bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu
Authors: Petrone Mary E. , Lucas Carolina , Menasche Bridget , Breban Mallery I. , Yildirim Inci , Campbell Melissa , Omer Saad B. , Ko Albert I. , Grubaugh Nathan D. , Iwasak Akiko , Wilen Craig B. , Vogels Chantal B.F. , Fauver Joseph R.
Published: March 2022

SARS-CoV-2 ‘Variants of Concern’ (VOCs) continue to reshape the trajectory of the COVID-19 pandemic. However, why some VOCs, like Omicron, become globally dominant while the spread of others is limited is not fully understood. To address this question, we investigated the VOC Mu, which was first identified in Colombia in late 2020. Our study demonstrates that, although Mu is less sensitive to neutralization compared to variants that preceded it, it did not spread significantly outside of South and Central America. Additionally, we find evidence that the response to Mu was impeded by reporting delays and gaps in the global genomic surveillance system. Our findings suggest that immune evasion alone was not sufficient to outcompete highly transmissible variants that were circulating concurrently with Mu. Insights into the complex relationship between genomic and epidemiological characteristics of previous variants should inform our response to variants that are likely to emerge in the future.
SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Authors: Ramuta Mitchell D. , Newman Christina M. , Brakefield Savannah F. , Stauss Miranda R. , Wiseman Roger W. , Kita-Yarbro Amanda , O’Connor Eli J. , Dahal Neeti , Lim Ailam , Poulsen Keith P. , Safdar Nasia , Marx John A. , Accola Molly A. , Rehrauer William M. , Zimmer Julia A. , Khubbar Manjeet , Beversdorf Lucas J. , Boehm Emma C. , Castañeda David , Rushford Clayton , Gregory Devon A. , Yao Joseph D. , Bhattacharyya Sanjib , Johnson Marc C. , Aliota Matthew T. , Friedrich Thomas C. , O’Connor David H. , O’Connor Shelby L.
Published: March 2022

Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.
Emerging Therapies for COVID-19: the value of information from more clinical trials
Authors: Dijk Stijntje W. , Krijkamp Eline , Kunst Natalia , Gross Cary P. , Wong John B. , Myriam Hunink M.G.
Published: March 2022

Objectives

The COVID-19 pandemic necessitates time-sensitive policy and implementation decisions regarding new therapies in the face of uncertainty. The aim of this study was to quantify consequences of approving therapies or pursuing further research: either immediate approval, use only in research, approval with research (e.g., Emergency Use Authorization), or reject.

Methods

Using a cohort state-transition model for hospitalized COVID-19 patients, we estimated quality-adjusted life years (QALYs) and costs associated with the following interventions: Hydroxychloroquine, Remdesivir, Casirivimab-Imdevimab, Dexamethasone, Baricitinib-Remdesivir, Tocilizumab, Lopinavir-Ritonavir, and Interferon beta-1a, and usual care. We used the model outcomes to conduct cost-effectiveness and value of information analyses from a US healthcare perspective and a lifetime horizon.

Results

Assuming a $100,000-per-QALY willingness-to-pay-threshold, only Remdesivir, Casirivimab-Imdevimab, Dexamethasone, Baricitinib-Remdesivir and Tocilizumab were (cost-) effective (incremental net health benefit 0.252, 0.164, 0.545, 0.668 and 0.524 QALYs and incremental net monetary benefit $25,249, $16,375, $54,526, $66,826 and $52,378). Our value of information analyses suggest that most value can be obtained if these 5 therapies are approved for immediate use rather than requiring additional RCTs (net value $20.6 Billion, $13.4 Billion, $7.4 Billion, $54.6 Billion and $7.1 Billion); Hydroxychloroquine (net value $198 Million) only used in further RCTs if seeking to demonstrate decremental cost-effectiveness, and otherwise rejected; and Interferon beta-1a and Lopinavir-Ritonavir are rejected (i.e., neither approved nor additional RCTs).

Conclusions and Relevance

Estimating the real-time value of collecting additional evidence during the pandemic can inform policymakers and clinicians about the optimal moment to implement therapies and whether to perform further research.
The origin of diffuse noxious inhibitory controls
Authors: Kucharczyk Mateusz Wojciech , Di Domenico Francesca , Bannister Kirsty
Published: March 2022

Pain alerts us to actual or potential tissue damage. During acute pain, our central nervous system acts endogenously to modulate pain processing, thus reducing or enhancing pain perception. However, during chronic pain, the balance between inhibitory and facilitatory processes are tipped in favour of pro-pain modulation.

Diffuse noxious inhibitory controls (DNIC) is a naturally occurring pain inhibitory pathway that projects from the brainstem to the spinal cord to inhibit neuronal activity therein in a manner that is 1) subserved by noradrenaline, and 2) dysfunctional in chronicity. To harness its high therapeutic potential, we aimed to anatomically and functionally define DNIC.

Through employing an intersectional opto- and chemogenetic approach to modulate activity in brainstem noradrenergic nuclei, here we show that spinal neuronal firing observed upon DNIC activation during electrophysiological experiments, and animal pain thresholds observed during behavioural experiments, are modulated in a pro-pain manner upon opto-manipulation of A5 spinally projecting noradrenergic neurons, thus evidencing the DNIC origin.

Given the plasticity of the functional expression of DNIC in disease, and the success of back and forward translation of paradigms that evoke DNIC in pre-clinical and clinical models, our findings offer an attractive avenue of studies for disease specific analgesic interventions.
Novel Adult Cortical Neuron Processing and Screening method illustrates Sex- and Age-dependent effects of pharmaceutical compounds
Authors: Sefiani Arthur , Rusyn Ivan , Geoffroy Cédric G.
Published: March 2022

Neurodegenerative diseases and neurotraumatic injuries are typically age-associated disorders that can reduce neuron survival, neurite outgrowth, and synaptic plasticity leading to loss of cognitive capacity, executive function, and motor control. In pursuit of reducing the loss of said neurological functions, novel compounds are sought that promote neuron viability, neuritogenesis, and/or synaptic plasticity. Current high content in vitro screenings typically use cells that are iPSC-derived, embryonic, or originate from post-natal tissues; however, most patients suffering from neurodegenerative diseases and neurotrauma are of middle-age and older. The chasm in maturity between the neurons used in drug screens and those in a target population is a barrier for translational success of in vitro results. It has been historically challenging to culture adult neurons let alone conduct screenings; therefore, age-appropriate drug screenings have previously not been plausible. We have modified Miltenyi’s protocol to increase neuronal yield, neuron purity, and neural viability at a reduced cost to expand our capacity to screen compounds directly in primary adult neurons. Furthermore, we have developed the first morphology-based screening system using adult cortical neurons. By using primary adult cortical neurons from mice that were 4 to 48 weeks old for screening of a library of pharmaceuticals, we have demonstrated age- and sex-dependent effects on neuritogenesis and neuron survival in vitro. Utilizing age- and sex-appropriate in vitro models to find novel compounds increasing neuron survival and neurite outgrowth, made possible by our modified adult neuron processing method, will greatly increase the relevance of in vitro screening for finding neuroprotective compounds.
On the Geometry of Interacting Axon Tracts in Relation to Their Functional Properties
Authors: Chawla Aman , Morgera Salvatore Domenic
Published: March 2022

It is well known that demyelination associated with multiple sclerosis alters coupling between axons in a diseased nerve tract due to exposure of ion channels. In this work we ask the question whether the presence of electric fields as a coupling mechanism between nerve axons, has any impact on the expected conduction properties of the nerve under focal demyelination. Using an approximate geometry for a bundle of three axons, we allow electric fields generated at a node of Ranvier to influence other nodes of Ranvier on different axons. In order to introduce focal demyelination, we allow a new type of structure, intermediate between a node and an internodal segment. We find that the nerve’s conduction profiles are different with and without field-based coupling. This is important because it opens up the possibility for an experimental investigation to study whether field-based coupling predominates over current-based coupling. Fields and currents may also be measured using different methods and so there are implications for bio-instrumentation. From a systems perspective, the study is based on a novel equation which allows electric fields to act as sources of current at axons’ nodes of Ranvier, thereby generating new behaviors from the set of coupled partial differential equations that model the electrodynamics of the nerve. In addition to our simulation study of focal demyelination, we present a justification for a certain geometric W-matrix used in our phenomenological 2019 model. We also provide the first simulations of a tract of tortuous axons, showing the impact of tract tortuosity on conduction velocity. The tortuous model is analyzed geometrically to illustrate the mechanism of synchronization. Finally, this same model is shown to be castable as a learning machine - a formulation that has neuroscience implications.
Behavioral and imaging analysis of Foxg1 heterozygous mice
Authors: Erickson Kirsty R. , Lifer Rebekah , Merritt Jonathan K. , Lanaghan Zeljka Miletic , Does Mark D. , Ramadass Karthik , Landman Bennett A. , Cutting Laurie E. , Neul Jeffrey L.
Published: March 2022

FOXG1 Syndrome (FS) is a devastating neurodevelopmental disorder that is caused by a heterozygous loss-of-function (LOF) mutation of theFOXG1gene, which encodes a transcriptional regulator important for telencephalic brain development. People with FS have marked developmental delays, impaired ambulation, movement disorders, seizures, and behavior abnormalities including autistic features. Current therapeutic approaches are entirely symptomatic, however the ability to rescue phenotypes in mouse models of other genetic neurodevelopmental disorders such as Rett syndrome, Angelman syndrome, and Phelan-McDermid syndrome by postnatal expression of gene products has led to hope that similar approaches could help modify the disease course in other neurodevelopmental disorders such as FS. While FoxG1 protein function plays a critical role in embryonic brain development, the ongoing adult expression of FoxG1 and behavioral phenotypes that present when FoxG1 function is removed postnatally provides support for opportunity for improvement with postnatal treatment. Here we generated a new mouse allele ofFoxg1that disrupts protein expression and characterized the behavioral and structural brain phenotypes in heterozygous mutant animals. These mutant animals display changes in locomotor behavior, gait, anxiety, social interaction, aggression, and learning and memory compared to littermate controls. Additionally, they have structural brain abnormalities reminiscent of people with FS. This information provides the framework for future studies to evaluate the potential for post-natal expression of FoxG1 to modify the disease course in this severe neurodevelopmental disorder.
NtrC expression at lag-phase improves competitive fitness under low and fluctuating nutrient condition
Authors: Mishra L K , Shashidhar R
Published: March 2022

The enteric pathogens cycle between nutrient rich host and nutrient poor external environment. These pathogens compete for nutrients in the host as well as in external environment and also often experience starvation. In this context, we have studied the role of a global nitrogen regulator (NtrC) of Salmonella Typhimurium. The ntrC mutation caused extended lag phase and slow growth in minimal media. In lag phase the wild-type cells showed ∼60 fold more expression of ntrC as compared to log phase cells. The role of ntrC gene is often studied with respect to nitrogen scavenging in a low nitrogen growing condition. However, our observation indicates that, even in the adequate supply of nitrogen, the ntrC null mutants failed to adapt to new nutrient conditions and were slow to exit from the lag phase. Gene expression studies at lag phase showed down-regulation of the genes involved in carbon/nitrogen transportation and metabolism in ΔntrC mutant. In the co-culture competition studies, we observed that ntrC knockout was unable to survive with the wild-type Salmonella and E. coli. We also observed that the ΔntrC mutant did not survive long term nitrogen starvation (150 days). Critical analysis of starvation survival revealed that, ntrC gene is essential for recycling of nutrients from the dead cells. The nutrient recycling efficiency of ΔntrC mutant was ∼ 12 times less efficient than wild-type. Hence, the current work establishes that ntrC expression at the lag phase is essential for competitive fitness of Salmonella to survive in an environment having low and fluctuating nutrient conditions.

Importance

Salmonella Typhimurium, both inside or outside of the host organism face enormous competition from other microorganisms. The competition may take place either in steady or in fluctuating climatic conditions. Thus, how Salmonella Typhimurium survive under such overlapping stress conditions, remained unclear. Therefore, here we report that, a global regulator NtrC, which is also a part of two-component system, activates the set of genes and operons involved in rapid adaptation and efficient nutrient recycling/scavenging. These properties, make cell able to compete with other microbes, under characteristic feast- or-famine life style of Salmonella Typhimurium. Therefore, this piece of work helps us to understand the starvation physiology of enteric bacterial pathogen Salmonella Typhimurium.
Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid
Authors: Lee Jonathan T. , Yang Qingyi , Gribenko Alexey , Perrin B. Scott , Zhu Yuao , Cardin Rhonda , Liberator Paul A. , Anderson Annaliesa S. , Hao Li
Published: March 2022

SARS-CoV-2 continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid™. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from ∼4,892,000 high-quality SARS-CoV-2 genomes in GISAID. Any mutations identified from comparison to the reference sequence (Wuhan-hu-1) were cataloged and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (alpha-, beta-, and gamma-coronaviruses). Additionally, we showed that over time the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the EUA approval of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals.

Importance

The recent authorization of oral SARS-CoV-2 antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. Emergence of new variants, as well as selective pressure imposed by antiviral drugs themselves, raise concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.
Effect of COVID-19 vaccination on menstrual periods in a prospectively recruited cohort
Authors: Von Woon Ee , Male Victoria
Published: March 2022

COVID-19 vaccination protects against the potentially serious consequences of SARS-CoV2 infection, but some people have been hesitant to receive the vaccine because of reports that it could affect menstrual bleeding. To determine whether this occurs, we prospectively recruited a cohort of 79 individuals, each of whom recorded details of at least three consecutive menstrual cycles, during which time they each received at least one dose of COVID-19 vaccine. We find that either dose of the COVID-19 vaccine is associated with a delay to the subsequent period in spontaneously cycling participants (2.3 days after dose 1; 1.3 days after dose 2) but this change rapidly reverses. No change to timing was detected in those on hormonal contraception. We detected no change in menstrual flow associated with either dose of the vaccine, in either spontaneously cycling participants or those on hormonal contraception. We detected no association between menstrual changes and other commonly-reported side effects of vaccination, such as sore arm, fever and fatigue.
Characterizing Photosynthetic Biofuel Production: Isotopically non-stationary13C metabolic flux analysis (INST-13CMFA) on limonene producingSynechococcussp. PCC 7002
Authors: Newman Darrian M. , Sake Cara L. , Metcalf Alex J. , Davies Fiona K. , Boyle Nanette R.
Published: March 2022

Synechococcussp. PCC 7002 is a unicellular cyanobacterium capable of fast growth, even under high light intensity and high salinity. These attributes along with genetic tractability makeSynechococcussp. PCC 7002 an attractive candidate for industrial scale production of specialty and commodity chemicals. One such strain produces limonene, an energy dense diesel jet fuel drop-in additive, at a titer of 4 mg/L over a four-day incubation period. In this study, we use the state-of-the-art whole-cell characterization tool, isotopically non-stationary13C metabolic flux analysis (INST-13CMFA) to determine intracellular fluxes through the pathways of central metabolism for the limonene producing strain and wild type strain ofSynechococcussp. PCC 7002. We find similar flux distribution in the Calvin-Benson-Bassham cycle, photorespiration, oxidative pentose phosphate pathway, and reductive tricarboxylic acid cycle. The key difference between strains is observed in the production of pyruvate. The limonene producing strain displays significantly higher flux through the amphibolic pathways of phosphoenolpyruvate carboxylase and the malic enzyme to synthesize pyruvate, while the wild type strain uses pyruvate kinase in a single step. Our findings suggest that this flux distribution is a mechanism to recover a physiologically optimal ratio of ATP to NADPH. The upregulation of this amphibolic pathway may act to restore the physiological ATP:NADPH ratio that has been disturbed by limonene biosynthesis.
A partnership of the lipid scramblase XK and of the lipid transfer protein VPS13A at the plasma membrane
Authors: Samander Andrés Guillén , Wu Yumei , Pineda S. Sebastian , García Francisco J. , Eisen Julia N. , Leonzino Marianna , Uğur Berrak , Kellis Manolis , Heiman Myriam , De Camilli Pietro
Published: March 2022

Chorea-acanthocytosis and McLeod syndrome are diseases with shared clinical manifestations caused by mutations in VPS13A and XK, respectively. Key features of these conditions are the degeneration of caudate neurons and the presence of abnormally shaped erythrocytes. XK belongs to a family of plasma membrane (PM) lipid scramblases whose action results in exposure of PtdSer at the cell surface. VPS13A is an ER-anchored lipid transfer protein with a putative role in the transport of lipids at contacts of the ER with other membranes. Recently VPS13A and XK were reported to interact by still unknown mechanisms. So far, however, there is no evidence for a colocalization of the two proteins at contacts of the ER with the PM, where XK resides, as VPS13A was shown to be localized at contacts between the ER and either mitochondria or lipid droplets. Here we show that VPS13A can also localize at ER-PM contacts via the binding of its PH domain to a cytosolic loop of XK, that such interaction is regulated by an intramolecular interaction within XK and that both VPS13A and XK are highly expressed in the caudate neurons. Binding of the PH domain of VPS13A to XK is competitive with its binding to intracellular membranes that mediate other tethering functions of VPS13A. Our findings support a model according to which VPS13A-dependent lipid transfer between the ER and the PM is coupled to lipid scrambling within the PM. They raise the possibility that defective cell surface exposure of PtdSer may be responsible for neurodegeneration.
Multiethnic Polygenic Risk Prediction in Diverse Populations through Transfer Learning
Authors: Tian Peixin , Chan Tsai Hor , Wang Yong-Fei , Yang Wanling , Yin Guosheng , Zhang Yan Dora
Published: March 2022

Polygenic risk scores (PRS) leverage the genetic contribution of an individual’s genotype to a complex trait by estimating disease risk. Traditional PRS prediction methods are predominantly for European population. The accuracy of PRS prediction in non-European populations is diminished due to much smaller sample size of genome-wide association studies (GWAS). In this article, we introduced a novel method to construct PRS for non-European populations, abbreviated as TL-Multi, by conducting transfer learning framework to learn useful knowledge from European population to correct the bias for non-European populations. We considered non-European GWAS data as the target data and European GWAS data as the informative auxiliary data. TL-Multi borrows useful information from the auxiliary data to improve the learning accuracy of the target data while preserving the efficiency and accuracy. To demonstrate the practical applicability of the proposed method, we applied TL-Multi to predict the risk of systemic lupus erythematosus (SLE) in Asian population and the risk of asthma in Indian population by borrowing information from European population. TL-Multi achieved better prediction accuracy than the competing methods including Lassosum and meta-analysis in both simulations and real applications.
Proteomic characterization of spinal cord synaptoneurosomes from Tg-SOD1/G93A mice supports a role for MNK1 and local translation in the early stages of amyotrophic lateral sclerosis
Authors: Casañas Juan José , Montesinos María Luz
Published: March 2022

The isolation of synaptoneurosomes (SNs) represents a useful means to study synaptic events. However, the size and density of synapses varies in different regions of the central nervous system (CNS), and this also depends on the experimental species studied, making it difficult to define a generic protocol for SNs preparation. To characterize synaptic failure in the spinal cord (SC) in the Tg-SOD1/G93A mouse model of amyotrophic lateral sclerosis (ALS), we applied a method we originally designed to isolate cortical and hippocampal SNs to SC tissue. Interestingly, we found that the SC SNs were isolated in a different gradient fraction to the cortical/hippocampal SNs. We compared the relative levels of synaptoneurosomal proteins in control (Tg-SOD1) animals, with Tg-SOD1/G93A mice at onset and those that were symptomatic using iTRAQ proteomics. The results obtained suggest that an important regulator of local synaptic translation, MNK1 (MAP kinase interacting serine/threonine kinase 1), might well influence the early stages of ALS.
The Structural and Biochemical Basis for FER Receptor Kinase Early Signaling Initiation in Arabidopsis
Authors: Kong Yanqiong , Chen Jia , Chen Hong , Shen Yanan , Wang Lifeng , Yan Yujie , Zhou Huan , Zheng Heping , Yu Feng , Ming Zhenhua
Published: March 2022

Accumulating evidence has indicated that receptor-like kinase (RLK) autophosphorylation and substrate phosphorylation triggered by RLK are early and essential events for RLK function. However, the structural and biochemical basis for these early events is largely unclear. Herein, we used RLK FERONIA (FER) as a model and crystallized its core kinase domain (FER-KD) in the dephosphorylated state. We found that FER-KD adopts an active conformation in its crystal structure. Moreover, FER-KD mutants with reduced or no catalytic activity also adopt an active conformation before phosphorylation. Collectively, these observations suggest that FER employs a phosphorylation-independent active state before ligand-induced phosphorylation and full activation. We further demonstrated that FER is a dual-specificity kinase and that autophosphorylation on Tyr residues lags somewhat behind Ser/Thr phosphorylation. More importantly, Tyr phosphorylation is essential for FER-KD to initiate substrate GRP7 phosphorylation. Our work provides a paradigm to study the mechanisms of the early steps of RLK signaling initiation and highlights its “active” form and Tyr phosphorylation-gated roles in response to signaling stimuli.
TGFβ limits Myc-dependent TCR-induced metabolic reprogramming in CD8+ T cells
Authors: Hope Helen Carrasco , Pickersgill Gabriella , Ginefra Pierpaolo , Vannini Nicola , Cook Graham P. , Salmond Robert J.
Published: March 2022

T cell activation is dependent upon the integration of antigenic, costimulatory and cytokine-derived signals and the availability and acquisition of nutrients from the environment. Furthermore, T cell activation is accompanied by reprogramming of cellular metabolism to provide the energy and building blocks for proliferation, differentiation and effector function. Transforming growth factor β (TGFβ) has pleiotropic effects on T cell populations, having both an essential role in the maintenance of immune tolerance but also context-dependent pro-inflammatory functions. We set out to define the mechanisms underpinning the suppressive effects of TGFβ on mouse CD8+ T cell activation. RNA-sequencing analysis of TCR-stimulated T cells determined that Myc-regulated genes were highly enriched within gene sets downregulated by TGFβ. Functional analysis demonstrated that TGFβ impeded TCR-induced upregulation of amino acid transporter expression, amino acid uptake and protein synthesis. Furthermore, TCR-induced upregulation of Myc-dependent glycolytic metabolism was substantially inhibited by TGFβ treatment with minimal effects on mitochondrial respiration or mTOR activation. Thus, our data suggest that inhibition of Myc-dependent metabolic reprogramming represents a major mechanism underpinning the suppressive effects of TGFβ on CD8+ T cell activation.
Comparative Structural and Dynamics Study of Free and gRNA-bound FnCas9 and SpCas9 Proteins
Authors: Panda Gayatri , Ray Arjun
Published: March 2022

The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, thereby hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. Here, we have compared the dynamics of a more specific naturally occurring Cas9 from Francisella novicida (FnCas9) to the most widely used, SpCas9 protein. Long-scale atomistic MD simulations of free and gRNA-bound forms of both the Cas9 proteins were performed, and their domain rearrangements and binding affinity with gRNA were compared to decipher the possible reason behind the enhanced specificity of FnCas9 protein. The greater binding affinity with gRNA, high domain electrostatics, and more volatility of FnCas9 than SpCas9 may explain its increased specificity and lower tolerance for mismatches.

Highlights

The gRNA binding led to the opening of the structure of Cas9 endonuclease and exposure of hydrophobic residues to accommodate it.

Concerted domain movement was observed in both SpCas9 (HNH-REC2 domains, CTD-Topo domains, and REC3-RuvC) and FnCas9 (HNH-REC3-REC1 and PI-WED-RuvC).

Both Cas9s have shown a decrease in percentage helicity and an increase in the percentage of structurally dynamic residues (more secondary structural transitions) post gRNA binding.

In the gRNA-bound form of FnCas9, the PAM-interacting domain was found to have a larger structural transition and increased coil%.

Electrostatic interactions have a major contribution to the high binding affinity of FnCas9 with gRNA.

Arginine-helix has shown a pivotal role in the binding of gRNA in FnCas9 protein.
A conserved PLK1 docking site in TopBP1 maintains genome integrity during mitosis
Authors: Li Jiayi , Bagge Jonas , Lisby Michael , Nilsson Jakob , Oestergaard Vibe H.
Published: March 2022

TopBP1 is a large scaffold protein with multiple functions in genome integrity. We previously identified a novel role for TopBP1 during M phase by showing that TopBP1 reduces carry-over of DNA damage to daughter cells. This function emerges as a critical backup pathway in BRCA deficient cells, yet many aspects of TopBP1 regulation during mitosis are unclear. The mitotic kinase PLK1 has been reported to interact with TopBP1 but the functional relevance of this is unclear. Here, we identify and characterize a conserved PLK1 docking site in TopBP1. Endogenous deletion of the PLK1 docking site in TopBP1 results in increased number of mitotic TopBP1 foci, increased DNA damage in daughter cells, deficient mitotic DNA repair synthesis and increased frequency of binucleation. At the same time, cell cycle distribution and ATR activation are normal in cells with the PLK1 docking site deletion in TopBP1. Interestingly, mutation of this site in TopBP1 renders cells sensitive to PARP inhibitors but not to camptothecin hinting to different cellular effects of the two chemotherapeutics. Altogether, our data indicate that the PLK1-TopBP1 interaction is critical for the mitotic function of TopBP1.
Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway
Authors: Xue Jan Y , Hind Katy , Lemay Matthew A. , Mcminigal Andrea , Jourdain Emma , Chan Cheong Xin , Martone Patrick T.
Published: March 2022

The discovery of lignins in the coralline red alga Calliarthron tuberculosum raised new questions about the deep evolution of lignin biosynthesis. Here we present the transcriptome of C. tuberculosum supported with newly generated genomic data to identify gene candidates from the monolignol biosynthetic pathway using a combination of sequence similarity-based methods. We identified candidates in the monolignol biosynthesis pathway for the genes 4CL, CCR, CAD, CCoAOMT, and CSE but did not identify candidates for PAL, CYP450 (F5H, C3H, C4H), HCT, and COMT. In gene tree analysis, we present evidence that these gene candidates evolved independently from their land plant counterparts, suggesting convergent evolution of a complex multistep lignin biosynthetic pathway in this red algal lineage. Additionally, we provide tools to extract metabolic pathways and genes from the newly generated transcriptomic and genomic datasets. Using these methods, we extracted genes related to sucrose metabolism and calcification. Ultimately, this transcriptome will provide a foundation for further genetic and experimental studies of calcifying red algae.
Species Distribution Modeling of Aedes aegypti in Maricopa County, Arizona from 2014-2020
Authors: Holeva-Eklund Whitney M. , Young Steven J. , Will James , Busser Nicole , Townsend John , Hepp Crystal M.
Published: March 2022

Aedes aegypti mosquitoes, which are of great importance to public health, have recently and rapidly expanded their global range; however, little is understood about the distribution of these mosquitoes in desert environments. Trapping records for Ae. aegypti in Maricopa County, Arizona from 2014-2020 were used to construct species distribution models using Maxent. Satellite imagery and socioeconomic factors were used as predictors. Maps of predicted habitat suitability were converted to binary presence/absence maps, and consensus maps were created that represent “core” habitat for the mosquito over six years of time. Generally, population density was the most important predictor in the models while median income was the least important. This study is the first step toward understanding the distribution of the vector in a desert environment.

One-Sentence Summary

This study uses satellite imagery and socioeconomic factors to identify core habitat over six years in a desert environment.
Liquid droplet aging and fibril formation of the stress granule protein TIA1 low complexity domain
Authors: Wittmer Yuuki , Jami Khaled M. , Stowell Rachelle K. , Le Truc , Hung Ivan , Murray Dylan T.
Published: March 2022

Protein domains biased toward a few amino acid types are vital for the formation of biomolecular condensates in living cells. These membraneless compartments are formed by molecules exhibiting a range of molecular motions and structural order. Missense mutations increase condensate persistence lifetimes or structural order, properties that are thought to underlie pathological protein aggregation. We examined seeded fibrils of the T-cell restricted intracellular antigen-1 low complexity domain and determined residues 338–357 compose the rigid fibril core. Aging of wild-type and P362L mutant low complexity domain liquid droplets resulted in fibril assemblies that are structurally distinct from the seeded fibril preparation. The results show that most disease mutations lie outside the region that forms homogeneous fibril structure, the droplets age into conformationally heterogenous fibrils, and the P362L disease mutation does not favor a specific fibril conformation.
Variations in antibody repertoires correlate with vaccine responses
Authors: Safonova Yana , Shin Sung Bong , Kramer Luke , Reecy James , Watson Corey T. , Smith Timothy P.L. , Pevzner Pavel A.
Published: March 2022

An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold the key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated data set, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.
4-Chloro-5-(dimethylamino)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyridazin-3(2H)-one
Authors: Song Jingjing , Jiang Xinyu , Wang Ziyi , Pei Jingyao , Li Hongsen
Published: March 2022

In the structure of the title compound, C15H14ClN5O2, the terminal phenyl ring and the adjacent furan ring subtend a dihedral angle of 6.77 (17)°. The 4-chloro-5-(dimethylamino)-pyridazin-3(2H)-one group is linked to the oxadiazole ring by a methylene bridge, and the dihedral angle between the pyridazine and oxadiazole rings is 88.66 (14)°. In the crystal, C—H...O and C—H...N hydrogen bonds extend the structure into a three-dimensional network.
The customer experience in Thailand's multichannel retail environments
Authors: Sombultawee Kedwadee , Tansakul Thanchanok
Published: March 2022

Purpose

The purpose of this paper is to investigate cognitive and affective customer service in Thailand's maltichannel retail environment. The research used the stimulus–organism–response model of consumer behaviour. The study's theoretical framework incorporated the multichannel service quality framework (Sousa and Voss, 2006) and a decomposed measure of customer experience, including cognitive and affective customer experience (Gao et al., 2021). Outcomes investigated included repurchase intention and word-of-mouth intention.

Design/methodology/approach

A quantitative survey of Thai consumers (aged 18 and over) who had purchased from multichannel retailers at least one time in the past year (n = 502) was conducted. Data were collected online and analysed using a structural equation modelling approach.

Findings

Significant factors in cognitive customer experience and affective customer experience included breadth of channel choice, transparency of channel, content consistency and process consistency. Effects differed in strength on these effects. Cognitive customer experience and affective customer experience influenced repurchase intention and word-of-mouth intention, with a stronger effect from affective customer experience.

Originality/value

This research presents an integrative model for customer experience in multichannel marketing, incorporating a well-established model of multichannel service quality and a decomposed measure of customer experience. It also illustrates the difference between cognitive customer experience and affective customer experience, which have different effect sizes from antecedents and different effects on outcome variables. This finding is a significant theoretical advancement.
Leader humility and team effectiveness: a moderated mediation model of leader-member exchange and employee satisfaction
Authors: Sheikh Aarif Mohd
Published: March 2022

Purpose

This research study examines the impact of leader humility (LH) on team effectiveness (TE) via the mediating mechanism of leader-member exchange (LMX). It also proposes employee satisfaction (ES) as a moderating variable in the relationship between LH and TE.

Design/methodology/approach

This study examines relationships among the study variables in the Indian context, using a sample of 589 employees serving the banking sector in Jammu and Kashmir, India. The data analysis was carried out via confirmatory factor analysis and structural equation modeling.

Findings

The results showed a significant positive influence of LH on TE. The results also posit a partial mediating effect of LMX on LH and TE interplay, and ES acts as a moderator between LH and TE. Thus, the results supported the hypothesized moderated mediation model and suggested implications for theory and practice. Further, the potential limitations and future directions are placed at the end.

Research limitations/implications

Organizational implications include that organizations should develop attractive organizational mechanisms to ensure better LMX and ES for enhancing employee effectiveness. Besides, organizations should attract and retain effective and humble leaders; and leaders should use humble attitude and behavior in dealing with employees, eventually ensuring higher TE.

Originality/value

This study tested LMX and job satisfaction as intervening variables in the relationship between LH and TE in the Indian context; the framework under context has received scarce research attention. The results suggest that organizations that focus on producing humble leaders succeed in enhancing and maintaining higher organizational effectiveness.
Concave or convex? The impact of display surface curvature on social appeals’ persuasion: the mediating role of self–other overlap
Authors: Zhang Yuli , Wang Chen
Published: March 2022

Purpose

Marketing persuasive materials are often displayed on a curved surface (e.g. a curved hallway). This study aims to investigate how the curvature (concave vs convex) of a display surface influences the persuasion of the marketing appeals presented on it.

Design/methodology/approach

The conceptual framework was tested in a field experiment, a lab experiment and two online experiments on Amazon Mechanical Turk. Analyses of variance and mediation analysis were used to test the hypotheses.

Findings

This research demonstrates that a concave (vs convex) display surface may increase persuasion for marketing materials with social appeals. This occurs because a concave surface enhances consumers’ perception of self–other overlap, which is matched with the content of the social appeal presented on it, thereby enhancing the appeal’s persuasiveness. It further identifies the appeal content as an important moderator of the effect; a convex (vs concave) display would enhance persuasion when the marketing materials contain personal appeals.

Research limitations/implications

Future research could investigate how a time delay (e.g. hours, days) and the curvature of a display board or wall would play a role in the effect of display curvature.

Practical implications

The findings offer a novel, simple and cost-effective approach to enhance persuasion for both nonprofit and for-profit marketing materials.

Originality/value

This research contributes to the persuasion literature by investigating the impact of one ubiquitous but overlooked aspect of the message setting (i.e. the curvature of the message’s display surface) on persuasion while holding the message source and content constant. It also advances knowledge on consumer shape perception by examining an underexplored shape (i.e. the curved shape of a display surface) that is nondiagnostic in message persuasion.
Examining the perspectives of adult working learners and key stakeholders using critical race theory
Authors: Jacobs Gloria E. , Castek Jill , Harris Kathy , Vanek Jen
Published: March 2022

Purpose

This article reports on a critical race theory (CRT) analysis of the perspectives of providers of employer-supported educational opportunities and adult learners, who identified as Black, indigenous or as a person of color, and were employed in service industries.

Design/methodology/approach

A review of the literature was used to shape an initial interview protocol. Data were collected from working learners in retail, hospitality, restaurants and healthcare industries. An “a priori” coding scheme that drew from CRT was applied to transcripts during analysis.

Findings

Analysis revealed that working learners' skills, experiential knowledge, learning mindset, language flexibility and knowledge gained from previous learning experiences were not consistently acknowledged by employers. CRT analysis illustrated that endemic racism exists within educational opportunities and in workplace learning.

Originality/value

CRT has not been widely used to examine adult education practice, especially for workforce development and employer-based education programs. This research expands the use of CRT in adult education and encourages critical conversations around equity in learning opportunities offered by employers. CRT informed data analysis uncovered barriers to equitable learning opportunities and workplace learning. A discussion of inequities in work-based learning illustrates there is insufficient awareness of implicit bias, which points to the need for initiatives focused on social justice.
Service beyond the status quo: the ripple effect of corporate social responsibility and internal marketing on employee's customer-oriented behavior
Authors: Olorunsola Victor Oluwafemi , Saydam Mehmet Bahri , Ogunmokun Oluwatobi A. , Ozturen Ali
Published: March 2022

Purpose

This paper proposes a research model in which work engagement (WE) mediates the effects of corporate social responsibility (CSR) and internal marketing (IM) simultaneously on customer-oriented boundary-spanning behavior (COBSB).

Design/methodology/approach

The study deploys structural equation modeling (SEM) to examine data acquired from 355 frontline bank employees (FBE) of private banks.

Findings

The findings of this study demonstrate that both FBE's perceptions of CSR and IM are positively related to their WE, proposing that adding CSR practices to existing IM programs is likely to boost anticipated employee work attitudes such as WE, which consecutively increase positive employee job outcomes such as COBSB. This research contributes to the body of knowledge by conceptually and empirically gauging CSR and IM practices simultaneously in the banking sector.

Originality/value

This study contributes to the existing body of knowledge by investigating the relationship between CSR and IM to COBSB via WE in frontline service roles in the retail banking sector.