bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA polymerase II pausing in development: orchestrating transcription
Authors: Abuhashem Abderhman , Garg Vidur , Hadjantonakis Anna-Katerina
Published: January 2022

The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.
Extracellular matrix guidance of autophagy: a mechanism regulating cancer growth
Authors: Chen Carolyn G. , Iozzo Renato V.
Published: January 2022

The extracellular matrix (ECM) exists as a dynamic network of biophysical and biochemical factors that maintain tissue homeostasis. Given its sensitivity to changes in the intra- and extracellular space, the plasticity of the ECM can be pathological in driving disease through aberrant matrix remodelling. In particular, cancer uses the matrix for its proliferation, angiogenesis, cellular reprogramming and metastatic spread. An emerging field of matrix biology focuses on proteoglycans that regulate autophagy, an intracellular process that plays both critical and contextual roles in cancer. Here, we review the most prominent autophagic modulators from the matrix and the current understanding of the cellular pathways and signalling cascades that mechanistically drive their autophagic function. We then critically assess how their autophagic functions influence tumorigenesis, emphasizing the complexities and stage-dependent nature of this relationship in cancer. We highlight novel emerging data on immunoglobulin-containing and proline-rich receptor-1, heparanase and thrombospondin 1 in autophagy and cancer. Finally, we further discuss the pro- and anti-autophagic modulators originating from the ECM, as well as how these proteoglycans and other matrix constituents specifically influence cancer progression.
Oxygen sensing with individual ZnO:Sb micro-wires: effects of temperature and light exposure on the sensitivity and stability
Authors: Chhetri Tej Poudel , Kerr Lei , Masmali Nada , Jaeger Herbert , Eid Khalid F.
Published: January 2022

Nanostructured ZnO has been widely investigated as a gas sensing material. Antimony is an important dopant for ZnO that catalyses its surface reactivity and thus strengthens its gas sensing capability. However, there are not enough studies on the gas sensing of antimony-doped ZnO single wires. We fabricated and characterized ZnO/ZnO:Sb core–shell micro-wires and demonstrated that individual wires are sensitive to oxygen gas flow. Temperature and light illumination strongly affect the oxygen gas sensitivity and stability of these individual wires. It was found that these micro- and nano-wire oxygen sensors at 200°C give the highest response to oxygen, yet a vanishingly small effect of light and temperature variations. The underlying physics and the interplay between these effects are discussed in terms of surface-adsorbed oxygen, oxygen vacancies and hydrogen doping.
Reparametrization of the Colle–Salvetti formula
Authors: Baskerville Adam L. , Targema Msugh , Cox Hazel
Published: January 2022

We investigate the Colle–Salvetti (CS) formula, the basis of the Lee, Yang and Parr (LYP) correlation functional used in approximate density functional theory. The CS formula is reparametrized using high-accuracy Hartree–Fock (HF) wavefunctions to determine the accuracy of the formula to calculate anions. Fitting to the hydride ion or the two-electron system just prior to electron detachment at the HF level of theory does not, in general, improve the calculated correlation energies using the parameters derived from the CS/LYP method. An analysis of the CS parameters used in the popular LYP functional demonstrates the ingenuity and perhaps fortuitousness of the original formulation by CS.
Sprinting with prosthetic versus biological legs: insight from experimental data
Authors: Beck Owen N. , Taboga Paolo , Grabowski Alena M.
Published: January 2022

Running-prostheses have enabled exceptional athletes with bilateral leg amputations to surpass Olympic 400 m athletics qualifying standards. Due to the world-class performances and relatively fast race finishes of these athletes, many people assume that running-prostheses provide users an unfair advantage over biologically legged competitors during long sprint races. These assumptions have led athletics governing bodies to prohibit the use of running-prostheses in sanctioned non-amputee (NA) competitions, such as at the Olympics. However, here we show that no athlete with bilateral leg amputations using running-prostheses, including the fastest such athlete, exhibits a single 400 m running performance metric that is better than those achieved by NA athletes. Specifically, the best experimentally measured maximum running velocity and sprint endurance profile of athletes with prosthetic legs are similar to, but not better than those of NA athletes. Further, the best experimentally measured initial race acceleration (from 0 to 20 m), maximum velocity around curves, and velocity at aerobic capacity of athletes with prosthetic legs were 40%, 1–3% and 19% slower compared to NA athletes, respectively. Therefore, based on these 400 m performance metrics, use of prosthetic legs during 400 m running races is not unequivocally advantageous compared to the use of biological legs.
The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain
Authors: Ruan Yongsen , Hou Mei , Tang Xiaolu , He Xionglei , Lu Xuemei , Lu Jian , Wu Chung-I , Wen Haijun
Published: January 2022

In new epidemics after the host shift, the pathogens may experience accelerated evolution driven by novel selective pressures. When the accelerated evolution enters a positive feedback loop with the expanding epidemics, the pathogen’s runaway evolution may be triggered. To test this possibility in COVID-19, we analyze the extensive databases and identify 5 major waves of strains, one replacing the previous one in 2020 – 2021. The mutations differ entirely between waves and the number of mutations continues to increase, from 3-4 to 21-31. The latest wave is the Delta strain which accrues 31 new mutations to become highly prevalent. Interestingly, these new mutations in Delta strain emerge in multiple stages with each stage driven by 6 – 12 coding mutations that form a fitness group. In short, the evolution of SARS-CoV-2 from the oldest to the youngest wave, and from the earlier to the later stages of the Delta wave, is a process of acceleration with more and more mutations. The global increase in the viral population size (M(t), at time t) and the mutation accumulation (R(t)) may have indeed triggered the runaway evolution in late 2020, leading to the highly evolved Alpha and then Delta strain. To suppress the pandemic, it is crucial to break the positive feedback loop between M(t) and R(t), neither of which has yet to be effectively dampened by late 2021. New waves beyond Delta, hence, should not be surprising.
Safety and immunogenicity of anti-SARS CoV-2 conjugate vaccine SOBERANA 02 in a two-dose or three-dose heterologous scheme in adults: Phase IIb Clinical Trial
Authors: Toledo-Romani María Eugenia , García-Carmenate Mayra , Verdecia-Sánchez Leslyhana , Pérez-Rodríguez Suzel , Rodriguez-González Meybis , Valenzuela-Silva Carmen , Paredes-Moreno Beatriz , Sanchez-Ramirez Belinda , González-Mugica Raúl , Hernández-Garcia Tays , Orosa-Vázquez Ivette , Díaz-Hernández Marianniz , Pérez-Guevara María Teresa , Enriquez-Puertas Juliet , Noa-Romero Enrique , Palenzuela-Diaz Ariel , Baro-Roman Gerardo , Mendoza-Hernández Ivis , Muñoz Yaima , Gómez-Maceo Yanet , Santos-Vega Bertha Leysi , Fernandez-Castillo Sonsire , Climent-Ruiz Yanet , Rodríguez-Noda Laura , Santana-Mederos Darielys , García-Vega Yanelda , Wu-Chen Guang , Doroud Delaram , Biglari Alireza , Boggiano-Ayo Tammy , Valdés-Balbín Yury , García-Rivera Daniel , García-Rivera Dagmar , Vérez-Bencomo Vicente ,   SOBERANA Research Group
Published: January 2022

Background

We report results of immunogenicity, safety and reactogenicity of SOBERANA 02 in a two-dose or three-dose heterologous scheme in adults in a phase IIb clinical trial.

Method

This phase IIb trial was designed as parallel, multicentre, adaptive, double blind, randomized and placebo-controlled. Subjects (N=810) aged 19-80 years were randomized to receive two doses of the recombinant SARS CoV-2 receptor binding domain (RBD) conjugated to tetanus toxoid (SOBERANA 02) and a third dose of dimeric RBD (SOBERANA Plus) 28 days apart; two production batches of active ingredient of SOBERANA 02 were evaluated. Primary outcome was the percentage of seroconverted subjects with ≥4-fold the anti-RBD IgG concentration. Secondary outcomes were safety, reactogenicity and neutralizing antibodies.

Results

Seroconversion rate in vaccinees was respectively 76.3 and 96.8% after two or three doses, compared with 7.3% in placebo group. Anti-RBD IgG increased significantly after first and second dose of SOBERANA 02 respect to placebo group; and the third dose with SOBERANA Plus boosts the response compared to the second dose. Neutralizing IgG antibodies were detected against D614G and VOCs α, β and δ. Specific and functional antibodies were detected at least until 7-8 months after the third dose. The frequency of serious adverse events (AEs) associated with vaccination was very low (0.1%); with only one serious AE consistent with vaccination. Local pain was the most frequent AE.

Conclusions

Two doses of SOBERANA 02 were well tolerated, safe an immunogenic in adults aged 19-80 years old. The heterologous combination with a third dose of SOBERANA Plus increased neutralizing antibodies, detectable 7-8 months after finishing the vaccination schedule.

Trial registry

https://rpcec.sld.cu/trials/RPCEC00000347
Seroresponse to third doses of SARS-CoV-2 vaccine among patients receiving maintenance dialysis
Authors: Hsu Caroline M. , Lacson Eduardo K. , Manley Harold J. , Aweh Gideon N. , Miskulin Dana , Johnson Doug , Weiner Daniel E.
Published: January 2022

Given the increased morbidity and mortality from COVID-19 among patients undergoing maintenance dialysis, we examined the seroresponse to an additional dose of SARS-CoV-2 mRNA vaccine, using a hypothesized protective anti-spike protein IgG antibody threshold of 7 based on prior work. Among 395 patients, 384 (97%) had seroresponse ≥7 following administration of the third dose. Among those with suboptimal (peak <7) and minimal (peak <1) seroresponse to an initial mRNA vaccine regimen, the rate of seroresponse ≥7 following a third dose was 97% (36 of 37) and 64% (14 of 22), respectively. Given ongoing high rates of COVID-19 and rapidly waning immunity after an initial vaccine series, we recommend a third mRNA vaccine dose be standard for all patients receiving maintenance dialysis.
The French Covid-19 vaccination policy did not solve vaccination inequities: a nationwide longitudinal study on 64.5 million individuals
Authors: Débarre F. , Lecoeur E. , Guimier L. , Jauffret-Roustide M. , Jannot A.-S.
Published: January 2022

Context

To encourage Covid-19 vaccination, France introduced during the Summer 2021 a “Sanitary Pass,” which morphed into a “Vaccine Passe” in early 2022. While the Sanity Pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French Sanitary and Vaccine Pass’ efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.

Methods

We considered the association between being a district above the median value of the first-dose vaccination rates and being above the median value of each indicator at different time points: just before the sanitary pass announcement (week 2021-W27), just before the sanitary pass came into force (week 2021-W31) and one month after (week 2021-W35), and the equivalent dates for the vaccine pass (weeks 2021-W49, 2022-W03, 2022-W07). We then considered the change over time of vaccination rates according to deciles of the three of the most associated indicators.

Results

The indicators most associated with vaccination rates were the share of local income coming from unemployment benefits, the proportion of overcrowded households, the proportion of immigrants in the district, and vote for an “anti-establishment” candidate at the 2017 Presidential election. Vaccination rate also were also contrasted along a North-West – South East axis, with lower vaccination coverage in the South-East of France.

Conclusion

Our analysis reveals that, both before and after the introduction of the French sanitary and vaccination passes, factors with the largest impact are related to poverty, immigration, and trust in the government.
ifCNV: a novel isolation-forest-based package to detect copy number variations from various NGS datasets
Authors: Cabello-Aguilar Simon , Vendrell Julie A. , Van Goethem Charles , Brousse Mehdi , Gozé Catherine , Frantz Laurent , Solassol Jérôme
Published: January 2022

Copy number variations (CNVs) are an essential component of genetic variation distributed across large parts of the human genome. CNV detection from next-generation sequencing data and artificial intelligence algorithms has progressed in recent years. However, only a few tools have taken advantage of machine learning algorithms for CNV detection, and none propose using artificial intelligence to automatically detect probable CNV-positive samples. Furthermore, in general, most CNV software that is developed for specific data types has sub-optimal reliability for routine practice. In addition, the most developed approach is to use a reference or normal dataset to compare with the samples of interest, and it is well known that selecting appropriate normal samples represents a challenging task which dramatically influences the precision of results in all CNV-detecting tools. With careful consideration of these issues, we propose here ifCNV, a new software based on isolation forests that creates its own reference, available in R and python with customisable parameters. ifCNV combines artificial intelligence using two isolation forests and a comprehensive scoring method to faithfully detect CNVs among various samples. It was validated using datasets from diverse origins (capture and amplicon, germline and somatic), and it exhibits high sensitivity, specificity and accuracy. ifCNV is a publicly available open-source software that allows the detection of CNVs in many clinical situations.

Key points

Copy number variation detection

Machine learning

Localisation scoring

Benchmark on various clinical situations and on various datasets

Easy-to-use R and Python open-source Package
Structural and computational insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction
Authors: Lan Jun , He Xinheng , Ren Yifei , Wang Ziyi , Zhou Huan , Fan Shilong , Zhu Chenyou , Liu Dongsheng , Shao Bin , Liu Tie-Yan , Wang Qisheng , Zhang Linqi , Ge Jiwan , Wang Tong , Wang Xinquan
Published: January 2022

Since SARS-CoV-2 Omicron variant (B.1.1.529) was reported in November 2021, it has quickly spread to many countries and outcompeted the globally dominant Delta variant in several countries. The Omicron variant contains the largest number of mutations to date, with 32 mutations located at spike (S) glycoprotein, which raised great concern for its enhanced viral fitness and immune escape[1–4]. In this study, we reported the crystal structure of the receptor binding domain (RBD) of Omicron variant S glycoprotein bound to human ACE2 at a resolution of 2.6 Å. Structural comparison, molecular dynamics simulation and binding free energy calculation collectively identified four key mutations (S477N, G496S, Q498R and N501Y) for the enhanced binding of ACE2 by the Omicron RBD compared to the WT RBD. Representative states of the WT and Omicron RBD-ACE2 systems were identified by Markov State Model, which provides a dynamic explanation for the enhanced binding of Omicron RBD. The effects of the mutations in the RBD for antibody recognition were analyzed, especially for the S371L/S373P/S375F substitutions significantly changing the local conformation of the residing loop to deactivate several class IV neutralizing antibodies.
Pathogens in exacerbations of chronic rhinosinusitis differ in sensitivity to silver nanoparticles
Authors: Szaleniec Joanna , Gibała Agnieszka , Stalińska Joanna , Oćwieja Magdalena , Żeliszewska Paulina , Drukała Justyna , Szaleniec Maciej , Gosiewski Tomasz
Published: January 2022

Purpose

The significance of the microbiome in chronic rhinosinusitis (CRS) is not clear. Antimicrobials are recommended in acute exacerbations of the disease (AECRS). Increasing rates of antibiotic resistance stimulate research on alternative therapeutic options including silver nanoparticles (AgNPs), sometimes referred to as “colloidal silver”. However, there are concerns regarding the safety of silver administration and the emergence of silver resistance. The aim of this cross-sectional observational study was to assess the sensitivity of sinonasal pathogens to AgNPs and compare it with the toxicity of AgNPs for nasal epithelial cells.

Methods

Negatively charged AgNPs (12±5 nm) were synthetized using tannic acid. The minimal inhibitory concentration (MIC) for pathogens isolated from patients with AECRS was approximated. Cytotoxicity of AgNPs was tested in vitro on human nasal epithelial cells line.

Results

48 clinical isolates and 4 reference strains were included in the study (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Acinetobacter baumanii, Serratia marcescens, Enterobacter cloacae). The MIC values differed between isolates, even within the same species. All the isolates (including antibiotic resistant) were sensitive to AgNPs in concentrations nontoxic to human cells during 24 h exposition. However, 48 h exposition to AgNPs increased toxicity to human cells, narrowing their therapeutic window and enabling 19% of pathogens to resist the AgNPs’ biocidal action.

Conclusions

AgNPs are effective against most pathogens isolated from patients with AECRS, but sensitivity testing may be necessary before application. Results of sensitivity testing for reference strains cannot be extrapolated to other strains of the same species.
Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series
Authors: Adamson Blythe , Sikka Robby , Wyllie Anne L. , Premsrirut Prem
Published: January 2022

The performance of Covid-19 diagnostic tests must continue to be reassessed with new variants of concern. The objective of this study was to describe the discordance in saliva SARS-CoV-2 PCR and nasal rapid antigen test results during the early infectious period. We identified a high-risk occupational case cohort of 30 individuals with daily testing during an Omicron outbreak in December 2021. Based on viral load and transmissions confirmed through epidemiological investigation, most Omicron cases were infectious for several days before being detectable by rapid antigen tests.
The onset of whole-body regeneration inBotryllus schlosseri: morphological and molecular characterization
Authors: Ricci Lorenzo , Salmon Bastien , Olivier Caroline , Andreoni-Pham Rita , Chaurasia Ankita , Alie Alexandre , Tiozzo Stefano
Published: January 2022

Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body.

In this manuscript, we characterized the onset of WBR inBotryllus schlosseri,one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization,in vivoobservations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR inB. schlosseriis initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis inB. schlosseriand allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.
The AMA1-RON complex drives Plasmodium sporozoite invasion in the mosquito and mammalian hosts
Authors: Fernandes Priyanka , Loubens Manon , Le Borgne Rémi , Marinach Carine , Ardin Beatrice , Briquet Sylvie , Vincensini Laetitia , Hamada Soumia , Hoareau-Coudert Bénédicte , Verbavatz Jean-Marc , Weiner Allon , Silvie Olivier
Published: January 2022

Plasmodium sporozoites that are transmitted by blood-feeding female Anopheles mosquitoes invade hepatocytes for an initial round of intracellular replication, leading to the release of merozoites that invade and multiply within red blood cells. Sporozoites and merozoites share a number of proteins that are expressed by both stages, including the Apical Membrane Antigen 1 (AMA1) and the Rhoptry Neck Proteins (RONs). Although AMA1 and RONs are essential for merozoite invasion of erythrocytes during asexual blood stage replication of the parasite, their function in sporozoites is still unclear. Here we show that AMA1 interacts with RONs in mature sporozoites. By using DiCre-mediated conditional gene deletion in P. berghei, we demonstrate that loss of AMA1, RON2 or RON4 in sporozoites impairs colonization of the mosquito salivary glands and invasion of mammalian hepatocytes, without affecting transcellular parasite migration. Our data establish that AMA1 and RONs facilitate host cell invasion across Plasmodium invasive stages, and suggest that sporozoites use the AMA1-RON complex to safely enter the mosquito salivary glands without causing cell damage, to ensure successful parasite transmission. These results open up the possibility of targeting the AMA1-RON complex for transmission-blocking antimalarial strategies.
Caveolae promote successful abscission by controlling intercellular bridge tension during cytokinesis
Authors: Andrade Virginia , Bai Jian , Gupta-Rossi Neetu , Jimenez Ana , Delevoye Cédric , Lamaze Christophe , Echard Arnaud
Published: January 2022

During cytokinesis, the intercellular bridge (ICB) connecting the daughter cells experiences pulling forces, which delay abscission by preventing the assembly of the ESCRT scission machinery. Abscission is thus triggered by tension release, but how ICB tension is controlled is unknown. Here, we report that caveolae, which are known to control membrane tension upon mechanical stress in interphase cells, are located at the midbody, at the abscission site and at the ICB/cell interface in dividing cells. Functionally, the loss of caveolae delays ESCRT-III recruitment during cytokinesis and impairs abscission. This is the consequence of a 2-fold increase of ICB tension measured by laser ablation, associated with a local increase in myosin II activity at the ICB/cell interface. We thus propose that caveolae buffer membrane tension and limit contractibility at the ICB to promote ESCRT-III assembly and cytokinetic abscission. Altogether, this work reveals an unexpected connection between caveolae and the ESCRT machinery and the first role of caveolae in cell division.

TEASER

Caveolae limit the tension in the intercellular bridge during cytokinesis to enable ESCRT-III assembly and successful abscission.
A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron
Authors: Yuan Tom Z. , Lucas Carolina , Monteiro Valter S. , Iwasaki Akiko , Yang Marisa L. , Nepita Hector F. , Lujan Hernandez Ana G. , Taft Joseph M. , Frei Lester , Reddy Sai T. , Weber Cédric R. , Malobisky Kevin P. , Mesquita Rodrigo , Sato Aaron K.
Published: January 2022

Bispecific antibodies have emerged as a promising strategy for curtailing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape. This brief report highlights RBT-0813 (also known as TB493-04), a synthetic, humanized, receptor-binding domain (RBD)-targeted bispecific antibody that retains picomolar affinity to the Spike (S) trimers of all major variants of concern and neutralizes both SARS-CoV-2 Delta and Omicron in vitro.
Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments
Authors: Yu Kai-Feng , Li Peng , Huang Yuansheng , Yang Jun , Li Han , Xie Yu , Li Rui , Zhang Bo , He Yiliang
Published: January 2022

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.
Cross-species analysis of LZTR1 loss-of-function mutants demonstrates dependency to RIT1 orthologs
Authors: Cuevas-Navarro Antonio , Rodriguez-Muñoz Laura , Grego-Bessa Joaquim , Cheng Alice , Rauen Katherine A. , Urisman Anatoly , McCormick Frank , Jimenez Gerardo , Castel Pau
Published: January 2022

RAS GTPases are highly conserved proteins involved in the regulation of mitogenic signaling. We have previously described a novel Cullin 3 RING E3 ubiquitin ligase complex formed by the substrate adaptor protein LZTR1 that binds, ubiquitinates, and promotes proteasomal degradation of the RAS GTPase RIT1. In addition, others have described that this complex is also responsible for the ubiquitination of canonical RAS GTPases. Here, we have analyzed the phenotypes of LZTR1 loss-of-function mutants in both fruit flies and mice and have demonstrated biochemical dependency on their RIT1 orthologs. Moreover, we show that LZTR1 is haplosufficient in mice and that embryonic lethality of the homozygous null allele can be rescued by deletion of RIT1.
Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis
Authors: Islam Md. Saiful , Hardwick Steven W. , Quell Laura , Chirgadze Dimitri Y. , Görke Boris , Luisi Ben F.
Published: January 2022

The biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled through intricate post-transcription networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthetase in Escherichia coli, but when bound by the protein RapZ, it becomes inactivated through cleavage by the endoribonuclease RNase E. Here we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the protein tetrameric quaternary structure to an imperfect structural repeat in the RNA. The RNA is contacted mostly through a highly conserved domain of RapZ that shares deep evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a pre-cleavage encounter intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised for cleavage. The structures suggest how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors are recognised for processing.
Plant speciation in the Namib Desert: origin of a widespread derivative species from a narrow endemic
Authors: Milton Joseph J. , Affenzeller Matthias , Abbott Richard J. , Comes Hans P.
Published: January 2022

Background

Parapatric (or ‘budding’) speciation is increasingly recognized as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented.

Aims

To test this speciation model in a hypothesized sister pair, the Southwest–North African disjunctSenecio flavusand its putative progenitor, the Namibian Desert endemicS. englerianus.

Methods

Phylogenetic inferences were combined with niche divergence tests, morphometrics, and experimental-genetic approaches. We also evaluated the potential role of an African Dry-Corridor (ADC) in promoting the hypothesized northward expansion ofS. flavus(from Namibia), using palaeodistribution models.

Results

Belonging to an isolated (potential ‘relict’) clade, the two morphologically distinct species show pronounced niche divergence in Namibia and signs of digenic-epistatic hybrid incompatibility (based on F2pollen fertility). The presence of ‘connate-fluked’ pappus hairs inS. flavus, likely increasing dispersal ability, is controlled by a single gene locus.

Conclusions

Our results provide support for a rare example of ‘budding’ speciation in which awider-ranged derivative (S. flavus) originated at the periphery of asmaller-ranged progenitor (S. englerianus) in the Namib Desert region. The Southwest–North African disjunction ofS. flavuscould have been established by dispersal across intermediate ADC areas during periods of (Late) Pleistocene aridification.
Exploring the onset of B12-based mutualisms using a recently evolved Chlamydomonas auxotroph and B12-producing bacteria
Authors: Bunbury Freddy , Deery Evelyne , Sayer Andrew , Bhardwaj Vaibhav , Harrison Ellen , Warren Martin J. , Smith Alison G.
Published: January 2022

Cobalamin (vitamin B12), is a cofactor for crucial metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonise the algal phycosphere, forming stable communities that gain preferential access to exudates and in return provide compounds, such as B12. Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12-dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12-independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesise that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12-dependent algae.

Originality-Significance statement

Microalgae are fundamental to the global carbon cycle, and yet despite being photosynthetic they often rely on other organisms for micronutrients. One of these micronutrients is vitamin B12 (cobalamin), which they receive from bacteria. Many environmental studies support the widespread role of B12 in algal-bacterial mutualisms, so here we wished to investigate how these mutualisms may arise evolutionarily by using an experimentally evolved B12-dependent alga and various B12-producers. A B12-producing rhizobium, Mesorhizobium loti, could stably support the B12-dependent Chlamydomonas reinhardtii metE7 strain, and vice versa, but nutrient supplementation increased growth of both species further. metE7 could also be supported by E. coli strains engineered to produce B12, and engineering a strain to release a higher proportion of B12 led to better algal growth, which increased bacterial growth in turn. We suggest that as B12-based mutualisms develop, increased B12 release may be selected for and therefore lead to more productive symbioses.
Control of bacterial immune signaling by a WYL domain transcription factor
Authors: Blankenchip Chelsea L. , Nguyen Justin V. , Lau Rebecca K. , Ye Qiaozhen , Gu Yajie , Corbett Kevin D.
Published: January 2022

Bacteria use diverse immune systems to defend themselves from ubiquitous viruses termed bacteriophages (phages). Many anti-phage systems function by abortive infection to kill a phage-infected cell, raising the question of how they are regulated to avoid cell killing outside the context of infection. Here, we identify a transcription factor associated with the widespread CBASS bacterial immune system, that we term CapW. CapW forms a homodimer and binds a palindromic DNA sequence in the CBASS promoter region. Two crystal structures of CapW suggest that the protein switches from an unliganded, DNA binding-competent state to a ligand-bound state unable to bind DNA. We show that CapW strongly represses CBASS gene expression in uninfected cells, and that phage infection causes increased CBASS expression in a CapW-dependent manner. Unexpectedly, this CapW-dependent increase in CBASS expression is not required for robust anti-phage activity, suggesting that CapW may mediate CBASS activation and cell death in response to a signal other than phage infection. Our results parallel concurrent reports on the structure and activity of BrxR, a transcription factor associated with the BREX anti-phage system, suggesting that CapW and BrxR are members of a family of universal defense signaling proteins.
Proteomic identification of phosphorylation dependent Septin 7 interactors that drive dendritic spine formation
Authors: Byeon Sujin , Werner Bailey , Falter Reilly , Davidsen Kristian , Snyder Calvin , Ong Shao-En , Yadav Smita
Published: January 2022

Septins are a family of cytoskeletal proteins that regulate several important aspects of neuronal development. Septin 7 (Sept7) is enriched at the base of dendritic spines in excitatory neurons and mediates both spine formation and spine-synapse maturation. Phosphorylation at a conserved C-terminal tail residue of Sept7 mediates its translocation into the dendritic spine head to allow spine-synapse maturation. The mechanistic basis for postsynaptic stability and compartmentalization conferred by phosphorylated Sept7, however, is not known. We report herein the proteomic identification of Sept7 phosphorylation dependent neuronal interactors. Using Sept7 C-terminal phosphopeptide pulldown and biochemical assays, we show that the 14-3-3 family of proteins specifically interact with Sept7 when phosphorylated at the T426 residue. Biochemically, we validate the interaction between Sept7 and 14-3-3 isoform gamma, and show that 14-3-3 gamma is also enriched in mature dendritic spine head. Further, we demonstrate that interaction of phosphorylated Sept7 with 14-3-3 protects it from dephosphorylation, as expression of a 14-3-3 antagonist significantly decreases phosphorylated Sept7 in neurons. This study identifies 14-3-3 proteins as an important physiological regulator of Sept7 function in neuronal development.
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein
Authors: Walter Marius , Chen Irene P , Vallejo-Gracia Albert , Kim Ik-Jung , Bielska Olga , Lam Victor L , Hayashi Jennifer M , Cruz Andrew , Shah Samah , Gross John D , Krogan Nevan J , Schilling Birgit , Ott Melanie , Verdin Eric
Published: January 2022

SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
Single Molecule Analysis of CENP-A Chromatin by High-Speed Atomic Force Microscopy
Authors: Melters Daniël P. , Neuman Keir C. , Rakshit Tatini , Dalal Yamini
Published: January 2022

Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated in the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamicsin vitroinform us about chromatin accessibilityin vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the MSD and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamicsin vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. Thus, changes which alter chromatin accessibilityin vitro, also correspondingly alter transcriptionin vivo. These data suggest a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance mobility.
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility
Authors: Coria Aaztli , Wienecke Anastacia , Borodavka Alexander , Laederach Alain
Published: January 2022

Due to genome segmentation, rotaviruses must co-package a set of eleven distinct genomic RNAs. The packaging is mediated by the RNA chaperone NSP2. While the activities of RNA chaperones are well studied with short RNAs, little is known about their global effect on the entire viral transcriptome. Here we used Selective 2′-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to systematically examine the secondary structure of the rotavirus transcriptome alone and in the presence of NSP2. Surprisingly, SHAPE-MaP data reveal that despite the well-characterized helix-unwinding activity of NSP2in vitro, its incubation with rotavirus transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of the per nucleotide mutation rate, from which SHAPE reactivities are derived, reveals a global five-fold rate increase in the presence of molar excess of NSP2. Further analysis of the mutation rate in the context of structural classification reveals a larger effect on stems rather than loop elements. Together, these data provide the first experimentally derived secondary structure model of the rotavirus transcriptome and reveal that NSP2 exerts a larger effect on stems, while acting by globally increasing RNA backbone flexibility in a protein concentration-dependent manner.
Asymmetric wall ingrowth deposition in Arabidopsis phloem parenchyma transfer cells is tightly associated with sieve elements
Authors: Wei Xiaoyang , Huang Yuan , Collings David A. , McCurdy David W.
Published: January 2022

In Arabidopsis, polarized deposition of wall ingrowths in phloem parenchyma (PP) transfer cells (TCs) occurs adjacent to cells of the sieve element/companion cell (SE/CC) complex. However, the spatial relationships between these different cell types in minor veins, where phloem loading occurs, are poorly understood. PP TC development and wall ingrowth localization were compared to other phloem cells in leaves of Col-0 and the transgenic lines AtSUC2::AtSTP9-GFP and AtSWEET11::AtSWEET11-GFP that identify CCs and PP respectively. The development of PP TCs in minor veins, indicated by deposition of wall ingrowths, proceeded basipetally in leaves. However, not all PP develop ingrowths and higher levels of wall ingrowth deposition occur in abaxial-compared to adaxial-positioned PP TCs. Furthermore, the deposition of wall ingrowths was exclusively initiated on and preferentially covered the PP TC/SE interface, rather than the PP TC/CC interface, and only occurred in PP cells that were adjacent to SEs. Collectively, these results demonstrate the dominant impact of SEs on wall ingrowth deposition in PP TCs and suggest the existence of two sub-types of PP cells in leaf minor veins. Compared to PP cells, PP TCs showed more abundant accumulation of AtSWEET11-GFP, indicating functional differences in phloem loading between PP and PP TCs.

Highlight

Wall ingrowth deposition in phloem parenchyma transfer cells of Arabidopsis leaf minor veins is initiated adjacent to sieve elements, rather than companion cells, and expands to preferentially cover this interface.
SARS-CoV-2 Infection of Microglia Elicits Pro-inflammatory Activation and Apoptotic Cell Death
Authors: Jeong Gi Uk , Lyu Jaemyun , Kim Kyun-Do , Chung Young Cheul , Yoon Gun Young , Lee Sumin , Hwang Insu , Shin Won-Ho , Ko Junsu , Lee June-Yong , Kwon Young-Chan
Published: January 2022

Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes various neurological symptoms in coronavirus disease 2019 (COVID-19) patients. The most dominant immune cells in the brain are microglia. Yet, the relationship between neurological manifestations, neuroinflammation, and host immune response of microglia to SARS-CoV-2 has not been well characterized. Here, we report that SARS-CoV-2 can directly infect human microglia, eliciting M1-like pro-inflammatory responses, followed by cytopathic effects. Specifically, SARS-CoV-2 infected human microglial clone 3 (HMC3), leading to inflammatory activation and cell death. RNA-seq analysis also revealed that ER stress and immune responses were induced in the early and apoptotic processes in the late phase of viral infection. SARS-CoV-2-infected HMC3 showed the M1 phenotype and produced pro-inflammatory cytokines such as interleukin (IL)-1β, IL-6, and tumour necrosis factor α (TNF-α), but not the anti-inflammatory cytokine IL-10. After this pro-inflammatory activation, SARS-CoV-2 infection promoted both intrinsic and extrinsic death receptor-mediated apoptosis in HMC3. Using K18-hACE2 transgenic mice, murine microglia were also infected by intranasal inoculation of SARS-CoV-2. This infection induced the acute production of pro-inflammatory microglial IL-6 and TNF-α and provoked a chronic loss of microglia. Our findings suggest that microglia are potential mediators of SARS-CoV-2-induced neurological problems and, consequently, can be targets of therapeutic strategies against neurological diseases in COVID-19 patients.

IMPORTANCE

Recent studies reported neurological manifestations and complications in COVID-19 patients, which are associated with neuroinflammation. As microglia are the dominant immune cells in brains, it needs to be elucidate the relationship between neuroinflammation and host immune response of microglia to SARS-CoV-2. Here, we suggest that SARS-CoV-2 can directly infect human microglia with cytopathic effect (CPE) using human microglial clone 3 (HMC3). The infected microglia were promoted to pro-inflammatory activation following apoptotic cell death. This pro-inflammatory activation was accompanied by the high production of pro-inflammatory cytokines, and led to neurotoxic-M1 phenotype polarization.In vivo, murine microglia were infected and produced pro-inflammatory cytokines and provoked a chronic loss using K18-hACE2 mice. Thus, our data present that SARS-CoV-2-infected microglia are potential mediators of neurological problems in COVID-19 patients. In addition, HMC3 cells are susceptible to SARS-CoV-2 and exhibit the CPE, which can be further used to investigate cellular and molecular mechanisms of neuroinflammation reported in COVID-19 patients.