bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibodies to Coagulase ofStaphylococcus aureuscrossreact to Efb and reveal different binding of shared Fibrinogen binding repeats
Authors: Bertoglio Federico , Ko Ya-Ping , Thomas Sheila , Giordano Liliana , Scommegna Francesca Romana , Meier Doris , Polten Saskia Helmsig , Becker Marlies , Arora Srishtee , Hust Michael , Höök Magnus , Visai Livia
Published: April 2022

Staphylococcus aureuspathology is caused by a plethora of virulence factors able to combat multiple host defence mechanisms. Fibrinogen (Fg), a critical component in the host coagulation cascade, plays an important role in the pathogenesis of this bacterium, as it is the target of multiple staphylococcal virulence proteins. Amongst its secreted virulence factors, Coagulase (Coa) and Extracellular fibrinogen-binding protein (Efb) share common Fg binding motives and have been described to form a Fg shield around staphylococcal cells, thereby allowing efficient bacterial spreading, phagocytosis escape and evasion of host immune system responses. Targeting these proteins with monoclonal antibodies thus represents a new therapeutic option againstS. aureus. To this end, here we report the selection and characterization of fully human, sequence-defined, monoclonal antibodies selected against the C-terminus of Coagulase. Given the functional homology between Coa and Efb, we also investigated if the generated antibodies bound the two virulence factors. Thirteen unique antibodies were isolated from naïve antibodies gene libraries by antibody phage display. As anticipated, most of the selected antibodies showed cross-recognition of these two proteins and among them, four were able to block the interaction between Coa/Efb and Fg. Furthermore, our monoclonal antibodies could interact with the two main Fg binding repeats present at the C-terminus of Coa and distinguish them, suggesting the presence of two functionally different Fg-binding epitopes.

Importance

The death toll related to methicillin-resistantS. aureuspiled to almost 1 million people in only one year (2019), ascribingS. aureusto the second leading cause of deaths associated with antimicrobial resistance. Therefore, new therapeutic strategies must be investigated. Blocking the adhesion step with the use of monoclonal antibodies is one promising alternative and Fg is a central plasma protein involved in staphylococcal infection. We present here a panel of monoclonal antibodies raised against Coa, cross-reacting to Efb and targeting the shared Fg binding repeats of Coa. In addition, we describe new epitope determinants in the repeated region of Coa, highlighted by differential binding of the newly selected antibodies.
Correlates of protection, viral load trajectories and symptoms in BA.1, BA.1.1 and BA.2 breakthrough infections in triple vaccinated healthcare workers
Authors: Marking Ulrika , Havervall Sebastian , Greilert Norin Nina , Bladh Oscar , Christ Wanda , Gordon Max , Ng Henry , Blom Kim , Phillipson Mia , Mangsbo Sara , Smed Sörensen Anna , Nilsson Peter , Hober Sophia , Åberg Mikael , Klingström Jonas , Thålin Charlotte
Published: April 2022

Background

Booster vaccine doses offer protection against severe COVID-19 caused by omicron but are less effective against infection. Characteristics such as serological correlates of protection, viral abundance, and clearance of omicron infection in triple vaccinated individuals are scarce.

Methods

We conducted a 4-week twice-weekly SARS-CoV-2 qPCR screening shortly after an mRNA vaccine booster in 368 healthcare workers. Spike-specific IgG levels and neutralization titers were determined at study start. qPCR-positive participants were sampled repeatedly for two weeks and monitored for symptoms.

Result

In total 81 (cumulative incidence 22%) omicron infections were detected, divided between BA.1, BA.1.1 and BA.2. Increasing post-booster antibody titers were protective against infection (p<0.05), linked to reduced viral load (p<0.01) and time to viral clearance (p<0.05). Only 10% of infected participants remained asymptomatic through the course of their infection. Viral load peaked at day 3 and live virus could be detected for up to 9 days after first PCR-positive sample. Presence of symptoms correlated to elevated viral load (p<0.0001), but despite resolution of symptoms most participants showed Ct levels <30 at day 9. No significant differences were observed for viral load and time to viral clearance between BA.1, BA.1.1 and BA.2 infected individuals.

Conclusion

We report a high incidence of omicron infection despite recent booster vaccination in triple vaccinated individuals. Increasing levels of vaccine-induced spike-specific WT antibodies entail increased protection against infection and reduce viral load if infected. High viral load and secretion of live virus for up to nine days may facilitate transmission in a triple vaccinated population.
Variation in National COVID-19 Mortality Rates Across Asian Subgroups in the United States, 2020
Authors: Xu Jay J.
Published: April 2022

Provisional U.S. national COVID-19 mortality data for the year 2020 analyzed by the CDC in March 2021 indicated that non-Hispanic Asians fared markedly better overall than other racial/ethnic minority groups–and marginally better than non-Hispanic Whites–in terms of age-adjusted mortality rates. However, Asians in the United States are composed of diverse array of origin subgroups with highly varying social, economic, and environmental experiences, which influence health outcomes. As such, lumping all Asians together into a single category can mask meaningful health disparities among more vulnerable Asian subgroups. To date, there has not been a national-level analysis of COVID-19 mortality outcomes between Asian subgroups. Utilizing final multiple cause of death data for 2020 and population projections from the U.S. Census Bureau’s Current Population Survey Annual Social and Economic Supplement for 2020, crude and age-adjusted national COVID-19 mortality rates, both overall and stratified by sex, were calculated for the six major single-race Asian origin subgroups (Asian Indian, Chinese, Filipino, Japanese, Korean, and Vietnamese) and a catch-all seventh category that comprises the remaining Asian subgroups (Other Asians), contrasting them to the corresponding mortality rates of other racial/ethnic groups. A substantially more nuanced picture emerges when disaggregating Asians into its diverse origin subgroups and stratifying by sex, with Filipino males and Asian males outside of the six major Asian subgroups in particular experiencing markedly higher age-adjusted mortality rates than their White male counterparts, whether comparisons were restricted to their non-Hispanic subsets or not. During the COVID-19 pandemic and in the post-pandemic recovery, it is imperative not to overlook the health needs of vulnerable Asian populations. Public health strategies to mitigate the effects of COVID-19 must avoid viewing Asians as a monolithic entity and recognize the heterogeneous risk profiles within the U.S. Asian population.
Chronotype and mortality - a 37-year follow-up study in Finnish adults
Authors: Hublin Christer , Kaprio Jaakko
Published: April 2022

Background

The only study on chronotype and mortality suggested small increases of all-cause and cardiovascular mortality in a 6.5-year follow-up. Our aim was to constructively replicate findings from it in a longer follow-up.

Methods

A questionnaire was administered to the population-based Finnish Twin Cohort in 1981 (response rate 84%, age 24–101 years). The study population included 23,854 participants who replied to the question: “Try to assess to what extent you are a morning person or an evening person”, with four response alternatives (clearly a morning person, to some extent a morning person, to some extent an evening person, and clearly an evening person). Vital status and cause of death data were provided by nationwide registers up to the end of 2018. Hazard ratios and their 95% confidence intervals for mortality were computed; there were 8728 deaths over the follow-up period. Adjustments were made for education, alcohol, smoking, body mass index, and sleep length.

Results

The model adjusted for all covariates showed a 9% increase in risk of all-cause mortality for the evening-type group (1.09, 1.01–1.18), with attenuation mainly due to smoking and alcohol, as they had larger consumption than those with morningness chronotypes. We observed no increase in cardiovascular mortality by chronotype. No increase in mortality was seen among the non-smokers who were at most light drinkers.

Conclusions

Our results from this 37-year follow-up study suggest that there is little or no independent contribution of chronotype to all-cause and cardiovascular mortality.

Key messages

There is little or no independent contribution of chronotype to mortality.

The increased risk of mortality associated with eveningness appears to be mainly mediated by a larger consumption of tobacco and alcohol than in those with a morningness chronotype.

It is important to be aware of the increased health risks of evening-type persons.
Multi-task deep autoencoder to predict Alzheimer’s disease progression using temporal DNA methylation data in peripheral blood
Authors: Chen Li
Published: April 2022

Motivation

Traditional approaches for diagnosing Alzheimer’s disease (AD) such as brain imaging and cerebrospinal fluid are invasive and expensive. It is desirable to develop a useful diagnostic tool by exploiting biomarkers obtained from peripheral tissues due to their noninvasive and easily accessible characteristics. However, the capacity of using DNA methylation data in peripheral blood for predicting AD progression is rarely known. It is also challenging to develop an efficient prediction model considering the complex and high-dimensional DNA methylation data in a longitudinal study.

Results

We develop two multi-task deep autoencoders, which are based on convolutional autoencoder and long short-term memory autoencoder to learn the compressed feature representations by jointly minimizing the reconstruction error and maximizing the prediction accuracy. By benchmarking on longitudinal methylation data collected from peripheral blood in Alzheimer’s Disease Neuroimaging Initiative, we demonstrate that the multi-task deep autoencoders outperform state-of-the-art machine learning approaches for both predicting AD progression and reconstructing the temporal methylation profiles. In addition, the proposed multi-task deep autoencoders can predict AD progression accurately using only historical data and the performance is further improved by including all temporal data.

Availability

https://github.com/lichen-lab/MTAE
Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling
Authors: Saha Suvrajit , Das Amit , Patra Chandrima , Anilkumar Anupama Ambika , Sil Parijat , Mayor Satyajit , Rao Madan
Published: April 2022

The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered GPI-anchored proteins (GPI-APs) form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drive the creation of active emulsions, mesoscale liquid ordered (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid-phase segregation. To test these ideas we use spatial imaging of homo-FRET combined with local membrane order and demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions, and exhibit significant lipid order, consistent with predictions of the active composite model.
Vimentin Intermediate Filaments Can Enhance or Abate Active Cellular Forces in a Microenvironmental Stiffness-Dependent Manner
Authors: Alisafaei Farid , Mandal Kalpana , Swoger Maxx , Yang Haiqian , Guo Ming , Janmey Paul A , Patteson Alison E , Shenoy Vivek B.
Published: April 2022

The mechanical properties of cells are largely determined by the cytoskeleton, which is a complex network of interconnected biopolymers consisting of actin filaments, microtubules, and intermediate filaments. While disruption of the actin filament and microtubule networks is known to decrease and increase cell-generated forces, respectively, the effect of intermediate filaments on cellular forces is not well understood. Using a combination of theoretical modeling and experiments, we show that disruption of vimentin intermediate filaments can either increase or decrease cell-generated forces, depending on microenvironment stiffness, reconciling seemingly opposite results in the literature. On the one hand, vimentin is involved in the transmission of actomyosin-based tensile forces to the matrix and therefore enhances traction forces. On the other hand, vimentin reinforces microtubules and their stability under compression, thus promoting the role of microtubules in suppressing cellular traction forces. We show that the competition between these two opposing effects of vimentin is regulated by the microenvironment stiffness. For low matrix stiffness, the force-transmitting role of vimentin dominates over their microtubule-reinforcing role and therefore vimentin increases traction forces. At high matrix stiffness, vimentin decreases traction forces as the microtubule-reinforcing role of vimentin becomes more important with increasing matrix stiffness. Our theory reconciles seemingly disparate experimental observations on the role of vimentin in active cellular forces and provides a unified description of stiffness-dependent chemo-mechanical regulation of cell contractility by vimentin.

Significance

Vimentin is a marker of the epithelial to mesenchymal transition which takes place during important biological processes including embryogenesis, metastasis, tumorigenesis, fibrosis, and wound healing. While the roles of the actin and microtubule networks in the transmission of cellular forces to the extracellular matrix are known, it is not clear how vimentin intermediate filaments impact cellular forces. Here, we show that vimentin impacts cellular forces in a matrix stiffness-dependent manner. Disruption of vimentin in cells on soft matrices reduces cellular forces, while it increases cellular forces in cells on stiff matrices. Given that cellular forces are central to both physiological and pathological processes, our study has broad implications for understanding the effect of vimentin on cellular forces in different microenvironments.
Thermal Effects on Neurons During Stimulation of the Brain
Authors: Kim Taeken , Kadji Herve , Whalen Andrew J. , Ashourvan Arian , Freeman Eugene , Fried Shelley I. , Tadigadapa Srinivas , Schiff Steven J.
Published: April 2022

All artificial stimulation of the brain deposits thermal energy in the brain. This occurs through either Joule heating of the conductors carrying current through electrodes and magnetic coils, or through dissipation of energy in the conductive brain. Similarly, temperature affects all biological processes and chemical reactions. Although electrical interaction with brain tissue is inseparable from thermal effects when electrodes are used, magnetic induction enables us to separate Joule heating from induction effects by contrasting AC and DC driving of magnetic coils using the same energy deposition within the conductors. Since mammalian cortical neurons have no known sensitivity to static magnetic fields, and if there is no evidence of effect on spike timing to oscillating magnetic fields, we can presume that the induced electrical currents within the brain are below the molecular shot noise where any interaction with tissue is purely thermal. In this study, we examined a range of frequencies produced from micromagnetic coils operating below the molecular shot noise threshold for electrical interaction with single neurons. We found that small temperature increases and decreases of 1°C caused consistent transient suppression and excitation of neurons during temperature change. Numerical modeling of the biophysics demonstrated that the Na-K pump, and to a lesser extent the Nernst potential, could account for these transient effects. Such effects are dependent upon compartmental ion fluxes, and the rate of temperature change. A new bifurcation is described in the model dynamics that accounts for the transient suppression and excitation; in addition, we note the remarkable similarity of this bifurcation’s rate dependency with other thermal rate-dependent tipping points in planetary warming dynamics. Furthermore, bifurcations in the steady state dynamics leading to stable firing suppression are described for slightly higher temperatures. These experimental and theoretical findings demonstrate that stimulation of the brain must take into account small thermal effects that are ubiquitously present in electrical and magnetic stimulation. More sophisticated models of electrical current interaction with neurons combined with thermal effects will be required in order to more accurately enable model-based control of neuronal circuitry.
A Low-Dose Triple Antibody Cocktail Against the Ectodomain of the Matrix Protein 2 of Influenza A Is A Universally Effective and Viral Escape Mutant Resistant Therapeutic Agent
Authors: Kim Teha , Bimler Lynn , Ronzulli Sydney L. , Song Amber Y. , Johnson Scott K. , Jones Cheryl A. , Tompkins S. Mark , Paust Silke
Published: April 2022

Influenza, a negative sense single-strand RNA virus of the genus Orthomyxoviridae, causes respiratory illness in humans and animals and significant morbidity and mortality worldwide. While exposure to a specific influenza A strain causes homologous protection, two immune-dominant influenza A virus (IAV)-encoded epitopes - Hemagglutinin (HA) and Neuraminidase (NA) - undergo antigenic shift and drift, resulting in IAVs to which humans lack pre-existing immunity. Without a universal vaccine or therapeutic agent, influenza virus infections will significantly threaten human health. The extracellular domain of the Matrix protein 2-ion channel (M2e) is an ideal antigenic target for a universal influenza therapy: it is highly conserved across influenza A serotypes, has a low mutation rate, and is essential for viral entry and replication. However, less than 20% of humans generate M2e-specific antibodies in response to IAV exposure, thus lacking the benefits of M2e-MAb-mediated immunity. To therapeutically address this deficit, we generated several non-neutralizing M2e-specific monoclonal antibodies (M2e-MAbs) with strong universal IAV treatment potential. Using three MAbs that bind to M2e differentially and competitively, we developed a low-dose M2e-MAb triple cocktail as an effective universal prophylactic and therapeutic agent. We identified the low-dose M2e-MAb triple cocktail’s optimal antibody-clone combination, isotype, minimum effective dosage, and administration time points in mouse models challenged with human and zoonotic BSL-2 and BSL-3 IAV strains, demonstrating its universal potential. Using the IgG2a isotype, which had proven most effective, we established FcγRI, FcγRIII, and FcγRIV as required for M2e-MAb-mediated protection of IAV-challenged mice. Importantly, we established individual M2e-MAbs and the resulting triple cocktail as effective and viral escape mutant-resistant treatments in immunocompetent and immunodeficient mice. These unique qualities provide precedence for prioritizing our M2e-MAbs for therapeutic development.

CONFLICT OF INTEREST STATEMENT

SP serves on the scientific advisory board for Shoreline Biosciences, Qihan Biotechnology and is a Scientific Consultant for Qihan Biotechnology and the Genomics Institute of the Novartis Research Foundation. The remaining authors declare no competing interests.
Dietary αKG inhibits SARS CoV-2 infection and rescues inflamed lungs to restore normal O2saturation in animals
Authors: Agarwal Sakshi , Kaur Simrandeep , Asuru Tejeswara Rao , Joshi Garima , Shrimali Nishith M , Singh Anamika , Singh Oinam Ningthemmani , Srivastva Puneet , Shrivastava Tripti , Vrati Sudhanshu , Surjit Milan , Guchhait Prasenjit
Published: April 2022

Our recent works described the rescue effect of α-ketoglutarate (αKG, a metabolite of Krebs cycle) on thrombosis and inflammation in animals. αKG augments activity of prolyl hydroxylase 2 (PHD2), which in turn degrades proline residues of substrates like phosphorylated Akt (pAkt) and hypoxia inducible factor (HIF)α. Here we describe the inhibitory effect of octyl αKG on pAkt as well as on HIF1α/HIF2α, and in turn decreasing SARS CoV-2 replication in Vero E6 cells. αKG failed to inhibit the viral replication and Akt phosphorylation in PHD2-knockdown U937 cells transiently expressing ACE2. Contrastingly, triciribine (TCN, an Akt-inhibitor) inhibited viral replication alongside a downmodulation of pAkt in PHD2-KD cells. Dietary αKG significantly inhibited viral infection and rescued hamsters from thrombus formation and inflammation in lungs, the known causes of acute respiratory distress syndrome (ARDS) in COVID-19. αKG supplementation also reduced the apoptotic death of lung tissues in infected animals, alongside a downmodulation of pAkt and HIF2α. αKG supplementation neither affected IgG levels against SARS CoV-2 RBD protein nor altered the neutralization antibody response against SARS CoV-2. It did not interfere with the percentage of interferon-γ positive (IFNγ+) CD4+ and IFNγ+CD8+ T cells in infected animals. The extended work in balb/c mice transiently expressing ACE2 showed a similar effect of αKG in reducing accumulation of inflammatory immune cells and cytokines, including IL6, IL1β and TNFα, in lungs as well as in circulation of infected animals. Pro-thrombotic markers like platelet microparticles and platelet-leukocyte aggregates were reduced significantly in infected mice after αKG supplementation. Importantly, αKG supplementation restored the O2saturation (SpO2) in circulation of SARS CoV-2 infected hamsters and mice, suggesting a potential therapeutic role of this metabolite in COVID-19 treatment.
Perturbed actin cap and nuclear morphology in primary fibroblasts of Huntington’s disease patients as a new phenotypic marker for personalized drug evaluation
Authors: Gharaba Saja , Paz Omri , Feld Lea , Abashidze Anastasia , Weinrab Maydan , Wolfenson Haguy , Weil Miguel
Published: April 2022

Human primary skin fibroblast cells from patient’s skin biopsies were used previously as a model to study different neurodegenerative diseases, including Huntington’s Disease (HD). These cells are directly isolated from the patient’s tissue without any alteration in the genome, retaining in culture conditions their endogenous cellular characteristics and biochemical properties, as well as their cellular proliferation capacity for several passages. The aim of this study was to identify a distinctive cellular phenotype in primary skin fibroblasts from various HD patients, using image-based high content analysis, which could be used in the future for personalized drug screening treatment evaluation. We show that HD fibroblasts have a distinctive nuclear morphology associated with a nuclear actin cap deficiency, which in turn affects cell motility in a similar manner to primary skin fibroblasts from Hutchinson-Gilford progeria syndrome (HGPS) patients used as known actin cap deficient cells. Moreover, treatment of the HD cells with either Latrunculin B, used to disrupt actin cap formation, or the antioxidant agent Mitoquinone, used to improve mitochondrial activity, show opposite effects on actin cap associated morphological features and cell motility. The former exacerbates the HD phenotype while the latter improves it. Deep data analysis of the HD nuclear and actin cap features using custom developed image analysis algorithms allow strong cluster classification distinct from HGPS and healthy matching controls, supporting the finding of a novel HD cellular phenotypic marker that could be modulated by pharmacological agents in this patient-based disease model.
Harnessing cellular perception apparatus for smart metabolic reprogramming
Authors: Tan Chunlin , Tao Fei , Xu Ping
Published: April 2022

Metabolic reprogramming (MRP) is a fundamental approach in synthetic biology that involves redirecting metabolic flux and remodeling metabolic networks. However, only few approaches have been made in effective metabolic operations, especially at global level of metabolic networks. Naturally existing cellular perception apparatuses (CPAs), such as histidine kinases (HKs), are considered to sit on sensitive nodes of the metabolic network, which can trigger natural MRP upon perceiving environmental fluctuations. We develop a plateform for global MRP by natural environmental stimulation based on the combinational interference of CPAs. The plateform consists of a CRISPRi-mediated dual-gene combinational knockdown (CDCK) strategy and survivorship-based metabolic interaction analysis (SMIA). A total of 35 histidine kinase (HK) genes and 24 glycine metabolism genes were selected as targets to determine effectiveness of our approach for fast-growing chassisVibrioFA2. Combined knockdown of several genes of HKs and glycine metabolism increased the glycine production. Other other hand, effects of CDCK on bacterial antibiotic resistance were assessed by targeting HKs. Many HKs were identified to be associated with antibiotic resistance inVibrioFA2, of which combinational knockdown of two HK genessasA_8and04288reduced the ampicillin resistance. This MRP strategy is powerful and cost-effective, and can be considered as a smart strategy capable of operating a broad range of metabolic networks in microorganisms.
Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies
Authors: Li Ruofan , Mor Michael , Ma Bingting , Clark Alex E. , Alter Joel , Werbner Michal , Lee Jamie Casey , Leibel Sandra L. , Carlin Aaron F. , Dessau Moshe , Gal-Tanamy Meital , Croker Ben A. , Xiang Ye , Freund Natalia T.
Published: April 2022

As new variants of SARS-CoV-2 continue to emerge, it is important to assess the neutralizing capabilities of naturally elicited antibodies against SARS-CoV-2. In the present study, we evaluated the activity of nine anti-SARS-CoV-2 monoclonal antibodies (mAbs), previously isolated from convalescent donors infected with the Wuhan-Hu-1 strain, against the SARS-CoV-2 variants of concern (VOC) Alpha, Beta, Gamma, Delta and Omicron. By testing an array of mutated spike receptor binding domain (RBD) proteins, cell-expressed spike proteins from VOCs, and neutralization of SARS-CoV-2 VOCs as pseudoviuses, or as the authentic viruses in culture, we show that mAbs directed against the ACE2 binding site (ACE2bs) are far more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which kept their potency against all VOCs tested. At the second part of our study, we reveal the neutralization mechanisms at high molecular resolution of two anti-SARS-CoV-2 neutralizing mAbs by structural characterization. We solved the structures of the Delta-neutralizing ACE2bs mAb TAU-2303 with the SARS-CoV-2 spike trimer and RBD at 4.5 Å and 2.42 Å, respectively, revealing a similar mode of binding to that between the RBD and the ACE2 receptor. Furthermore, we provide five additional structures (at resolutions of 5.54 Å, 7.76 Å, 6.47 Å, 3.45 Å, and 7.32 Å) of a second antibody, non-ACE2bs mAb TAU-2212, complexed with the SARS-CoV-2 spike trimer. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunits. Our study provides new mechanistic insights about how antibodies neutralize SARS-CoV-2 and its emerging variants and provides insight about the likelihood of reinfections.
Compound interaction screen on a photoactivatable cellulose membrane (CISCM) identifies drug targets
Authors: Melder Teresa , Lindemann Peter , Welle Alexander , Trouillet Vanessa , Heißler Stefan , Nazaré Marc , Selbach Matthias
Published: April 2022

Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.
RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia
Authors: McMillan M , Gomez N , Bekier M , Li X , Miguez R , Tank EM , Barmada SJ
Published: April 2022

Methylation of RNA at the N6 position of adenosine (m6A) is one of the most common RNA modifications, impacting RNA stability as well as its transport and translation. Previous studies uncovered RNA destabilization in models of amyotrophic lateral sclerosis (ALS), in association with accumulation of the RNA-binding protein TDP43, which is itself mislocalized from the nucleus in >95% of those with ALS. Here, we show that TDP43 recognizes m6A-modified RNA, and that RNA methylation is critical for both TDP43 binding and autoregulation. We also observed extensive hypermethylation of coding and non-coding transcripts in ALS spinal cord, many of which overlap with methylated TDP43 target RNAs. Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via a single-cell CRISPR/Cas9 candidate-based screen in primary neurons. The most promising genetic modifier among these—the canonical m6A reader YTHDF2— accumulated within spinal motor neurons in ALS postmortem sections, and its knockdown prolonged the survival of human neurons carrying ALS-associated mutations. Collectively, these data show that m6A modifications modulate RNA binding by TDP43, and that m6A is pivotal for TDP43-related neurodegeneration in ALS.
Protein-Peptide Turnover Profiling reveals wiring of phosphorylation during protein maturation
Authors: Hammarén Henrik M. , Geissen Eva-Maria , Potel Clement , Beck Martin , Savitski Mikhail M.
Published: April 2022

Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods that rely on pulsed metabolic labeling are very popular to quantify turnover rates on a proteome-wide scale. Such data have often been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein’s lifetime—a fundamentally different metric. We use this framework to identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results open up an entirely new aspect in the study of PTMs, by tying them into the context of a protein’s lifetime.
The Bcvic1 and Bcvic2 vegetative incompatibility genes in Botrytis cinerea encode proteins with domain architectures involved in allorecognition in other filamentous fungi
Authors: Arshed Saadiah , Cox Murray P , Beever Ross E , Parkes Stephanie L , Pearson Michael N , Bowen Joanna Katharine , Templeton Matthew David
Published: April 2022

Vegetative incompatibility is a fungal allorecognition system characterised by the inability of genetically distinct conspecific fungal strains to form a viable heterokaryon, and is controlled by multiple polymorphic loci termed vic (vegetative incompatibility) or het (heterokaryon incompatibility). We have genetically identified and characterised the first vic locus in the economically important, plant-pathogenic, necrotrophic fungus Botrytis cinerea. A bulked segregant approach coupled with whole genome Illumina sequencing in near-isogenic lines of B. cinerea was used to map a 60-kb genomic region for a vic locus. Within that locus, we identified two adjacent, highly polymorphic open reading frames, Bcvic1 and Bcvic2, which encode predicted proteins that contain domain architectures implicated in vegetative incompatibility in other filamentous fungi. Bcvic1 encodes a predicted protein containing a putative serine esterase domain, a NACHT family of NTPases domain, and several Ankyrin repeats. Bcvic2 encodes a putative syntaxin protein containing a SNARE domain; such proteins typically function in vesicular transport. Deletion of Bcvic1 and Bcvic2 individually had no effect on vegetative incompatibility. However, deletion of the region containing both Bcvic1 and Bcvic2 resulted in mutant lines that were severely restricted in growth and showed loss of vegetative incompatibility. Complementation of these mutants by ectopic expression restored the growth and vegetative incompatibility phenotype, indicating that Bcvic1 and Bcvic2 are controlling vegetative incompatibility at this vic locus.
CD169+ macrophages orchestrate plasmacytoid dendritic cell arrest and retention for optimal priming in the bone marrow of malaria-infected mice
Authors: Fried Jamie , Paul Mahinder , Jing Zhixin , Fooksman David , Lauvau Grégoire
Published: April 2022

Plasmacytoid dendritic cells (pDC) are the most potent producer of type I interferon (IFN), but how pDC are primed in vivo is poorly defined. Using a mouse model of severe malaria, we have previously established that upon priming by CD169+ macrophages (MP), pDC initiate type I IFN-I secretion in the bone marrow (BM) of infected mice via cell-intrinsic TLR7 sensing and cell-extrinsic STING sensing. Herein we show that CD169+ MP and TLR7-sensing are both required for pDC arrest during priming, suggesting CD169+ MP are the source of TLR7 ligands. We establish that TLR7 sensing in pDC and chemotaxis are both required for pDC arrest and functional clustering with CD169+ MP in the BM. Lastly, we demonstrate that STING-sensing in CD169+ MP control pDC initiation of type I IFN production while also regulating pDC clustering and egress from the BM. Collectively, these results link pDC acquisition of type I IFN secreting capacity with changes in their motility, homing and interactions with CD169+ MP during infection. Thus, targeting this cellular interaction may help modulate type I IFN to improve outcomes of microbial infections and autoimmune diseases.
Estimating the number of breakthrough COVID-19 deaths in the United States
Authors: Smith Jinkinson
Published: April 2022

While there is compelling evidence of the effectiveness of COVID-19 vaccines, increasing attention has also been paid to the fact that, like all vaccines, they are not 100% effective. Therefore, some fully vaccinated people have developed “breakthrough” cases of COVID-19, and some of these individuals have died as a result. The purpose of this study was to estimate the number of fully vaccinated or “breakthrough” deaths from COVID-19 in the United States. Data was compiled from state COVID-19 dashboards and various other sources for as many states as possible. As of March 27, 2022 based on data from 46 U.S. states and the District of Columbia, an estimated minimum of 57,617 breakthrough COVID-19 deaths had occurred in the United States. Furthermore, based on this incomplete data, a total of 12.8% of all COVID-19 deaths in the included regions and time periods were among fully vaccinated individuals (whether boosted or not). Extrapolating this data to the entire United States implies that the minimum total number of such deaths as of March 27, 2022 was 79,917. Data from a MMWR article, if similarly extrapolated to the entire country, implies a significantly larger number of breakthrough deaths throughout the United States: 99,152.
A simple algorithm based on initial Ct values predicts the duration to SARS-CoV-2 negativity and allows more efficient test-to-release and return-to-work schedules
Authors: Anastasiou Olympia E. , Khanh Le-Trilling Vu Thuy , Trilling Mirko
Published: April 2022

Especially during global pandemics but also in the context of epidemic waves, the capacity for diagnostic qRT-PCRs rapidly becomes a limiting factor. Furthermore, excessive testing incurs high costs and can result in an overstrained work force in diagnostics departments. Obviously, people aim to shorten their isolation periods, hospitals need to discharge convalescent people, and re-employ staff members after infection. The aim of the study was to optimize retesting regimens for test-to-release from isolation and return-to-work applications. For this purpose, we investigated the association between Ct values at the first diagnosis of SARS-CoV-2 infection and the period until test negativity was reached, or at least until the Ct value exceeded 30, which is considered to indicate the transition to a non-infectious state. We included results from the testing of respiratory material samples for the detection of SARS-CoV-2 RNA, tested from 01 March 2020 to 31 January 2022.

Lower initial Ct values were associated with longer periods of SARS-CoV-2 RNA positivity. Starting with Ct values of <20, 20-25, 25-30, 30-35, and >35, it took median intervals of 20 (interval: 14-25), 16 (interval: 10-21), 12 (interval: 7-16), 7 (interval: 5-14), and 5 (interval: 2-7) days, respectively, until the person tested negative. Accordingly, a Ct threshold of 30 was surpassed after 13 (interval: 8-19), 9 (interval: 6-14), 7 (interval: 6-11), 6 (interval: 4-10), and 3 (interval: 1-6) days, respectively, in individuals with aforementioned start Ct values. Furthermore, the time to negativity was longer for adults versus children, wild-type SARS-CoV-2 variant versus other variants of concern, and in patients who were treated in the intensive care units.

Based on these data, we propose an adjusted retesting strategy according to the initial Ct value in order to optimize available PCR resources.
Dark accumulation of downstream glycolytic intermediates confers robust initiation of photosynthesis in cyanobacteria
Authors: Tanaka Kenya , Shirai Tomokazu , Vavricka Christopher J. , Matsuda Mami , Kondo Akihiko , Hasunuma Tomohisa
Published: April 2022

Photosynthesis must maintain stability and robustness throughout fluctuating natural environments. In cyanobacteria, dark-to-light transition leads to drastic metabolic changes from dark respiratory metabolism to CO2 fixation through the Calvin-Benson-Bassham (CBB) cycle using energy and redox equivalents provided by photosynthetic electron transfer. Previous studies showed that catabolic metabolism supports the smooth transition into CBB cycle metabolism. However, metabolic mechanisms for robust initiation of photosynthesis are poorly understood due to lack of dynamic metabolic characterizations of dark-to-light transitions. Here, we show rapid (on a time scale of seconds) dynamic changes in absolute metabolite concentrations and 13C tracer incorporation after strong or weak light irradiation in the cyanobacterium Synechocystis sp. PCC 6803. Integration of this data enables estimation of time-resolved nonstationary metabolic flux underlying CBB cycle activation. This dynamic metabolic analysis indicates that downstream glycolytic intermediates including phosphoglycerate and phosphoenolpyruvate accumulate under dark conditions as major substrates for initial CO2 fixation. Compared with wild-type Synechocystis, significant delays in the initiation of oxygen evolution are observed in 12 h dark preincubated mutants deficient in glycogen degradation or oxidative pentose phosphate pathway (Δzwf, Δgnd, and ΔglgP). Accordingly, the degree of delay in the oxygen evolution initiation is proportional to the accumulated pool size of the glycolytic intermediates. These observations indicate that the accumulation of glycolytic intermediates is essential for efficient metabolism switching under fluctuating light environments.
Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography
Authors: Faragó Tomáš , Gasilov Sergey , Emslie Iain , Zuber Marcus , Helfen Lukas , Vogelgesang Matthias , Baumbach Tilo
Published: April 2022

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.
A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities
Authors: Mobley B. R. , Schmidt K. E. , Chen J. P. J. , Kirian R. A.
Published: April 2022

Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand–maximize–compress (EMC) algorithm is highly effective at merging single-particle diffraction patterns with missing orientation values, but most implementations exhaustively sample the space of missing parameters and may become computationally prohibitive as the number of degrees of freedom extends beyond orientation angles. This paper describes how the EMC algorithm can be modified to employ Metropolis Monte Carlo sampling rather than grid sampling, which may be favorable for reconstruction problems with more than three missing parameters. Using simulated data, this variant is compared with the standard EMC algorithm.
(How) do advanced data and analyses enable HR analytics success? A neo-configurational analysis
Authors: Strohmeier Stefan , Collet Julian , Kabst Rüdiger
Published: April 2022

Purpose

Enabled by increased (“big”) data stocks and advanced (“machine learning”) analyses, the concept of human resource analytics (HRA) is expected to systematically improve decisions in human resource management (HRM). Since so far empirical evidence on this is, however, lacking, the authors' study examines which combinations of data and analyses are employed and which combinations deliver on the promise of improved decision quality.

Design/methodology/approach

Theoretically, the paper employs a neo-configurational approach for founding and conceptualizing HRA. Methodically, based on a sample of German organizations, two varieties (crisp set and multi-value) of qualitative comparative analysis (QCA) are employed to identify combinations of data and analyses sufficient and necessary for HRA success.

Findings

The authors' study identifies existing configurations of data and analyses in HRM and uncovers which of these configurations cause improved decision quality. By evidencing that and which combinations of data and analyses conjuncturally cause decision quality, the authors' study provides a first confirmation of HRA success.

Research limitations/implications

Major limitations refer to the cross-sectional and national sample and the usage of subjective measures. Major implications are the suitability of neo-configurational approaches for future research on HRA, while deeper conceptualizing and researching both the characteristics and outcomes of HRA constitutes a core future task.

Originality/value

The authors' paper employs an innovative theoretical-methodical approach to explain and analyze conditions that conjuncturally cause decision quality therewith offering much needed empirical evidence on HRA success.
Patanjali Ayurved Limited: role reversal in competitive advertising
Authors: Singh Harvinder , Aggarwal Rashmi Kumar , Rishi Bikramjit
Published: April 2022

Learning outcomes

Leraning outcomes are as follows: demonstrating how companies in the Indian market are using competitive advertising; giving participants an overview of the regulatory framework for advertising in India; highlighting the complexities arising out of the multiplicity of advertising regulations and institutions in India; appreciating the legal and ethical perspectives of advertisements and self-regulation; and evaluating the stance taken by both the parties in this particular case to develop multi-stakeholder perspective.

Case overview/Synopsis

A recent advertisement by international conglomerate Hindustan Unilever Limited was severely criticized for insulting Indian values by Baba Ramdev, promoter of India's largest Ayurvedic Company selling Indian indigenous and natural alternate medicinal products. It was in a complete reversal of the scenario between 2015 and 2018 when other Indian consumer goods companies complained against advertisements released by Patanjali. Indian fast moving consumer goods sector is witnessing a trend of competitive advertising in which companies are downplaying and criticizing the competitors. Though quite old, this trend caught momentum when Patanjali Ayurved Limited, a new player in the market, started advertising aggressively in 2015–2016. It resulted in many complaints by the aggrieved parties in the industry bodies and different courts of law in India. A part of the confusion comes from the diversity of advertising regulations across different Indian platforms and the absence of a clearly defined institutional framework for resolving such disputes. Consequently, most such disputes land up in the court of law in India. The case study builds an understanding of the legal framework within which companies are governed for brand promotions and creates a contextual ethical dilemma to drive the discourse on advertising through self-regulation in India.

Complexity academic level

This case is meant to benefit students pursuing a graduate or upper-level undergraduate degree in management or law/business law.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 8: Marketing.