bluuebunny/crossref_metadata_2025 huggingface dataset:
Human genetic diversity alters therapeutic gene editing off-target outcomes
Authors: Cancellieri Samuele , Zeng Jing , Lin Linda Yingqi , Tognon Manuel , Nguyen My Anh , Lin Jiecong , Bombieri Nicola , Maitland Stacy A. , Ciuculescu Marioara-Felicia , Katta Varun , Tsai Shengdar Q. , Armant Myriam , Wolfe Scot A. , Giugno Rosalba , Bauer Daniel E. , Pinello Luca
Published: May 2021

CRISPR gene editing holds great promise to modify somatic genomes to ameliorate disease. In silico prediction of homologous sites coupled with biochemical evaluation of possible genomic off-targets may predict genotoxicity risk of individual gene editing reagents. However, standard computational and biochemical methods focus on reference genomes and do not consider the impact of genetic diversity on off-target potential. Here we developed a web application called CRISPRme that explicitly and efficiently integrates human genetic variant datasets with orthogonal genomic annotations to nominate and prioritize off-target sites at scale. The method considers both single-nucleotide variants (SNVs) and indels, accounts for bona fide haplotypes, accepts spacer:protospacer mismatches and bulges, and is suitable for personal genome analyses. We tested the tool with a guide RNA (gRNA) targeting theBCL11Aerythroid enhancer that has shown therapeutic promise in clinical trials for sickle cell disease (SCD) and β-thalassemia1. We find that the top candidate off-target site is produced by a non-reference allele common in African-ancestry populations (rs114518452, minor allele frequency (MAF)=4.5%) that introduces a protospacer adjacent motif (PAM) for SpCas9. We validate that SpCas9 generates indels (∼9.6% frequency) and chr2 pericentric inversions in a strictly allele-specific manner in edited CD34+ hematopoietic stem/progenitor cells (HSPCs), although a high-fidelity Cas9 variant mitigates this off-target. The CRISPRme tool highlights alternative allele-specific off-target editing as a prevalent risk of gRNAs considered for therapeutic gene editing. Our report illustrates how population and private genetic variants should be considered as modifiers of genome editing outcomes. We suggest that variant-aware off-target assessment should be considered in therapeutic genome editing efforts going forward and provide a powerful approach for comprehensive off-target nomination.
Robust Prediction of Patient-Specific Clinical Response to Unseen Drugs From
in vitro Screens Using Context-aware Deconfounding
Autoencoder
Authors: He Di , Liu Qiao , Xie Lei
Published: May 2021

Accurate and robust prediction of patient-specific responses to drug
treatments is critical for drug development and personalized medicine. However,
patient data are often too scarce to train a generalized machine learning model.
Although many methods have been developed to utilize cell line data, few of them
can reliably predict individual patient clinical responses to new drugs due to
data distribution shift and confounding factors. We develop a novel
Context-aware Deconfounding Autoencoder (CODE-AE) that can extract common
biological signals masked by context-specific patterns and confounding factors.
Extensive studies demonstrate that CODE-AE effectively alleviates the
out-of-distribution problem for the model generalization, significantly improves
accuracy and robustness over state-of-the-art methods in both predicting
patient-specific ex vivo and in
vivo drug responses purely from in
vitro screens and disentangling intrinsic biological signals
from confounding factors. Using CODE-AE, we screened 50 drugs for 9,808 cancer
patients and discovered novel personalized anti-cancer therapies and
drug-response biomarkers.

Contact:lxie@iscb.org
On exploring effects of coevolving residues on DNA binding specificity of transcription factors
Authors: Luan Yizhao , Xie Zhi
Published: May 2021

Transcription factors (TFs) regulate gene expression by specifically binding to DNA targets. Many factors have been revealed to influence TF-DNA binding specificity. Coevolution of residues in proteins occurs due to a common evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically analyzed TF-DNA interactions from high-throughput experiments for seven TF families, including Homeobox, HLH, bZIP_1, Ets, HMG_box, zf-C4 and Zn_clus TFs. Based on TF-DNA interactions, we detected TF subclass determining sites (TSDSs) defining the heterogeneity of DNA binding preference for each TF family. We showed that the TSDSs were more likely to be coevolving with TSDSs than with non-TSDSs, particularly for Homeobox, HLH, Ets, bZIP_1 and HMG_box TF families. Mutation of the highly coevolving residues could significantly reduce the stability of TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence of the functional importance of coevolved residues in refining transcriptional regulation and provided clues to the application of engineered DNA-binding domains and protein.
Leveraging single-cell ATAC-seq to identify disease-critical fetal and adult brain cell types
Authors: Kim Samuel S. , Jagadeesh Karthik , Dey Kushal K. , Shen Amber Z. , Raychaudhuri Soumya , Kellis Manolis , Price Alkes L.
Published: May 2021

Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at high resolution, and early work on integrating GWAS with scRNA-seq has shown promise, but work on integrating GWAS with scATAC-seq has been limited. Here, we identify disease-critical fetal and adult brain cell types by integrating GWAS summary statistics from 28 brain-related diseases and traits (average N =298K) with 3.2 million scATAC-seq and scRNA-seq profiles from 83 cell types. We identified disease-critical fetal (resp. adult) brain cell types for 22 (resp. 23) of 28 traits using scATAC-seq data, and for 8 (resp. 17) of 28 traits using scRNA-seq data. Notable findings using scATAC-seq data included highly significant enrichments of fetal photoreceptor cells for major depressive disorder, fetal ganglion cells for BMI, fetal astrocytes for ADHD, and adult VGLUT2 excitatory neurons for schizophrenia. Our findings improve our understanding of brain-related diseases and traits, and inform future analyses of other diseases/traits.
Spatiotemporal evaporating droplet dynamics on fomites enhances long term bacterial pathogenesis
Authors: Majee Sreeparna , Chowdhury Atish Roy , Pinto Roven , Chattopadhyay Ankur , Agharkar Amey Nitin , Chakravortty Dipshikha , Basu Saptarshi
Published: May 2021

Naturally drying bacterial droplets on inanimate surfaces representing fomites are the most consequential mode for transmitting infection through oro-fecal route. We provide a multiscale holistic approach to understand flow dynamics induced bacterial pattern formation on fomites leading to pathogenesis. The most virulent gut pathogen,SalmonellaTyphimurium (STM), typically found in contaminated food and water, is used as model system in the current study. Evaporation-induced flow in sessile droplets facilitates the transport of STM, forming spatio-temporally varying bacterial deposition patterns based on droplet medium’s nutrient scale. Mechanical and low moisture stress in the drying process, reduced bacterial viability but interestingly induced hyper-proliferation of STM in macrophages, augmenting virulence in fomites. In vivo studies of fomites in mice confirm that STM maintains virulence. This work demonstrates that stressed bacterial deposit morphologies formed over small timescale (minutes) on organic and inorganic surfaces, plays significant role in enhancing fomite’s pathogenesis over hours and days.
Rational Drug Design of Targeted and Enzyme Cleavable Vitamin E Analogs as Neoadjuvant to Chemotherapy: In Vitro and In Vivo Evaluation on Reduction of Cardiotoxicity of Doxorubicin.
Authors: Pandurangi Raghu S , Cseh Orsolya , Luchman Artee , Xu siguang , Ma Cynthia , Senedheera Sanjeeva , Forrest laird
Published: May 2021

Traditional drug design focus on specific target (s) expressed by cancer cells. However, cancer cells outsmart the interventions by activating survival pathways and/or downregulating cell death pathways. As the research in molecular biology of cancer grows exponentially, new methods of drug designs are needed to target multiple pathways/targets which are involved in survival of cancer cells. Vitamin E analogues including a-tocopheryl succinate (TOS) is a well-known anti-tumoregenic agent which is well studied both in vitro and in vivo tumor models. However, lack of targeting cancer cells and unexpected toxicity along with the poor water solubility of TOS compelled a rational drug design using both targeting and cleavable technologies incorporated in the new drug design. A plethora of Vitamin E derivatives (AMP-001, 002 and 003) were synthesized, characterized and studied for the improved efficacy and lowered toxicity in various cancer cells in vitro. Preliminary studies revealed AAAPT leading candidates reduced the invasive potential of brain tumor stem cells, synergized with different drugs and different treatments. AAAPT leading drug AMP-001 enhanced the therapeutic index of front-line drug Doxorubicin in triple negative breast cancer (TNBC) tumor rat model preserving the ventricular function when used as a neoadjuvant to Doxorubicin. These results may pave the way for reducing the cardiotoxicity of chemotherapy in clinical settings.
6′,6′-Difluoro-aristeromycin is a potent inhibitor of MERS-coronavirus replication
Authors: Ogando Natacha S. , Zevenhoven-Dobbe Jessika C. , Jarhad Dnyandev B. , Tripathi Sushil Kumar , Lee Hyuk Woo , Jeong Lak Shin , Snijder Eric J. , Posthuma Clara C.
Published: May 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has highlighted the lack of treatments to combat infections with human or (potentially) zoonotic CoVs. Thus, it is critical to develop and evaluate antiviral compounds that either directly target CoV functions or modulate host functions involved in viral replication. Here, we demonstrate that low-micromolar concentrations of 6′,6′-difluoro-aristeromycin (DFA), an adenosine nucleoside analogue, strongly inhibit the replication of Middle East respiratory syndrome coronavirus (MERS-CoV) in a cell-based infection assay. DFA was designed to target S-adenosylhomocysteine (SAH) hydrolase and, consequently, may affect intracellular levels of the methyl donor S-adenosylmethionine, which is used by two CoV methyltransferases involved in the capping of the 5’ end of the viral mRNAs. Passaging of wild-type MERS-CoV in the presence of DFA selected a virus population with a ∼100-fold decreased DFA sensitivity, which carried various amino acid substitutions in viral nonstructural proteins (nsps). Specifically, mutations were present in the RNA polymerase subunit (nsp12) and in nsp13, the helicase subunit containing a nucleoside triphosphate hydrolase activity that has been implicated in CoV capping. We hypothesize that DFA directly or indirectly affects viral cap methylation, either by inhibiting the viral enzymes involved or by binding to SAH hydrolase. We also evaluated the antiviral activity of DFA against other betacoronaviruses, but found it to have limited impact on their replication, while being quite cytotoxic to the Calu-3 cells used for this comparison. Nevertheless, our results justify the further characterization of DFA derivatives as an inhibitor of MERS-CoV replication.

Importance

Currently, there is a lack of antiviral drugs with proven efficacy against human CoV infections including the MERS-CoV that is endemic in the Middle East, the pandemic SARS-CoV-2 and potential future zoonotic CoV. This highlights the importance to investigate new drug targets and identify compounds that can be used to inhibit CoV replication. In this study, we characterize the inhibitory effect of DFA on MERS-CoV replication by phenotypic studies, time-of-addition studies, and the generation and genotyping of a DFA-resistant virus population. Our results revealed that DFA needs further improvement to reduce its cytotoxic side-effects and potentially enhance its broad-spectrum activity. Despite this observation, we think that DFA can be used to understand the function and metabolic interactions of the CoV RNA-synthesizing machinery, or as a starting point for the design of new compounds of the same class.
Macrophage-produced peroxynitrite induces antibiotic tolerance and supersedes intrinsic mechanisms of persister formation
Authors: Beam Jenna E. , Wagner Nikki J. , Shook John C. , Bahnson Edward S.M. , Fowler Vance G. , Rowe Sarah E. , Conlon Brian P.
Published: May 2021

Staphylococcus aureus is a leading human pathogen that frequently causes chronic and relapsing infections. Antibiotic tolerant persister cells contribute to frequent antibiotic failure in patients. Macrophages represent an important niche during S. aureus bacteremia and recent work has identified a role for oxidative burst in the formation of antibiotic tolerant S. aureus. We find that host-derived peroxynitrite, the reaction product of superoxide and nitric oxide, is the main mediator of antibiotic tolerance in macrophages. Using a collection of S. aureus clinical isolates, we find that, despite significant variation in persister formation in pure culture, all strains were similarly enriched for antibiotic tolerance following internalization by activated macrophages. Our findings suggest that host interaction strongly induces antibiotic tolerance and may negate bacterial mechanisms of persister formation, established in pure culture. These findings emphasize the importance of studying antibiotic tolerance in the context of bacterial interaction with the host suggest that modulation of the host response may represent a viable therapeutic strategy to sensitize S. aureus to antibiotics.
Rapid identification of Sars-CoV-2 variants of concern using the portable peakPCR platform
Authors: Hosch Salome , Bechtold Philippe , Wagner Philipp , Ruiz-Serrano Amalia , Gregorini Michele , Siegrist Denise , Engler Olivier , Stark Wendelin J. , Daubenberger Claudia A. , Schindler Tobias
Published: May 2021

The need for tools which allow rapid detection and continuous monitoring of Sars-CoV-2 variants of concern (VOC) is greater than ever, as these variants are more transmissible and therefore increase the pressure of COVID-19 on healthcare systems. To address this demand, we aimed to develop and evaluate a robust and fast diagnostic approach for identification of Sars-CoV-2 VOC-associated spike gene mutations. Our diagnostic assays detect the E484K and N501Y SNPs as well as a spike gene deletion (HV69/70) and can be run on standard laboratory equipment or on the portable rapid diagnostic technology platform peakPCR. The assays achieved excellent diagnostic performance when tested with RNA extracted from culture-derived Sars-CoV-2 VOC lineages. Simplicity of usage and the relatively low costs are advantages which make our approach well-suited for decentralized and rapid testing, especially in resource limited settings.
The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions
Authors: Sachak-Patwa R. , Byrne H.M. , Dyson L. , Thompson R.N.
Published: May 2021

Countries around the world have introduced travel restrictions to reduce SARS-CoV-2 transmission. As vaccines are gradually rolled out, attention has turned to when travel restrictions and other non-pharmaceutical interventions (NPIs) can be relaxed. Here, using SARS-CoV-2 as a case study, we develop a mathematical branching process model to assess the risk that, following the removal of NPIs, cases introduced into new locations initiate a local outbreak. Our model accounts for changes in background population immunity due to vaccination. We consider two locations in which the vaccine rollout has progressed quickly – specifically, the Isle of Man (a British crown dependency in the Irish Sea) and the country of Israel. Rather than aiming to make exact quantitative predictions about the outbreak risk in different locations, we instead use data from these locations to demonstrate the general principle that the outbreak risk is unlikely to be eliminated completely when travel restrictions and other NPIs are removed in low prevalence settings. This conclusion holds even once vaccine programmes are completed. Key factors underlying these results are the potential for transmission even following vaccination, incomplete vaccine uptake, and the recent emergence of SARS-CoV-2 variants with increased transmissibility. Combined, these factors suggest that when travel restrictions are relaxed, it will still be necessary to implement surveillance of incoming passengers to identify infected individuals quickly. This measure, as well as tracing and testing (and/or isolating) contacts of detected infected passengers, should remain in place to suppress potential outbreaks until case numbers globally are reduced.
Wnt/β-catenin inhibition disrupts drug-tolerance in isogenic carboplatin-resistant models of Triple-Negative Breast Cancer
Authors: de Oliveira Willy Antoni Abreu , Moens Stijn , El Laithy Youssef , van der Veer Bernard K. , Athanasouli Paraskevi , Cortesi Emanuela Elsa , Baietti Maria Francesca , Koh Kian Peng , Ventura Juan-Jose , Amant Frédéric , Annibali Daniela , Lluis Frederic
Published: May 2021

Triple-Negative Breast Cancer (TNBC) is the most aggressive breast cancer subtype, characterized by both limited treatment options and higher relapse rates than hormone-receptor-positive breast cancers. Chemotherapy remains the mainstay treatment for TNBC, and platinum salts have been explored as a therapeutic alternative in neo-adjuvant and metastatic settings. However, primary and acquired resistance to chemotherapy in general and platinum-based regimens specifically strongly hampers TNBC management. In this study, we used carboplatin-resistant in vivo patient-derived xenograft and isogenic TNBC cell-line models and detected enhanced Wnt/β-catenin activity correlating with an induced expression of stem cell markers in both resistant models. In accordance, the activation of canonical Wnt signaling in parental TNBC cell lines increases stem cell markers’ expression, formation of tumorspheres, and promotes carboplatin resistance. Finally, we prove that Wnt signaling inhibition resensitizes resistant models to carboplatin both in vitro and in vivo, suggesting the synergistic use of Wnt inhibitors and carboplatin as a therapeutic option in TNBC. Here we provide evidence for a prominent role of Wnt signaling in mediating resistance to carboplatin, and we establish that combinatorial targeting of Wnt signaling overcomes carboplatin resistance enhancing chemotherapeutic drug efficacy.
NMR solution structure and analysis of isolated S3b-S4a motif of repeat IV of the human cardiac sodium channel
Authors: Hussein Adel K. , Bhuiyan Mohammed H. , Arshava Boris , Zhuang Jianqin , Poget Sébastien F.
Published: May 2021

Voltage-gated sodium channels are membrane proteins that play an important role in the propagation of electrical signals by mediating the rising phase of an action potential. Numerous diseases, including epilepsy, extreme pain, and certain cardiac arrhythmias have been linked to defects in these channels. The S3b-S4a helix-turn-helix motif (paddle motif) is a region of the channel that is involved in voltage sensing and undergoes significant structural changes during gating. It is also the binding site for many gating-modifier toxins. We determined the solution structure of the paddle motif from the fourth repeat of NaV1.5 in dodecylphosphocholine micelles by NMR spectroscopy and investigated its dynamics and micelle interactions. The structure displays a helix hairpin with a short connecting loop, and likely represents the activated conformation with three of the first four gating charges facing away from S3. Furthermore, paramagnetic relaxation measurements show that the paddle motif is mainly interacting with the interface region of the micelle. NMR relaxation studies reveal that the paddle motif is mostly rigid, with some residues around the loop region and the last 4 residues on the C-terminus displaying heightened mobility. The structural findings reported here allowed the interpretation of three disease-causing mutations in this region of the human cardiac sodium channel, S1609W, F1617del and T1620M. The establishment of this model system for NMR studies of the paddle region offers a promising platform for future toxin interaction studies in the cardiac sodium channels, and similar approaches may be applied to other sodium channel isoforms.
Dynamic profiling and functional interpretation of histone lysine crotonylation and lactylation during neural development
Authors: Dai Shang-Kun , Liu Pei-Pei , Teng Zhao-Qian , Liu Chang-Mei
Published: May 2021

Background

Metabolites such as crotonyl-CoA and lactyl-CoA influence gene expression through covalently modifying histones, known as histone lysine crotonylation (Kcr) and histone lysine lactylation (Kla). However, their existence patterns, dynamic changes, biological functions, as well as associations with histone lysine acetylation (Kac) and gene expression during mammalian development remain largely unknown, which imped us from understanding the epigenetic regulations of histone lysine acylations.

Results

Histone Kcr and Kla are widely distributed and undergo global changes during neural development. By profiling genome-wide dynamics of H3K9ac, H3K9cr and H3K18la in combination with ATAC sequencing and RNA sequencing, we reveal that these histone marks cooperatively regulate chromatin state and gene expression, as well as promote transcriptome remodelling to favour cell fate transition in the developing telencephalon. Importantly, we demonstrate that global histone Kcr and Kla are not consequence of transcription and furtherly identify histone deacetylase 1-3 (HDAC1-3) as novel “erasers” of H3K18la. Taking advantage of induced differentiation system of P19 embryonal carcinoma (EC) cells, we find that a selective inhibitor of HDAC1-3, MS-275 pre-activates neural fate-related transcriptional programs via stimulating multiple histone lysine acylations simultaneously.

Conclusions

Our study uncover the interplays between histone lysine acylations to regulate gene expression and the differentiation-promoting functions of histone Kcr and Kla during development, and provide evidence that multiple histone lysine actlations synchronously alternate to orchestrate transcriptome responding under HDACs inhibition.
Urinary Metabolomics from a Dose-Fractionated Polymyxin B Rat Model of Acute Kidney Injury
Authors: Locci Emanuela , Liu Jiajun , Pais Gwendolyn M. , Chighine Alberto , Kahnamoei Dariusc Andrea , Xanthos Theodoros , Chalkias Athanasios , Lee Andrew , Hauser Alan R. , Chang Jack , Rhodes Nathaniel J. , d’Aloja Ernesto , Scheetz Marc H.
Published: May 2021

Background

Polymyxin B remains an important antimicrobial against multi-drug resistant bacteria; however, kidney injury is often a treatment limiting event with kidney failure rates that range from 5-13%.

Methods

Samples were obtained from a previously conducted study of male Sprague-Dawley rats that received dose fractionated polymyxin B (12 mg/kg/day subcutaneously) once daily (QD), twice daily (BID), and thrice daily (TID) for three days. In the original study, urinary biomarkers and kidney histopathology scores were determined. Urine was sampled daily and analyzed for urinary metabolites via 1H NMR analysis.

Unsupervised Principal Components Analysis was applied for exploratory data analysis to identify trends and outliers in the spectral data. Then, supervised Orthogonal Partial Least Square Discriminant Analysis was applied to classify the samples collected in different days and identify metabolic differences during the treatment. Metabolomes were compared across study groups (i.e. those receiving QD, BID, TID, and control) using a mixed-effects models. Spearman correlation was performed for injury biomarkers and the metabolome.

Results

A total of 27 rats contributed 77 urinary samples; n=25 rats were included that were treated with Polymyxin B and n=2 received saline. Pre-dosing samples clustered well and were characterized by higher amounts of citrate, 2-oxoglutarate, and Hippurate. On day 1 post treatment, day 1 samples showed higher taurine; day 3 samples had higher lactate, acetate and creatine. Taurine was the only metabolite significantly increased in both BID and TID compared to QD group. Taurine on day 1 correlated with increasing histopathology scores (Spearman’s rho = 0.4167, P=0.038) and KIM-1 (Spearman’s rho =0.4052, P=0.036); whereas KIM-1 on day one and day 3 did not reach significance with histopathology (Spearman’s rho = 0.3248, P=0.11 and Spearman’s rho = 0.3739, P=0.066).

Conclusion

Polymyxin B causes increased amounts of urinary taurine on day 1 which then normalizes to baseline concentrations. Taurine may provide one of the earlier signals of acute kidney damage caused by polymyxin B.
A semi-variance approach to visualising phylogenetic autocorrelation
Authors: Noonan M. J. , Fagan W. F. , Fleming C. H.
Published: May 2021

Comparing traits across species has been a hallmark of biological research for centuries. While inter-specific comparisons can be highly informative, phylogenetic inertia can bias estimates if not properly accounted for in comparative analyses. In response, researchers typically treat phylogenetic inertia as a form of autocorrelation that can be detected, modelled, and corrected for. Despite the range of methods available for quantifying the strength of phylogenetic autocorrelation, no tools exist for visualising these autocorrelation structures.

Here we derive variogram methods suitable for phylogenic data, and show how they can be used to straightforwardly visualise phylogenetic autocorrelation. We then demonstrate their utility for three empirical examples: sexual size dimorphism (SSD) in the Musteloidea, maximum per capita rate of population growth,r, in the Carnivora, and brain size in the Artiodactyla.

When modelling musteloid SSD, the empirical variogram showed a tendency for the variance in SSD to stabilise over time, a characteristic feature of Ornstein-Uhlenbeck (OU) evolution. In agreement with this visual assessment, model selection identified the OU model as the best fit to the data. In contrast, the infinitely diffusive Brownian Motion (BM) model did not capture the asymptotic behaviour of the variogram and was less supported than the OU model. Phylogenetic variograms proved equally useful in understanding why an OU model was selected when modellingrin the Carnivora, and why BM was the selected evolutionary model for brain size in the Artiodactyla.

Because the variograms of the various evolutionary processes each have different theoretical profiles, comparing fitted semi-variance functions against empirical semi-variograms can serve as a useful diagnostic tool, allowing researchers to understand why any given evolutionary model might be selected over another, which features are well captured by the model, and which are not. This allows for fitted models to be compared against the empirical variogram, facilitating model identification prior to subsequent analyses. We therefore recommend that any phylogenetic analysis begin with a non-parametric estimate of the autocorrelation structure of the data that can be visualized. The methods developed in this work are openly available in the newRpackagectpm.
The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments
Authors: Waltz Florent , Salinas-Giegé Thalia , Englmeier Robert , Meichel Herrade , Soufari Heddy , Kuhn Lauriane , Pfeffer Stefan , Förster Friedrich , Engel Benjamin D. , Giegé Philippe , Drouard Laurence , Hashem Yaser
Published: May 2021

Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green algaChlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Novel proteins, mainly helical repeat proteins, including OPR, PPR and mTERF proteins are found in Chlamydomonas mitoribosome, revealing the first structure of an OPR protein in complex with its RNA target. Targeted amiRNA silencing indicated that the novel ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the mitochondrial inner membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of the mitoribosome diversity and the various strategies they adopt for membrane tethering.

Highlights

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Structure of theChlamydomonas reinhardtiimitoribosome

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Fragmented ribosomal RNAs are stabilized by highly intertwined interactions with Chlamydomonas-specific proteins

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Specific r-proteins are essential for rRNA homeostasis and respiratory fitness

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Cryo-ET reveals the mitoribosome association to the inner mitochondrial membrane
Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution
Authors: Ansari Narjes , Rizzi Valerio , Carloni Paolo , Parrinello Michele
Published: May 2021

The main protease from SARS-CoV-2 is a homodimer. Yet, a recent 0.1 ms long molecular dynamics simulation shows that it readily undergoes a symmetry breaking event on passing from the solid state to the aqueous solution. As a result, the subunits present distinct conformations of the binding pocket. By analysing this long time simulation, here we uncover a previously unrecognised role of water molecules in triggering the transition. Interestingly, each subunit presents a different collection of long-lived water molecules. Enhanced sampling methods performed here, along with machine learning approaches, further establish that the transition to the asymmetric state is essentially irreversible.
Decoding activity in Broca’s area predicts the occurrence of auditory hallucinations across subjects
Authors: Fovet Thomas , Yger Pierre , Lopes Renaud , de Pierrefeu Amicie , Duchesnay Edouard , Houenou Josselin , Thomas Pierre , Szaffarczyk Sébastien , Domenech Philippe , Jardri Renaud
Published: May 2021

BACKGROUND

Functional magnetic resonance imaging (fMRI) capture aims at detecting auditory-verbal hallucinations (AVHs) from continuously recorded brain activity. Establishing efficient capture methods with low computational cost that easily generalize between patients remains a key objective in precision psychiatry. To address this issue, we developed a novel automatized fMRI-capture procedure for AVHs in schizophrenia patients.

METHODS

We used a previously validated, but labor-intensive, personalized fMRI-capture method to train a linear classifier using machine-learning techniques. We benchmarked the performances of this classifier on 2320 AVH periods vs. resting-state periods obtained from schizophrenia patients with frequent symptoms (n=23). We characterized patterns of BOLD activity that were predictive of AVH both within- and between-subjects. Generalizability was assessed with a second independent sample gathering 2000 AVH labels (n=34 schizophrenia patients), while specificity was tested with a nonclinical control sample performing an auditory imagery task (840 labels, n=20).

RESULTS

Our between-subject classifier achieved high decoding accuracy (area-under-the-curve, AUC = 0.85) and discriminated AVH from rest and verbal imagery. Optimizing the parameters on the first schizophrenia dataset and testing its performance on the second dataset led to a 0.85 out-of-sample AUC (0.88 for the converse test). We showed that AVH detection critically depends on local BOLD activity patterns within Broca’s area.

CONCLUSIONS

Our results demonstrate that it is possible to reliably detect AVH-states from BOLD signals in schizophrenia patients using a multivariate decoder without performing complex regularization procedures. These findings constitute a crucial step toward brain-based treatments for severe drug-resistant hallucinations.
Polo-like kinase 2 inhibition reduces serine-129 phosphorylation of physiological nuclear alpha-synuclein but not of the aggregated alpha-synuclein
Authors: Elfarrash Sara , Jensen Nanna Møller , Ferreira Nelson , Schmidt Sissel Ida , Gregersen Emil , Vestergaard Marie Vibeke , Nabavi Sadegh , Meyer Morten , Jensen Poul Henning
Published: May 2021

Accumulation of aggregated alpha-synuclein (α-syn) is believed to play a pivotal role in the pathophysiology of Parkinson’s disease (PD) and other synucleinopathies. α-Syn is a key constituent protein of Lewy pathology, and α-syn phosphorylated at serine-129 (pS129) constitutes more than 90% of α-syn in Lewy bodies and hence, it is used extensively as a pathological marker for the aggregated form of α-syn. However, the exact role of pS129 remains controversial as well as the kinase(s) responsible for the phosphorylation.

In this study, we investigated the effect of Polo-like kinase 2 (PLK2) inhibition on formation of pS129 using ex-vivo organotypic brain slice model of synucleinopathy. Our data demonstrated that PLK2 inhibition has no effect on α-syn aggregation, pS129 or inter-neuronal spreading of the aggregated α-syn seen in the organotypic slices. Instead, PLK2 inhibition reduced the soluble nuclear pS129 level confined in the nuclei. The same finding was replicated in an in-vivo mouse models of templated α-syn aggregation and human dopaminergic neurons, suggesting that PLK2 is more likely to be involved in S129 phosphorylation of soluble non-pathology related fraction of α-syn. We also demonstrated that reduction of nuclear pS129 but not the aggregates specific pS129 following PLK2 inhibition for a short time before sample collection improves the signal to noise ratio when quantifying pS129 aggregate pathology.
Vegetation characteristics control sediment and nutrient retention on but not underneath vegetation in floodplain meadows
Authors: Kretz Lena , Bondar-Kunze Elisabeth , Hein Thomas , Richter Ronny , Schulz-Zunkel Christiane , Seele-Dilbat Carolin , van der Plas Fons , Vieweg Michael , Wirth Christian
Published: May 2021

Sediment and nutrient retention are essential ecosystem functions that floodplains provide and that improve river water quality. During floods, the floodplain vegetation retains sediment, which settles on plant surfaces and the soil underneath plants. Both sedimentation processes require that flow velocity is reduced, which may be caused by the topographic features and the vegetation structure of the floodplain. However, the relative importance of these two drivers and their key components have rarely been both quantified. In addition to topographic factors, we expect vegetation height and density, mean leaf size and pubescence, as well as species diversity of the floodplain vegetation to increase the floodplain’s capacity for sedimentation. To test this, we measured sediment and nutrients (carbon, nitrogen and phosphorus) both on the vegetation itself and on sediment traps underneath the vegetation after a flood at 24 sites along the River Mulde (Germany). Additionally, we measured biotic and topographic predictor variables. Sedimentation on the vegetation surface was positively driven by plant biomass and the height variation of the vegetation, and decreased with the hydrological distance (total R2=0.56). Sedimentation underneath the vegetation was not driven by any vegetation characteristics but decreased with hydrological distance (total R2=0.42). Carbon, nitrogen and phosphorus content in the sediment on the traps increased with the total amount of sediment (total R2=0.64, 0.62 and 0.84, respectively), while C, N and P on the vegetation additionally increased with hydrological distance (total R2=0.80, 0.79 and 0.92, respectively). This offers the potential to promote sediment and especially nutrient retention via vegetation management, such as adapted mowing. The pronounced signal of the hydrological distance to the river emphasises the importance of a laterally connected floodplain with abandoned meanders and morphological depressions. Our study improves our understanding of the locations where floodplain management has its most significant impact on sediment and nutrient retention to increase water purification processes.
Larval dispersal of Brachyura in the largest estuarine / marine system in the world
Authors: de Lima Francielly Alcântara , Butturi-Gomes Davi , das Neves Pantoja Marcela Helena , Martinelli-Lemos Jussara Moretto
Published: May 2021

For the first time, this study monitored six sites in a wide transect with approximately 240 km radius on the Amazon Continental Shelf (ACS) every three months. The objective was to analyze the larval composition of Brachyura, its abundance in shallow/subsurface and oblique hauls, the extent of larval dispersion related to the estuary/plume, and to predict the probability of occurrence and abundance for the temperature, salinity, and chlorophyll-aprofiles of the water column. A total of 17,759 identified larvae are distributed in 8 families and 25 taxa. The water salinity was the best predictor of larval distribution. The statistical models used indicated that Panopeidae and Portunidae larvae are more frequent and more likely to occur in shallow water layers, while Calappidae occur in deeper layers, and Grapsidae, Ocypodidae, Sesarmidae, Pinnotheridae and Leucosiidae occur similarly in both strata. The larval dispersion extent varies among families and throughout the year while the groups are distributed in different salinities along the platform. The probability of occurrence of Portunidae is higher in ocean water (> = 33.5); Grapsidae, Panopeidae, and Pinnotheridae is higher in intermediate and ocean salinity waters (25.5 to 33.5); Ocypodidae, Sesarmidae and Calappidae is higher in estuarine and intermediate salinity waters (5 to 25.5), whereas Leucosiidae, euryhaline, occur in all salinities (5 to 33.5). Furthermore, the Amazon River seasonal flow and plume movement throughout the year not only regulate the larval distribution and dispersion of estuarine species but are fundamental for the ACS species, providing the necessary nutrient input for larval development in the region plankton.
Pursuit of chlorovirus genetic transformation and CRISPR/Cas9-mediated gene editing
Authors: Noel Eric A. , Weeks Donald P. , Van Etten James L.
Published: May 2021

The ability to carry out genetic and molecular modifications of the large dsDNA chloroviruses, with genomes of 290 to 370 kb, would expedite studies to elucidate the functions of both identified and unidentified virus-encoded proteins. These plaque-forming viruses replicate in certain unicellular, eukaryotic chlorella-like green algae and are present in freshwater environments throughout the world. However, to date, only a few of these algal species and virtually none of their viruses have been genetically manipulated due to lack of practical methods for genetic transformation and genome editing. In an effort to develop gene editing tools for modifying specific chlorovirus CA-4B genes using preassembled Cas9 protein-sgRNA ribonucleoproteins (RNPs), we first tested multiple methods for delivery of Cas9/sgRNA RNP complexes into infected cells including cell wall-degrading enzymes, electroporation, silicon carbide (SiC) whiskers, and cell-penetrating peptides (CPPs). Agrobacterium -mediated transfection of chlorovirus host Chlorella variabilis NC64A with a binary vector containing a chlorovirus-encoded glycosyltransferase mutant gene was also examined. Attempts at developing a reliable chlorovirus transformation system were unsuccessful. However, in one experiment two independent virus mutants were isolated from macerozyme-treated NC64A cells incubated with Cas9/sgRNA RNPs targeting CA-4B-encoded gene 034r, which encodes a putative glycosyltransferase. Selection of these mutants using antibodies was dependent on a specific change in the pattern of glycans attached to the virus’ major capsid protein (MCP). Analysis of DNA sequences from the two mutant viruses showed highly targeted nucleotide sequence modifications in the 034r gene of each virus that were fully consistent with Cas9/RNP-directed gene editing. However, we were unable to duplicate these results and therefore unable to achieve a reliable system to genetically edit chloroviruses. Nonetheless, these observations provide strong initial suggestions that Cas9/RNPs may function to promote editing of the chlorovirus genome, and that further experimentation is warranted and worthwhile.
Analyzing Biomarker Discovery: Estimating the Reproducibility of Biomarker Sets
Authors: Forouzandeh Amir , Rutar Alex , Kalmady Sunil V , Greiner Russell
Published: May 2021

Many researchers try to understand a biological condition by identifying biomarkers. This is typically done using univariate hypothesis testing over a labeled dataset, declaring a feature to be a biomarker if there is a significant statistical difference between its values for the subjects with different outcomes. However, such sets of proposed biomarkers are often not reproducible – subsequent studies often fail to identify the same sets. Indeed, there is often a very small overlap between the biomarkers proposed in pairs of related studies that explore the same phenotypes over the same distribution of subjects. This paper first defines the Reproducibility Score for a labeled dataset as a measure (taking values between 0 and 1) of the reproducibility of the results produced by an arbitrary fixed biomarker discovery process for a given distribution of subjects. We then provide ways to reliably estimate this score by defining algorithms that produce an over-bound and an under-bound for this score for a given dataset and biomarker discovery process, for the case of univariate hypothesis testing on dichotomous groups. We confirm that these approximations are meaningful by providing empirical results on a large number of datasets and show that these predictions match known reproducibility results. We have also created a publicly available website, hosted at https://biomarker.shinyapps.io/BiomarkerReprod/, that produces these Reproducibility Score approximations for any given dataset (with continuous or discrete features and binary class labels).
Vascular epiphytes contribute disproportionately to global centres of plant diversity
Authors: Taylor Amanda , Zotz Gerhard , Weigelt Patrick , Cai Lirong , Karger Dirk Nikolaus , König Christian , Kreft Holger
Published: May 2021

Aim

Vascular epiphytes are ubiquitous features of wet tropical forests where they contribute substantially to local and regional plant diversity. While some basic epiphyte distribution patterns are relatively well studied, little effort has been made to understand the drivers responsible for constraining their global distribution. This study quantifies the substantial contribution of epiphytes to global gradients and centres of vascular plant diversity and explores whether epiphytes vary from terrestrial plants in relation to contemporary and historical environmental variables.

Location

Global.

Time period

Present.

Major taxa studied

Vascular epiphytes.

Methods

We integrated EpiList 1.0, a comprehensive list comprising > 30,000 vascular epiphyte species, and species distributions derived from the GIFT database to describe the global biogeography of epiphytes. We used generalized linear mixed effects models to assess the relationship between epiphytic and terrestrial plant diversity, and contemporary and historical environmental predictors.

Results

We find that epiphytes substantially contribute to global centres of vascular plant diversity, accounting for up to 39% of the vascular flora in the Neotropics. Epiphytes decrease in species numbers with increasing latitude at a rate three times faster than terrestrial plants, a trend that is driven mainly by the distribution of tropical forests and precipitation. Further, large regional differences emerge that are explained by several large endemic angiosperm families (e.g., Neotropical Bromeliaceae) that are absent in other tropical regions.

Main conclusions

Our results show that epiphytes are disproportionately diverse in most global centres of plant diversity and play an important role in driving the global latitudinal diversity gradient for plants. The distribution of precipitation and tropical forests emerge as major drivers of the latitudinal diversity gradient in epiphyte species richness. Finally, our findings demonstrate how epiphyte floras in different biogeographical realms are composed of different families and higher taxa revealing an important signature of historical biogeography.
A dentate gyrus– CA3 inhibitory circuit promotes evolution of hippocampal-cortical ensembles during memory consolidation
Authors: Twarkowski Hannah , Steininger Victor , Kim Min Jae , Sahay Amar
Published: May 2021

Memories encoded in the dentate gyrus (DG) – CA3 circuit of the hippocampus are routed from CA1 to anterior cingulate cortex (ACC) for consolidation. Although CA1 parvalbumin inhibitory neurons (PV INs) orchestrate hippocampal-cortical communication, we know less about CA3 PV INs or DG – CA3 principal neuron – IN circuit mechanisms that contribute to evolution of hippocampal-cortical ensembles during memory consolidation. Using viral genetics to selectively mimic and boost an endogenous learning-dependent circuit mechanism, DG cell recruitment of CA3 PV INs and feed-forward inhibition (FFI) in CA3, in combination with longitudinal in vivo calcium imaging, we demonstrate that FFI facilitates formation and maintenance of context-associated neuronal ensembles in CA1. Increasing FFI in DG – CA3 promoted context specificity of neuronal ensembles in ACC over time and enhanced long-term contextual fear memory. In vivo LFP recordings in mice with increased FFI in DG – CA3 identified enhanced CA1 sharp-wave ripple – ACC spindle coupling as a potential network mechanism facilitating memory consolidation. Our findings illuminate how FFI in DG – CA3 dictates evolution of ensemble properties in CA1 and ACC during memory consolidation and suggest a teacher-like function for hippocampal CA1 in stabilization and re-organization of cortical representations.