bluuebunny/crossref_metadata_2025 huggingface dataset:
Lineage-specific genes are clustered with allorecognition loci and respond to G × E factors regulating the switch from asexual to sexual reproduction inNeurospora
Authors: Wang Zheng , Wang Yaning , Kasuga Takao , Wang Yen-Wen , Lopez-Giraldez Francesc , Zhang Yang , Zhang Zhang , Dong Caihong , Sil Anita , Trail Frances , Yarden Oded , Townsend Jeffrey P.
Published: June 2022

Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. However, there is a lack of working hypotheses as to how they might play that role. In the genome ofNeurospora crassa, most of the 670NeurosporaLSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, which regulate self-recognition and define vegetative incompatibility groups. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural and HMF—wildfire-produced chemicals that are a strong inducer of sexual development. Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts ofadv-1andpp-1that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. Accordingly, we propose a gene-by-environment interaction model encouraging further investigation of the roles of LSGs and HET-domain genes in speciation inNeurospora. This gene-by-environment interaction model emphasizes the roles of the LSGs in response to genetic and environmental factors, leading to the regulation of the switch from the asexual growth and fusion, such that vegetative incompatibility governed by allorecognition promotes allelic homogeneity, sexual reproduction, and outbreeding, whereas VI repression and meiotic recombination promotes allelic polymorphism.
Impaired Neutralization of SARS-CoV-2 Including Omicron Variants after COVID-19 mRNA Booster Immunization under Methotrexate Therapy
Authors: Habermann Elisa , Gieselmann Lutz , Tober-Lau Pinkus , Hagen Alexander ten , Albach Fredrik N , Zernicke Jan , Ahmadov Elvin , de Silva Amanthi Nadira Arumahandi , Frommert Leonie Maria , Klotsche Jens , Kurth Florian , Sander Leif Erik , Burmester Gerd , Klein Florian , Biesen Robert
Published: June 2022

Objective

To determine the immediate need for a fourth COVID-19 vaccination based on the neutralizing capacity in patients on methotrexate (MTX) therapy after mRNA booster immunization.

Methods

In this observational cohort study, neutralizing serum activity against SARS-CoV-2 wildtype (Wu01) and variant of concern (VOC) Omicron BA.1 and BA.2 were assessed by pseudovirus neutralization assay before, 4 and 12 weeks after mRNA booster immunization in 50 rheumatic patients on MTX, 26 of whom paused the medication. 44 non-immunosuppressed persons (NIP) served as control group.

Results

While the neutralizing serum activity against SARS-CoV-2 Wu01 and Omicron variants increased 67-to 73-fold in the NIP after booster vaccination, the serum activity in patients receiving MTX increased only 20-to 23-fold. As a result, significantly lower neutralizing capacities were measured in patients on MTX compared to the NIP at week 4. Patients who continued MTX treatment during vaccination had significantly lower neutralizing serum titres against all three virus strains at week 4 and 12 compared to patients who paused MTX and the control group, except for BA.2 at week 12. Patients who paused MTX reached comparably high neutralization titres as the NIP, except for Wu01 at week 12. Neutralization of omicron variants was significantly lower in comparison to wildtype in both groups.

Conclusion

Patients pausing MTX showed a similar vaccine response to NIP. Patients who continued MTX demonstrated an impaired booster response indicating a potential benefit of a second booster vaccination.
HEALTH ECONOMIC BURDEN ON HEPATITIS B IMMUNOGLOBULIN VACCINATION
Authors: Laurito Arbeen A. , Bett Lourdes L.
Published: June 2022

Abstract of the Study

Background

Chronic Hepatitis B infection comprises the mortality among viral hepatitis despite primary hepatitis B vaccination was implemented in different states health programs. Different modalities of combining active and passive hepatitis B vaccination were conducted. Pregnant women hepatitis screening was not yet streamlined in the clinical management due to social and economic challenges. Fetal to maternal vertical transmission of hepatitis B virus is still a burden to our health system. It is the objective of the study to present the cost of incorporating hepatitis B immunoglobulin vaccine in the current vaccination program, as strengthen the preventive measures of hepatitis infection locally and nationally.

Methods

Survey questionnaires were utilized to gather demographic data among randomly selected pregnant women during their prenatal visits at the hospital. Hospital and city-based census were used for projecting cost and revenues of having hepatitis B immunoglobulin vaccination.

Results

A total of 74 respondents were identified. A financial 5-year was forecast would show a revenue of Php 1,494,500.00 ($28,869.5) on the 5th year and would spare the mothers from OOP expenses with a total amount of Php 945,500 ($18,264.40). Moreover, the monthly revenue of Hep B Ig vaccination (based on 2016 census) on a city-wide was forecasted. The difference of the total amount of PHIC reimbursement from the amount of vaccine purchasing would give the facility a projected revenue of Php 3,381,123.00 ($65,313.62) or a monthly average of Php (281,760.25). A total of 1,380 newborns would be at risk to hepatitis B-reactive mothers and would be protected by securing hepatitis B immunoglobulin and be made available in the hospital pharmacy. Furthermore, pregnant women are protected against financial risk of unnecessary out-of-pocket expenses.

Conclusion

This study found that the pregnant women was aware of the economic burden of hepatitis B immunoglobulin vaccine and it would benefit the healthcare facility by strategically addressing the external factors for a sustained vaccination program.
Separation of transcriptional repressor and activator functions in HDAC3
Authors: Tang Min , Regadas Isabel , Belikov Sergey , Shilkova Olga , Xu Lei , Wernersson Erik , Liu Xuewen , Wu Hongmei , Bienko Magda , Mannervik Mattias
Published: June 2022

The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex and its canonical function is in transcriptional repression, but it can also activate transcription. Here we show that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N-terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhance repressor activity beyond wild-type in the early embryo. We conclude that the critical functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery.
Structure of SARS-CoV-2 M protein in lipid nanodiscs
Authors: Dolan Kimberly A. , Dutta Mandira , Kern David M. , Kotecha Abhay , Voth Gregory A. , Brohawn Stephen G.
Published: June 2022

SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.
The adipose-neural axis is critically involved in cardiac arrhythmias
Authors: Fan Yubao , Huang Shanshan , Li Suhua , Wu Bingyuan , Huang Li , Zhao Qi , Zheng Zhenda , Xie Xujing , Liu Jia , Huang Weijun , Sun Jiaqi , Zhu Xiulong , Wang Maosheng , Zhu Jieming , Xiang Andy Peng , Li Weiqiang
Published: June 2022

Dysfunction of the sympathetic nervous system and increase of epicardial adipose tissue (EAT) have been independently associated with the occurrence of cardiac arrhythmia. However, their exact roles in triggering arrhythmia remain elusive due to a lack of appropriate human disease models. Here, using the in vitro co-culture system with sympathetic neurons, cardiomyocytes, and adipocytes, we show that adipocyte-derived leptin could activate sympathetic neurons and increase the release of NPY, which in turn trigger arrhythmia of cardiomyocytes by interaction with NPY1R and subsequently enhancing the activity of NCX and CaMKII. The arrhythmic phenotype could be partially blocked by leptin neutralizing antibody, or an inhibitor of NPY1R, NCX or CaMKII. More importantly, increased EAT thickness accompanied with higher leptin/NPY blood levels was detected in atrial fibrillation patients compared to control group. Our study provides the first evidence that adipose-neural axis would contribute to arrhythmogenesis and represent a potential therapeutic target for arrhythmia.
Glaucoma cases reported post-COVID-19 vaccination : A VAERS database analysis
Authors: Singh Rohan Bir , Parmar Uday Pratap Singh , Ichhpujani Parul
Published: June 2022

Objective

To evaluate glaucoma cases reported post-COVID-19 vaccination and describe the clinical presentations in these cases.

Design

An analysis of the Centers for Disease Control and Prevention (CDC) Vaccine Adverse Event Reporting System (VAERS) database

Participants

The study includes 161 individuals who were reported for glaucoma after administration of COVID-19 vaccines [BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna) and Ad26.COV2.S (Janssen)] between December 2020 and April 2022.

Main Outcome Measures

Estimated crude reporting rate of glaucoma, clinical presentations, onset duration and associated risk factors.

Results

A total of 2,061,557,270 doses of COVID-19 vaccines were administered during the study timeframe. During this period, 161 glaucoma cases were reported with an estimated crude reporting rate (per million doses) of 0.09, 0.06 and 0.07 for BNT162b2, mRNA-1273 and Ad26.COV2.S, respectively. The majority of patients (n=130, 80.7%) received BNT162b2, vaccine, while 27 patients (16.8%) received mRNA-1273 and four patients (2.5%) received rAd26.COV2.S vaccines. The mean age of patients in the cohort was 60.41±17.56 years and 67.7% (n=109) were women. More than half (56.6%) were reported within the first week after vaccination. The glaucoma onset interval was significantly shorter in patients who received BNT162b2 and rAd26.COV2.S vaccines compared to mRNA-1273 (p=0.013). A higher risk of glaucoma incidence was observed in the short term in patients who received BNT162b2 vaccines compared to mRNA-1273 (p=0.05). In patients vaccinated with mRNA-1273, a significantly higher frequency of glaucoma cases was reported in older patients (p=0.047) compared to younger age groups.

Conclusions

The CDC-VAERS data suggest an extremely low safety concern for glaucoma on receiving BNT162b2, mRNA-1273, or Ad26.COV2.S vaccines. The onset interval of adverse events was shorter in patients who received BNT162b2 and rAd26.COV2.S vaccines compared to mRNA-1273. The glaucoma cases after mRNA-1273 vaccination were more commonly reported in older patients. These findings are subject to the limitations of passive reporting systems, under reporting and presumptive case definition, and should be considered preliminary without the medical record analysis for establishing a definitive diagnosis.
Atlas of plasma nuclear magnetic resonance biomarkers for health and disease in 118,461 individuals from the UK Biobank
Authors: Julkunen Heli , Cichońska Anna , Tiainen Mika , Koskela Harri , Nybo Kristian , Mäkelä Valtteri , Nokso-Koivisto Jussi , Kristiansson Kati , Perola Markus , Salomaa Veikko , Jousilahti Pekka , Lundqvist Annamari , Kangas Antti J. , Soininen Pasi , Barrett Jeffrey C. , Würtz Peter
Published: June 2022

Blood lipids and metabolites are both markers of current health and indicators of risk for future disease. Here, we describe plasma nuclear magnetic resonance (NMR) biomarker data for 118,461 participants in the UK Biobank, an open resource for public health research with extensive clinical and genomic data. The biomarkers cover 249 measures of lipoprotein lipids, fatty acids, and small molecules such as amino acids, ketones, and glycolysis metabolites. We provide a systematic atlas of associations of these biomarkers to prevalence, incidence, and mortality of over 700 common diseases (biomarker-atlas.nightingale.cloud/). The results reveal a plethora of biomarker associations, including susceptibility to infectious diseases and risk for onset of various cancers, joint disorders, and mental health outcomes, indicating that abundant circulating lipids and metabolites are risk markers well beyond cardiometabolic diseases. Clustering analyses indicate similar biomarker association patterns across different types of diseases, such as liver diseases and polyneuropathies, suggesting latent systemic connectivity in the susceptibility to a diverse set of diseases. The release of NMR biomarker data at scale in the UK Biobank highlights the promise of metabolic profiling in large cohorts for public health research and translation.
Predictive value of automated coronary calcium scoring in lung cancer screening with low dose computed tomography
Authors: Sabia Federica , Balbi Maurizio , Ledda Roberta E. , Milanese Gianluca , Ruggirello Margherita , Valsecchi Camilla , Marchianò Alfonso , Sverzellati Nicola , Pastorino Ugo
Published: June 2022

Coronary artery calcium (CAC) is a known risk factor for cardiovascular events, but not yet routinely evaluated in Low Dose Computed Tomography (LDCT) screening. The present analysis compared the accuracy of a new automated CAC quantification versus prior manual quantification on baseline LDCT screening images as predictors of all-cause mortality at 12 years.

The study included 1129 volunteers of the Multicentric Italian Lung Detection (MILD) trial who underwent a baseline LDCT scan from September 2005 to September 2006, already analyzed in a previous paper on CAC scoring. The initial manual CAC (mCAC) had been scored by one operator using a dedicated software, while the new automated CAC (aCAC) score was measured by a fully automated artificial intelligence software. All CAC scores were stratified in four categories: 0, 0.1- 19.9, 20-399, and ≥ 400.

The study showed a high correlation between aCAC and mCAC scores, with an Intraclass Correlation Coefficient of 0.887. Of 613 negative mCAC score, 87.6% had aCAC score >0, and 14.0% >20. A CAC score >20 revealed a higher risk of 12-year all-cause mortality both with mCAC and aCAC. Focusing on the 535 individuals with false negative mCAC score, aCAC identified a subset of volunteers with a significantly poorer survival of 86% (aCAC 20-399, p=0.0007).

CAC quantification could be accurately and safely performed with a fully automated software on baseline LDCT screening images to predict all-cause mortality risk.
Interferon Beta-1α ring prophylaxis to reduce household transmission of SARS-CoV-2: the Containing Coronavirus Disease-19 randomized clinical trial
Authors: Castro-Rodriguez José A. , Fish Eleanor N. , Kollmann Tobi , Iturriaga Carolina , Karpievitch Yuliya , Shannon Casey , Chen Virginia , Balshaw Robert , Montgomery Samuel T. , Ho Joseph , Othman Rym Ben , Aniba Radhouana , Gidi-Yunge Francisca , Hartnell Lucy , Pérez-Mateluna Guillermo , Urzúa Marcela , Tebbutt Scott , García-Huidobro Diego , Perret Cecilia , Borzutzky Arturo , Stick Stephen M.
Published: June 2022

Importance

Evidence suggests that early, robust type 1 interferon responses to SARS-CoV-2 are critical determinants for COVID-19 disease outcomes, accelerating viral clearance and limiting viral shedding.

Objective

We undertook a ring prophylaxis study to determine whether pegylated IFNβ-1α could reduce SARS-CoV-2 household transmission.

Design

A cluster randomized clinical trial of pegylated IFNβ-1α conducted in Santiago, Chile. Recruitment was conducted between December 4th2020, and 31stMay 2021, with the last follow-up completed June 29th2021.

Setting

The study was conducted across 341 households in the metropolitan area of Santiago, Chile.

Participants

Index cases were identified from databases of those with confirmed SARS-CoV-2 from COVID-19 clinics and emergency room visits in Santiago, Chile. 5,154 index cases were assessed for eligibility, 1,372 index cases were invited to participate, and 341 index cases and their household contacts (n = 831) were enrolled in the study.

Intervention

Households were cluster randomized to receive 125µg subcutaneous pegylated IFNβ-1α (n = 172 households, 607 participants), or standard care (n = 169 households, 565 participants).

Main Outcome(s) and Measure(s)

Frequentist and Bayesian analyses were undertaken to determine the effects of treatment on (i) reducing viral shedding in index cases and (ii) reducing viral transmission to treatment-eligible household contacts. Four secondary outcomes were assessed including duration of viral shedding, effects on viral transmission and seroconversion, incidence of hospitalization, and incidence and severity of reported adverse events. A post-hoc ‘at risk population’ was defined as households where the index case was positive at the start of the study and there was at least one treatment eligible contact in a household who tested negative for SARS-CoV-2.

Results

In total, 1172 participants in 341 households underwent randomization, with 607 assigned to receive IFNβ-1α and 565 to standard care. Based on intention to treat and per protocol analyses, IFNβ-1α treatment was ineffective. However, in the ‘at risk’ population, the relative risk of infection was reduced by 23% in treated individuals and that there was a 95% probability that IFNβ-1α reduced household transmission

Conclusions and Relevance

Ring prophylaxis with IFNβ-1α reduces the probability of SARS-CoV-2 transmission within a household.

Trial Registration

Clinicaltrials.govidentifier:NCT04552379
A general, highly efficient and facile synthesis of biocompatible rhodamine dyes and probes for live-cell multicolor nanoscopy
Authors: Bucevičius Jonas , Gerasimaitė Rūta , Kiszka Kamila A. , Pradhan Shalini , Kostiuk Georgij , Koenen Tanja , Lukinavičius Gražvydas
Published: June 2022

The development of live-cell fluorescence nanoscopy is powered by the availability of suitable fluorescent probes. Rhodamines are among the best fluorophores for labeling intracellular structures. Isomeric tuning is a powerful method for optimizing biocompatibility of the rhodamine-containing probes without affecting their spectral properties. However, the efficient synthesis pathway for rhodamine 4-isomers is still lacking. Herein, we present a facile protecting-group-free 4-carboxyrhodamines’ synthesis based on nucleophilic addition of lithium dicarboxybenzenide to the corresponding xanthone. This approach drastically reduces the number of synthesis steps and expands the achievable structural diversity, increases overall yields and permits a cheap gram-scale synthesis of the dyes. We prepared a wide range of symmetric and asymmetric 4-carboxyrhodamines covering the whole visible spectrum and targeted them to multiple structures in living cells – microtubules, DNA, actin, mitochondria, lysosomes, Halo-tagged and SNAP-tagged proteins. The enhanced permeability fluorescent probes operate at submicromolar concentrations allowing high contrast STED and confocal microscopy of living cells and tissues.
The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes
Authors: Gupta Yogesh K. , Marcelino-Guimarães Francismar C. , Lorrain Cécile , Farmer Andrew , Haridas Sajeet , Ferreira Everton Geraldo Capote , Lopes-Caitar Valéria S. , Oliveira Liliane Santana , Morin Emmanuelle , Widdison Stephanie , Cameron Connor , Inoue Yoshihiro , Thor Kathrin , Robinson Kelly , Drula Elodie , Henrissat Bernard , LaButti Kurt , Bini Aline Mara Rudsit , Paget Eric , Singan Vasanth , Daum Christopher , Dorme Cécile , van Hoek Milan , Janssen Antoine , Chandat Lucie , Tarriotte Yannick , Richardson Jake , do Vale Araújo Melo Bernardo , Wittenberg Alexander , Schneiders Harrie , Peyrard Stephane , Zanardo Larissa Goulart , Holtman Valéria Cristina , Coulombier-Chauvel Flavie , Link Tobias I. , Balmer Dirk , Müller André N. , Kind Sabine , Bohnert Stefan , Wirtz Louisa , Chen Cindy , Yan Mi , Ng Vivian , Gautier Pierrick , Meyer Maurício Conrado , Voegele Ralf Thomas , Liu Qingli , Grigoriev Igor V. , Conrath Uwe , Brommonschenkel Sérgio H. , Loehrer Marco , Schaffrath Ulrich , Sirven Catherine , Scalliet Gabriel , Duplessis Sébastien , van Esse H. Peter
Published: June 2022

Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizi’s genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.
Dynamics of SARS-CoV-2 genetic mutations and their information entropy
Authors: Vopson Melvin M.
Published: June 2022

We report an investigation of the mutations dynamics of the SARS-CoV-2 virus using Shannon’s information theory. Our study includes seventeen RNA genetic sequences collected at different geographic locations and timeframes ranging from Dec. 2019 to Oct. 2021. The data shows a previously unobserved relationship between the information entropy of genomes and their mutation dynamics. The information entropy of the mutated variants decreases linearly with the number of genetic mutations with a negative slope of 1.52 × 10-5bits / mutations, pointing to a possible deterministic approach to the dynamics of genetic mutations. The method proposed here could be used to develop a predictive algorithm of genetic mutations.
Two Rac1 pools integrate the direction and coordination of collective cell migration
Authors: Zhou Sijia , Li Peng , Liu Jiaying , Li Hao , Liao Juan , Chen Lin , Yi Bin , Wang Xiaobo
Published: June 2022

Integration of collective cell direction and coordination is believed to ensure collective guidance for efficient movement. Previous studies demonstrated that chemokine receptors PVR and EGFR govern a gradient of Rac1 activity essential for collective guidance of Drosophila border cells, whose mechanistic insight is unknown. By monitoring and manipulating subcellular Rac1 activity, here we reveal two switchable Rac1 pools at border cell protrusions and supracellular cables, two important structures responsible for direction and coordination. Rac1 and Rho1 form a positive feedback loop that guides mechanical coupling at cables to achieve migration coordination. Rac1 cooperates with Cdc42 to control protrusion growth for migration direction, as well as to regulate the protrusion-cable exchange, linking direction and coordination. PVR and EGFR guide correct Rac1 activity distribution at protrusions and cables. Therefore, our studies emphasize the existence of a balance between two Rac1 pools, rather than a Rac1 activity gradient, as an integrator for the direction and coordination of collective cell migration.
B-Myb association with DNA is mediated by its negative regulatory domain and Cdk phosphorylation
Authors: Wijeratne Tilini U. , Guiley Keelan Z. , Lee Hsiau-Wei , Müller Gerd A. , Rubin Seth M.
Published: June 2022

B-Myb is a highly conserved member of the vertebrate Myb family of transcription factors that plays a critical role in cell-cycle progression and proliferation. Myb proteins activate Myb-dependent promoters by interacting specifically with Myb binding site (MBS) sequences using their DNA binding domain (DBD). Transactivation of MBS promoters by B-Myb is repressed by its negative regulatory domain (NRD), and phosphorylation of the NRD by Cdk2-CyclinA relieves the repression to activate B-Myb dependent promoters. The structural mechanisms underlying autoinhibition and activation have been poorly characterized. We determined that a region in the B-Myb NRD (residues 510-600) directly associates with the DBD and inhibits DBD binding to the MBS DNA sequence. We demonstrate that phosphorylation of the NRD at T515, T518, and T520 is sufficient to disrupt the interaction between the NRD and the DBD, which results in increased affinity for MBS DNA and increased B-Myb-dependent promoter activation. Our biochemical characterization of B-Myb autoregulation and the activating effects of phosphorylation provides insight into how B-Myb functions as a site-specific transcription factor.
Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles
Authors: Vettkötter Dennis , Schneider Martin , Liewald Jana , Zeiler Sandra , Guldan Julia , Watanabe Shigeki , Gottschalk Alexander
Published: June 2022

Silencing neurons acutely and specifically informs about their functional roles in circuits and behavior. Existing optogenetic silencers include ion pumps or channels, and tools that damage the neurotransmitter release machinery. While the former hyperpolarize the cell and can alter ionic gradients, the latter allow only slow recovery, requiring de novo synthesis. Thus, there is a need for other strategies combining fast activation and reversibility. Here, we use light-evoked homo-oligomerization of cryptochrome CRY2 to silence synaptic transmission, by clustering synaptic vesicles (SVs). We benchmark this tool, optoSynC, by electrophysiology and locomotion in Caenorhabditis elegans. optoSynC clusters SVs within 25 s, causing approximation, observable by electron microscopy. Locomotion silencing is rapid (tauon ∼15 s) and recovers quickly (tauoff ∼10 min) after light-off. Further, optoSynC can inhibit exocytosis for several hours, at very low light intensities. optoSynC is a highly efficient, ‘non-ionic’ optogenetic silencer that may further allow to manipulate different SV pools.
Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for Label-Free Detection of Molecules across Entire Cell Sections
Authors: Elferich Johannes , Schiroli Giulia , Scadden David , Grigorieff Nikolaus
Published: June 2022

A major goal of biological imaging is localization of biomolecules inside a cell. Fluorescence microscopy can lo-calize biomolecules inside whole cells and tissues, but its ability to count biomolecules and accuracy of the spatial coordinates is limited by the wavelength of visible light. Cryo-electron microscopy (cryo-EM) provides highly accurate position and orientation information of biomolecules but is often confined to small fields of view inside a cell, limiting biological context. In this study we use a new data-acquisition scheme called “Defocus-Corrected Large-Area cryo-EM” (DeCo-LACE) to collect high-resolution images of entire sections (100 – 200 nm thick lamel-lae) of neutrophil-like mouse cells, representing 1-2% of the total cellular volume. We use 2D template matching (2DTM) to determine localization and orientation of the large ribosomal subunit in these sections. These data provide “maps” of ribosomes across entire sections of mammalian cells. This high-throughput cryo-EM data collection approach together with 2DTM will advance visual proteomics and provide biological insight that cannot be obtained by other methods.
Immediate early proteins of herpes simplex virus transiently repress viral transcription before subsequent activation
Authors: Dunn Laura E.M. , Birkenheuer Claire H. , Dufour Rachel , Baines Joel D.
Published: June 2022

Herpes simplex virus 1 (HSV-1) utilizes cellular RNA polymerase II (Pol) to transcribe its genes in one of two phases. In the latent phase, viral transcription is highly restricted but during the productive lytic phase, more than 80 genes are expressed in a temporally coordinated cascade. In this study, we used precision nuclear Run On followed by deep Sequencing (PRO-Seq) to characterize early viral transcriptional events using HSV-1 immediate early (IE) gene mutants, corresponding genetically repaired viruses, and wild type virus. Unexpectedly, in the absence of the IE genes ICP4, ICP22 or ICP0 at 1.5 hpi we observed high levels of aberrant transcriptional activity across the mutant viral genomes, but substantially less on either wild type or the congenic repaired virus genomes. This feature was particularly prominent in the absence of ICP4 expression. Cycloheximide treatment during infection with both the ICP4 and ICP22 mutants and their respective genetic repairs did not alter the relative distribution of Pol activity, but increased overall activity across both viral genomes, indicating that both virion components and at least some de novo protein synthesis were required for full repression. Overall, these data reveal that prior to their role in transcriptional activation, IE gene products and virion components first repress transcription and that the HSV-1 lytic transcriptional cascade is mediated through subsequent de-repression steps.

Importance

Herpes simplex virus 1 (HSV-1) transcription during productive replication is believed to comprise a series of activation steps leading to a specific sequence of gene expression. Here we show that virion components and immediate early (IE) gene products ICP0, ICP4 and ICP22 first repress viral gene transcription to varying degrees before subsequently activating specific gene subsets. It follows that the entire HSV transcriptional program involves a series of steps to sequentially reverse this repression. This previously uncharacterized repressive activity of IE genes very early in infection may represent an important checkpoint allowing HSV-1 to orchestrate either the robust lytic transcriptional cascade or the more restricted transcriptional program during latency.
Juvenile Shank3 KO mice adopt distinct hunting strategies during prey capture learning
Authors: Kuhnle Chelsea Groves , Grimes Micaela , Casanova Victor Manuel Suárez , Turrigiano Gina G. , Van Hooser Stephen D.
Published: June 2022

Mice are opportunistic omnivores that readily learn to hunt and eat insects such as crickets. The details of how mice learn these behaviors and how these behaviors may differ in strains with altered neuroplasticity are unclear. We quantified the behavior of juvenile wild type and Shank3 knockout mice as they learned to hunt crickets during the critical period for ocular dominance plasticity. This stage involves heightened cortical plasticity including homeostatic synaptic scaling, which requires Shank3, a glutamatergic synaptic protein that, when mutated, produces Phelan-McDermid syndrome and is often comorbid with autism spectrum disorder (ASD). Both strains showed interest in examining live and dead crickets and learned to hunt. Shank 3 knockout mice took longer to become proficient, and, after 5 days, did not achieve the efficiency of wild type mice in either time-to-capture or distance-to-capture. Shank3 knockout mice also exhibited different characteristics when pursuing crickets that defied explanation as a simple motor deficit. Although both genotypes moved at the same average speed when approaching a cricket, Shank3 KO mice paused more often during approaches, did not begin final accelerations toward crickets as early, and did not close the distance gap to the cricket as quickly as wild type mice. These differences in Shank3 KO mice are reminiscent of some behavioral characteristics of individuals with ASD as they perform complex tasks, such as slower action initiation and completion. This paradigm will be useful for exploring the neural circuit mechanisms that underlie these learning and performance differences in monogenic ASD rodent models.
Kinetic Characterization and Computational Modeling of the Escherichia coli Heptosyltransferase II: Exploring the Role of Protein Dynamics in Catalysis for a GT-B Glycosyltransferase
Authors: Hassan Bakar A. , Liu Zhiqi A. , Milicaj Jozafina , Kim Mia S. , Tyson Meka , Sham Yuk Y. , Taylor Erika A.
Published: June 2022

Glycosyltransferases (GTs) are enzymes that are uniquely adapted to promote the formation of a glycosidic bond between a sugar molecule and a wide variety of substrates. Heptosyltransferase II (HepII) is a GT involved in the lipopolysaccharide (LPS) biosynthetic pathway that transfers the seven-carbon sugar (L-glycero-D-manno-heptose; Hep) onto a lipid anchored glycopolymer (heptosylated Kdo2-Lipid A, Hep-Kdo2-Lipid A or HLA). LPS plays a key role in Gram-negative bacterial sepsis as a stimulator of the human immune response and has been used as an adjuvant in vaccines. As such, ongoing efforts towards inhibition of LPS biosynthetic enzymes to aid development of novel antimicrobial therapeutics has driven significant effort towards the characterization of these enzymes. Three heptosyltransferases are involved in the inner-core biosynthesis, with E. coli HepII being the last to be quantitatively characterized in vivo, as described herein. HepII shares modest sequence similarity with heptosyltransferase I (HepI) while maintaining a high degree of structural homology. Here we report the first kinetic and biophysical characterization of HepII and demonstrate the properties of HepII that are shared by HepI to include sugar donor promiscuity, and sugar acceptor induced secondary structural changes which results in significant thermal stabilization. HepII also has an increased catalytic efficiency and a significantly tighter binding affinity for both of its substrates, with an insensitivity to the number of acyl chains on the sugar acceptor. Additionally, a structural model of the HepII ternary complex, refined by molecular dynamics simulations, was developed to probe potentially important substrate-protein contacts and revealed the potential of Tryptophan (Trp) residues responsible for reporting on ligand binding. As was previously described for HepI, Tryptophan fluorescence in HepII allowed observation of substrate induced changes in Trp fluorescence intensity which enabled determination of substrate dissociation constants. Combined, these efforts meaningfully enhance our understanding of the Heptosyltransferase family of enzymes and will aid in future efforts to design novel, potent and specific inhibitors for this family of enzymes.
Extensive protein dosage compensation in aneuploid human cancers
Authors: Schukken Klaske M. , Sheltzer Jason M.
Published: June 2022

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins show dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has a moderate effect on the expression of oncogenes and tumor suppressors, showing that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.
Synthesis and crystal structure of [(Sp
)-(2-phenylferrocenyl)methyl]trimethylammonium iodide dichloromethane monosolvate
Authors: Lachguar Abdelhak , Deydier Eric , Labande Agnès , Manoury Eric , Poli Rinaldo , Daran Jean-Claude
Published: June 2022

As a follow-up to our research on the chemistry of disubstituted ferrocene derivatives, the synthesis and the structure of the title compound, [Fe(C5H5)(C15H19N)]I·CH2Cl2, is described. The cation molecule is built up from a ferrocene disubstituted by a trimethylammonium methyl group and a phenyl ring. The asymmetric unit contains the iodide to equilibrate the charge and a disordered dichloromethane solvate. The disordered model results from a roughly statistical exchange (0.6/0.4) between one Cl and one H. The packing of the structure is stabilized by weak C—H...X (X = I, Cl), C—H...π(Cp) and C—Cl...π(phenyl) interactions, building a three-dimensional network. The cation has planar chirality with Sp
(Fc) absolute configuration. The structure of the title compound is compared with related disubstituted (trimethylammonio)methyl ferrocenes.
Psychiatric symptoms influence the performance on the Screener Intelligence and Learning Disabilities in general mental health care in The Netherlands
Authors: Nieuwenhuis Jeanet , Noorthoorn Eric , Lepping Peter , Mulder Niels , Nijman Henk
Published: June 2022

Purpose

A recently published study showed a 41% prevalence of mild intellectual disability (MID) and borderline intellectual functioning (BIF) in a large sample of Dutch psychiatric patients. This study aims to examine if the outcomes of the Screener for Intelligence and Learning Disabilities (SCIL) were affected by the severity of psychiatric symptoms during admission.

Design/methodology/approach

The authors administered the SCIL and the Kennedy Axis V (domain psychological impairment) at two moments when patients were sufficiently stabilised and just before discharge.

Findings

A total of 86% of the respondents had the same outcome regardless of the time of administration. The Kennedy score correlated modestly with changes in the SCIL scores, suggesting that the severity of psychiatric symptoms just modestly affected the performance.

Practical implications

Recognising MID/BIF in mental health care is essential but challenging for clinicians. The authors concluded that screening with the SCIL allows clinicians to identify patients with MID/BIF at an early stage of their admission, which helps to individualise treatment and reduce the risk of aggression, coercive measures and prolonged admissions. However, the authors prefer to assess all patients on cognitive impairment as early as possible after referral at a more stable moment in time.

Originality/value

To the best of the authors’ knowledge, there is no research concerning screening instruments on MID/BIF used at admission wards in Mental Health Care.
Importance of first-line employees in lean implementation in SMEs: a systematic literature review
Authors: Knapić Viktorija , Rusjan Borut , Božič Katerina
Published: June 2022

Purpose

Existing research evidence shows a fragmented understanding of the roles of first-line employees (FLEs) as essential factors for successful lean implementation in small- and medium-sized enterprises (SMEs), provoking recent calls for additional research on the identification of enablers and barriers for lean acceptance among workers. Therefore, this paper aims to identify related enablers and barriers to lean implementation among FLEs and determine future research avenues for improving the understanding of lean methodology implementation in SMEs.

Design/methodology/approach

Relying on a systematic literature review methodology, the authors aimed to synthesize and evaluate available peer-reviewed papers on the role of FLEs in lean implementation in SMEs. General descriptive and thematic analysis comprehensively depicted the selected research topic and identified the main themes within collected papers and potential future research questions.

Findings

The authors identified four main themes related to FLEs’ role in lean implementation: cultural change factors, employee characteristics, management involvement and lean job design. Within each theme, the authors present a comprehensive overview of FLE-related factors and associated enablers and barriers that should be considered for a successful lean implementation in SMEs.

Practical implications

The research outcomes are important to practicing managers in SMEs, helping them facilitate lean acceptance and enhance the likelihood of successful lean implementation.

Originality/value

The insights from this study present building blocks in developing a lean implementation model for SMEs that considers the FLEs’ role more comprehensively.
The importance of adopting an intersectionality approach to refugee status determination procedures: lessons from Greece, Israel and Uganda
Authors: Sarkin Jeremy Julian , Morais Tatiana
Published: June 2022

Purpose

This paper argues that intersectionality ought to be a vital tool to identify and recognise those who are refugees. It provides a useful way to distinguish refugees from migrants as well as making it possible to screen for asylum seekers who are at greater risk of experiencing specific vulnerable situations, such as sexual and gender-based violence. This study therefore argues that intersectionality is useful for risk assessment processes as well as for triggering special protection mechanisms.

Design/methodology/approach

This research article draws from a cross-cultural empirical study conducted in Greece, Uganda, and Israel on problems asylum seekers and refugees face in host countries.

Findings

It is argued that while it is important to identify and screen for asylum seekers who have survived or are at greater risk of experiencing sexual and gender-based violence to provide special protection, it may lead to what has been called a “categorical fetishism”, in this case, applied to vulnerability. Such stigmatising and disempowering perceptions of refugees and their experiences may lead to the view that there are “good” refugees and asylum seekers who are worthy of protection, as opposed to “others”.

Originality/value

This original empirical article provides a new way of examining issues of refugee status determination to ensure fairer ways of doing so.
Supervisor bottom line mentality, self-regulation impairment and unethical pro-organizational behavior: investigating the moderating effect of perceived employability
Authors: Kamran Komal , Farasat Mobina , Azam Akbar , Atif Mian Muhammad
Published: June 2022

Purpose

Unethical pro-organizational behavior (UPB) is one of the major reasons behind high-profile financial frauds in the recent past. This study aims to explore how an exclusive focus on financial outcomes, i.e. supervisor bottom-line mentality (BLM) leads to UPB among employees and highlights the critical role of self-regulation impairment and perceived employability in the process. Drawing on self-regulation theory, this study examines how BLM and perceived employability interactively impact self-regulatory strength, which ultimately influences UPB.

Design/methodology/approach

The theoretical model is tested through a time-lagged field study of 171 employees and hypothesis testing in SPSS PROCESS Macros.

Findings

Results suggest that self-regulation impairment mediates a positive relationship between supervisor BLM and employee UPB and perceived employability moderates this indirect association between BLM and UPB, wherein the indirect positive relationship is stronger when perceived employability is low (than high).

Originality/value

This study contributes to the BLM and UPB literature by identifying the critical role of perceived employability and suggesting that UPB is an impulsive action rather than an intentional move.
Memetic algorithm for unrelated parallel machine scheduling problem with grey processing times
Authors: Arık Oğuzhan Ahmet
Published: June 2022

Purpose

This paper aims to provide a promising memetic algorithm (MA) for an unrelated parallel machine scheduling problem with grey processing times by using a simple dispatching rule in the local search phase of the proposed MA.

Design/methodology/approach

This paper proposes a MA for an unrelated parallel machine scheduling problem where the objective is to minimize the sum of weighted completion times of jobs with uncertain processing times. In the optimal schedule of the problem’s single machine version with deterministic processing time, the machine has a sequence where jobs are ordered in their increasing order of weighted processing times. The author adapts this property to some of their local search mechanisms that are required to assure the local optimality of the solution generated by the proposed MA. To show the efficiency of the proposed algorithm, this study uses other local search methods in the MA within this experiment. The uncertainty of processing times is expressed with grey numbers.

Findings

Experimental study shows that the MA with the swap-based local search and the weighted shortest processing time (WSPT) dispatching rule outperforms other MA alternatives with swap-based and insertion-based local searches without that dispatching rule.

Originality/value

A promising and effective MA with the WSPT dispatching rule is designed and applied to unrelated parallel machine scheduling problems where the objective is to minimize the sum of the weighted completion times of jobs with grey processing time.