberli D. , Bayliss K. L.
Published: May 2022

Cold plasma is an ionised gas that can be used to control a range of microorganisms. In this study, a protocol was developed for cold plasma treatment of in vitro growth of Fusarium graminearum, a global mycotoxic species generally associated with cereal grain. Four F. graminearum isolates on potato dextrose agar (PDA) were treated with cold plasma for 70 s from a distance of 21 cm in a closed environment, and their radial colony growth was measured. To consider whether cold plasma modified the culture media, non-inoculated half-strength PDA plates were also treated with cold plasma prior to inoculation with the F. graminearum isolates. Similarly, to determine if a rise in temperature during the treatment impacted the growth of the isolates or the culture media itself, the plates were treated with dry heat before and after inoculation with the isolates. Treatment of F. graminearum isolates with cold plasma inhibited their growth and was not associated with the culture media or the rise in temperature during the treatment. Optical emission spectroscopy of cold plasma identified reactive (ionised) species of argon, nitrogen, hydrogen, oxygen, copper, and carbon with the highest number of peaks produced for argon. These results demonstrate that cold plasma can significantly reduce the in vitro growth of F. graminearum isolates when treated in a closed environment and suggest there is potential to control the in vivo growth of F. graminearum.
The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma
Authors: Tiberti Matteo , Di Leo Luca , Vistesen Mette Vixø , Kuhre Rikke , Cecconi Francesco , De Zio Daniela , Papaleo Elena
Published: May 2022

Cancer genomics and cancer mutation databases have made a wealth of information about missense mutations found in cancer patient samples. Contextualizing by means of annotation and predicting the effect of amino acid change help identify which ones are more likely to have a pathogenic impact. Those can be validated by means of experimental approaches that assess the impact of protein mutations on the cellular functions or their tumorigenic potential. Here, we propose the integrative bioinformatic approach Cancermuts, implemented as a Python package. Cancermuts is able to gather known missense cancer mutations from databases such as cBioPortal and COSMIC, and annotate them with the pathogenicity score REVEL as well as information on their source. It is also able to add annotations about the protein context these mutations are found in, such as post-translational modification sites, structured/ustructured regions, presence of short linear motifs and more. We applied Cancermuts to the intrinsically disordered protein AMBRA1, a key regulator of many cellular processes tightly (de)regulated in cancer. By these means, we classified mutations of AMBRA1 in melanoma, where AMBRA1 is highly mutated and displays a tumor-suppressive role. Next, based on REVEL score, position along the sequence and their local context, we applied cellular and molecular approaches to validate the predicted pathogenicity of a subset of mutations in an in vitro melanoma model. By doing so, we have identified two AMBRA1 mutations which show enhanced tumorigenic potential and are worth further investigation, highlighting the usefulness of the tool. Cancermuts can be used on any protein targets starting from minimal information, and it is available at https://www.github.com/ELELAB/cancermuts as free software.
Engineering aSinorhizobium melilotichassis with monopartite, single replicon genome configuration
Authors: Wagner Marcel , Döhlemann Johannes , Geisel David , Sobetzko Patrick , Serrania Javier , Lenz Peter , Becker Anke
Published: May 2022

Multipartite bacterial genomes pose challenges for genome engineering and establishment of additional replicons. We simplified the tripartite genome structure (3.65 Mbp chromosome, 1.35 Mbp megaplasmid pSymA, 1.68 Mbp chromid pSymB) ofSinorhizobium meliloti. Strains with bi- and monopartite genome configurations were generated by targeted replicon fusions. Our design preserved key genomic features, such as replichore ratios, GC skew, and KOPS and coding sequence distribution. Under standard culture conditions, growth rates of these strains and the wild type were nearly comparable. Spatiotemporal replicon organization and segregation were maintained in the triple replicon fusion strain. Deletion of the replication initiator-encoding genes including theoriVsof pSymA and pSymB from this strain resulted in a monopartite genome withoriCas the sole origin of replication, a strongly unbalanced replichore ratio, slow growth and an aberrant cellular localization oforiC. Suppressor mutation R436H in the cell cycle histidine kinase CckA and a 3.2 Mbp inversion, both individually, largely restored growth. These strains will facilitate integration of secondary replicons inS. meliloti,and thus be useful for genome engineering applications, such as generating hybrid genomes.

Graphical Abstract
On Weighted K-Mer Dictionaries
Authors: Pibiri Giulio Ermanno
Published: May 2022

We consider the problem of representing a set of k-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a k-mer is efficient. The representation is called a weighted dictionary of k-mers and finds application in numerous tasks in Bioinformatics that usually count k-mers as a pre-processing step. In fact, k-mer counting tools produce very large outputs that may result in a severe bottleneck for subsequent processing.

In this work we extend the recently introduced SSHash dictionary (Pibiri, Bioinformatics 2022) to also store compactly the weights of the k-mers. From a technical perspective, we exploit the order of the k-mers represented in SSHash to encode runs of weights, hence allowing (several times) better compression than the empirical entropy of the weights. We also study the problem of reducing the number of runs in the weights to improve compression even further and illustrate a lower bound for this problem. We propose an efficient, greedy, algorithm to reduce the number of runs and show empirically that it performs well, i.e., very similarly to the lower bound. Lastly, we corroborate our findings with experiments on real-world datasets and comparison with competitive alternatives. Up to date, SSHash is the only k-mer dictionary that is exact, weighted, associative, fast, and small.
Sustainable elk harvests in Alberta with increasing predator populations
Authors: Trump Tyler , Knopff Kyle , Morehouse Andrea , Boyce Mark S.
Published: May 2022

Large predators often are believed to cause declines in hunter harvests of ungulates due to direct competition for prey with hunters. In Alberta, predators of elk (Cervus elaphus), including grizzly bear (Ursus arctos), cougar (Puma concolor), and wolf (Canis lupus), have increased in recent years. We used trend analysis replicated by Wildlife Management Unit (WMU) to examine regional trends in elk harvest and hunter success. Over a 26-year period, average harvest of elk increased for both unrestricted bull (5.46% yr-1) and limited-quota (6.64% yr-1) hunting seasons. Average hunter success also increased for both unrestricted bull (0.2% yr-1) and limited-quota (0.3% yr-1) seasons, but no trend was detected in hunter effort (P> 0.05). Our results show that increasing large-predator populations do not necessarily reduce hunter harvest of elk, and we only found evidence for this in Alberta’s mountain WMUs where predation on elk calves has reduced recruitment. Furthermore, data indicate that Alberta’s elk harvest management has been sustainable, i.e., hunting has continued while populations of elk have increased throughout most of the province. Wildlife agencies can justify commitments to long-term population monitoring because data allow adaptive management and can inform stakeholders on the status of populations.
Fission yeast Smi1p participates in the synthesis of the primary septum by regulating β-1,3-glucan synthase Bgs1p function
Authors: Sethi Kriti , Cortés Juan C. G. , Sato Mamiko , Osumi Masako , Naqvi Naweed I. , Ribas Juan Carlos , Balasubramanian Mohan
Published: May 2022

Cytokinesis is the concluding step of the cell cycle. Coordination between multiple cellular processes is essential for the success of cytokinesis. The fission yeast, Schizosaccharomyces pombe, like other fungal cells is contained within a cell wall. During cell division, the external cell wall is extended inwards to form a special septum wall structure in continuity with the cell wall. The primary septum, the central component of the three-layered division septum, is enriched with linear β-1,3-glucan formed by Bgs1p, a β-1,3-glucan synthase. In this study we uncover a novel essential protein, Smi1p, that functions as a suppressor of the Bgs1p temperature-sensitive mutant, cps1-191. We observe a rescue in the cell wall composition and ultrastructure and also in actomyosin ring dynamics. Further, we identify a colocalization and physical association between Bgs1p and Smi1p. Altogether, our results indicate that Smi1p regulates the function of Bgs1p during cytokinesis.
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-Cell Epitopes
Authors: Xu Haodong , Zhao Zhongming
Published: May 2022

Identification of B-cell epitopes (BCEs) plays an essential role in the development of peptide vaccines, immuno-diagnostic reagents, and antibody design and production. In this work, we generated a large benchmark dataset comprising 126,779 experimentally-supported, linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell assays. Analysis of this curated dataset showed large pathogen diversity covering 176 different families. The accuracy in linear BCE prediction was found to strongly vary with different features, while the performance by sequence features was superior to that by structural features. To search more efficient and interpretive feature representations, a ten-layer deep learning framework for linear BCE prediction, namely NetBCE, was developed. NetBCE achieved high accuracy and robust performance with the average area under the curve (AUC) value of 0.846 in five-fold cross validation through automatically learning the informative classification features. NetBCE substantially outperformed the conventional machine learning algorithms and other tools, with an over 22.06% improvement of AUC value compared to other tools using an independent dataset. Through investigating the output of important network modules in NetBCE, epitopes and non-epitopes tended to present in distinct regions with efficient feature representation along the network layer hierarchy. The NetBCE tool will be useful for linear B-cell epitopes identification and more generally, immunological and computational biology research.
Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat
Authors: Hooy Richard M. , Iwamoto Yuichiro , Tudorica Daniel , Ren Xuefeng , Hurley James H.
Published: May 2022

The AP adaptor complexes are best known for forming the inner layer of clathrin coats on spherical vesicles. AP complexes also have many clathrin-independent roles in tubulovesicular membrane traffic, whose structural and mechanistic basis has been a mystery. HIV-1 Nef hijacks the AP-1 complex to sequester MHC-I internally, evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes in the absence of clathrin, and determined its structure by cryo-ET. The coat assembles both laterally and axially via an Arf1 dimer interface not seen before. Nef recruits MHC-I, but is not essential for the underlying AP-1:Arf1 lattice. Consistent with a role for AP-1:Arf1 coated tubules as intermediates in clathrin coated vesicle formation, AP-1 positive tubules are enriched in cells upon clathrin knockdown, with or without Nef. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef can sequester MHC-I. The coat contact residues are conserved across Arf isoforms and across the Arf-dependent AP adaptors AP-1, 3, and 4. These findings reveal that AP complexes can self-assemble with Arf1 into tubular coats in the absence of clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats, as an intermediate in clathrin vesicle formation from internal membranes, and as a MHC-I sequestration mechanism in HIV-1 infection.
Tissue-specific modifier alleles determineMertkloss-of-function traits
Authors: Akalu Yemsratch T. , Mercau Maria E. , Ansems Marleen , Wagage Sagie , Hughes Lindsey D. , Nevin James , Alberto Emily , Liu Xinran , He Li-Zhen , Alvarado Diego , Keler Tibor , Kong Yong , Philbrick William M. , Finnemann Silvia C. , Iavarone Antonio , Lasorella Anna , Rothlin Carla V. , Ghosh Sourav
Published: May 2022

Knockout (KO) mouse models play critical roles in elucidating biological processes behind disease-associated or disease-resistant traits. As a consequence of gene KO, mice display certain phenotypes. Based on insight into the molecular role of said gene in a biological process, it is inferred that the particular biological process causally underlies the trait. This approach has been crucial towards understanding the basis of pathological and/or advantageous traits associated withMertkKO. MERTK is a receptor tyrosine kinase with a critical role in phagocytosis of apoptotic cells or cellular debris. Therefore, early-onset, severe retinal degeneration was described to be a direct consequence of failed phagocytosis of photoreceptor outer segments by retinal pigment epithelia. Similarly, enhanced anti-tumor immunity was inferred to result from the failure of macrophages to dispose cancer cell corpses, resulting in a pro-inflammatory tumor microenvironment. Here we report that the loss ofMertkalone is not sufficient for retinal degeneration. This trait only manifests when the function of the paralogTyro3is concomitantly lost. Additionally, the dramatic resistance against two syngeneic mouse tumor models observed inMertkKO cannot, at least entirely, be ascribed to the loss ofMertk. The widely usedMertkKO carries multiple coincidental changes in its genome that affect the expression of a number of genes, includingTyro3. Nonetheless, neitherTyro3, nor macrophage phagocytosis by alternate genetic redundancy, accounts for the absence of anti-tumor immunity in two independentMertkKOs. Collectively, our results indicate that context-dependent epistasis of independent modifier alleles determineMertkKO traits.
Thirty years of deforestation within the entire ranges of nine endangered lemur species (3 CR, 4 EN, 2 VU) in northwestern Madagascar
Authors: Schüßler Dominik , Andriamalala Yves Rostant , van der Bach Robin , Katzur Cheyenne , Kolbe Christoph , Rabe Maheritafika Mamy Hasina , Rasolozaka Misa , Razafitsalama Mamy , Renz Marten , Steffens Travis S. , Radespiel Ute , Brenner Jana
Published: May 2022

Forest cover change is of particular concern in tropical regions. In this study, we investigate the degree of deforestation in the entire ranges of nine highly threatened lemur species in northwestern Madagascar. Landsat satellite images were acquired from four different time stages (1990, 2000, 2011, 2020), classified into forest/non-forest, and changes quantified. Forest cover declined from 17.5% to 9.3% within the last 30 years. This decline varied across four protected areas (PAs) investigated: the forest cover of Ankarafantsika National Park (ANP) declined only moderately over time (from 76.3% to 67.4%), while it declined drastically in other PAs (e.g., from 54.9% to 18.9%, Bongolava Forest Corridor). Two lemur taxa are most affected (Lepilemur otto, Microcebus bongolavensis) by having only very few isolated forest patches left within their ranges (approximately 542.7 km²). For two other species (L. ahmansoni, L. aeeclis), most of the remaining forest is concentrated in two coastal PAs (in total 627.2 and 477.9 km², respectively), while those species occurring inside ANP (5 taxa) experienced rather stable forest coverage until 2020. A reversal of these deforestation trends and active reforestation measures are desperately needed to reduce habitat loss for these nine lemur species. A practical experience-based guideline is therefore provided.
Derivation of the immortalized cell line-UM51-PrePodo-hTERT and its responsiveness to Angiotensin II and activation of RAAS
Authors: Erichsen Lars , Friedel Kloss Lea Doris , Thimm Chantelle , Bohndorf Martina , Schichel Kira , Wruck Wasco , Adjaye James
Published: May 2022

Recent demographic studies predict there will be a considerable increase of elderly people within the next decades. Aging has been recognized as one of the main risk factors of the world’s most prevalent diseases, including neurodegenerative disorders, cancer, cardiovascular disease, and metabolic disease. During the process of aging a gradual loss of tissue volume and organ function is observed, which is partially caused by replicative senescence. The capacity of cellular proliferation and replicative senescence is tightly regulated by their telomere length. When the telomere length with progressive cell division is critically shortened, the cell becomes proliferative arrested and DNA damage response and cellular senescence are triggered. At this time point the so called “Hayflick limit” is attained.

Podocytes are a cell type that is found in the kidney glomerulus where they have major implications in blood filtration. Mature podocytes are terminal differentiated cells that are unable to undergo cell division in vivo. For this reason, the establishment of podocyte cell cultures has been very challenging. In our present study, we present the successful immortalization of a human podocyte progenitor cell line, of which the primary cell cells were isolated directly from the urine of a 51-year-old male. The immortalized cell line has been cultured over the course of one year (∼100 passages) with high proliferation capacity, while still endowed with contact inhibition and P53 expression and activation. Furthermore, by immunofluorescent-based expression and quantitative Real-Time PCR for the podocyte markers NPHS1, SYNPO and WT1 we confirmed the differentiation capacity of the immortalized cells. Finally, we evaluated and confirmed the responsiveness of the immortalized cells on the main mediator Angiotensin II (ANGII) of the renin-angiotensin-system (RAS). Elevated levels of ANGII have been identified as a main risk factor for the initiation and progression of chronic kidney disease (CKD). CKD is characterized by an impairment of podocyte function and subsequently podocyte apoptosis. As a major risk factor for patients to develop CKD, diabetes, hypertension, heart disease and stroke have been recognized - all of which show increased incidence in elderly people. In conclusion, we have shown that it is possible to by-pass cellular replicative senescence (Hayflicks limit) by TERT-driven immortalization of human urine-derived pre-podocyte cells from a 51-year-old African male.