Initial Step Research Articles

Diagnosing and Treating IgAN: Steroids, Budesonide, or Maybe Both?

IgA nephropathy (IgAN), the most common primary glomerulonephritis worldwide, is characterized by a mesangial IgA deposit and a variety of histological lesions, as described by the Oxford classification system. Despite the well-described "four-hit hypothesis", there are still plenty of less or undescribed mechanisms that participate in the disease pathogenesis, such as B-cell priming, which seems to be initiated by different antigens in the intestinal microbiota. Diagnosis of the disease is currently based on kidney biopsy findings, as the sensitivity and specificity of the many serum and urinary biomarkers described so far do not seem to have diagnostic accuracy. Therapeutic strategies consist of the initial step of non-immune medication, aiming to reduce both the intraglomerular pressure and proteinuria to below 0.5 g/day, followed by systemic corticosteroid administration in patients who remain at high risk for progressive chronic kidney disease despite the maximum non-immune treatment. The 6-month systemic corticosteroid treatment reduces proteinuria levels; however, the increased possibility of adverse events and increased relapse rate after treatment raises the need for a new therapeutic approach. Targeted-release budesonide is a therapeutic modality that aims to inhibit disease pathogenetic pathways at early stages; it has minor systemic absorption and proven beneficial effects on renal function and proteinuria. In the present systemic review, the benefits and adverse events of steroids and budesonide are described, and the possibility of combined treatment is questioned in selected cases with active histologic lesions.

Analyzing Variances in User Story Characteristics: A Comparative Study of Stakeholders with Diverse Domain and Technical Knowledge in Software Requirements Elicitation

Background: In Agile software development, an essential initial stage is eliciting software requirements. This process engages stakeholders to achieve comprehensive results. However, a common issue is the variance in domain and technical knowledge among stakeholders, potentially impacting the quality of software requirements elicitation. Objective: Understanding the characteristics of user stories produced by stakeholders becomes crucial, particularly considering the differences in domain and technical knowledge. This study aims to compare the characteristics of user stories generated by stakeholders with varying backgrounds in domain and technical expertise. Methods: The initial step involves categorizing respondents into distinct stakeholder groups. Three stakeholders are involved in this study, constituting a combination of those with high and low technical and domain knowledge. Subsequently, data collection of user stories is conducted across various case studies. Finally, the acquired user stories are analyzed for further insights. Results: The analysis reveals variations in user stories generated by the three stakeholder categories across the three case studies. Stakeholders with domain knowledge tend to focus on 'what' aspects with task elements and 'why' aspects with hard-goal elements. Meanwhile, technical knowledge crafts user stories with capability elements in the 'what' aspect. Utilizing the QUS framework, it is evident that technical knowledge consistently produces a higher number of high-quality user stories across all quality categories, Conclusion: The contribution offered by this study lies in determining the distinct characteristics of user stories produced by different types of stakeholders, focusing on disparities in domain and technical knowledge. The study highlights the comparison of various characteristics of user story elements, such as hard-goals, soft-goals, tasks, or capabilities, and assesses the quality of user stories based on the user story framework. Additionally, it endorse the importance of process innovation in shaping the requirements gathering process and subsequently influencing the quality of user stories. Keywords: User story, Agile Software Development, Requirements Elicitation, Stakeholder, Domain Knowledge, Process Innovation Background: In Agile software development, an essential initial stage is eliciting software requirements. This process engages stakeholders to achieve comprehensive results. However, a common issue is the variance in domain and technical knowledge among stakeholders, potentially impacting the quality of software requirements elicitation. Objective: Understanding the characteristics of user stories produced by stakeholders becomes crucial, particularly considering the differences in domain and technical knowledge. This study aims to compare the characteristics of user stories generated by stakeholders with varying backgrounds in domain and technical expertise. Methods: The initial step involves categorizing respondents into distinct stakeholder groups. Three stakeholders are involved in this study, constituting a combination of those with high and low technical and domain knowledge. Subsequently, data collection of user stories is conducted across various case studies. Finally, the acquired user stories are analyzed for further insights. Results: The analysis reveals variations in user stories generated by the three stakeholder categories across the three case studies. Stakeholders with domain knowledge tend to focus on 'what' aspects with task elements and 'why' aspects with hard-goal elements. Meanwhile, technical knowledge crafts user stories with capability elements in the 'what' aspect. Utilizing the QUS framework, it is evident that technical knowledge consistently produces a higher number of high-quality user stories across all quality categories, Conclusion: The contribution offered by this study lies in determining the distinct characteristics of user stories produced by different types of stakeholders, focusing on disparities in domain and technical knowledge. The study highlights the comparison of various characteristics of user story elements, such as hard-goals, soft-goals, tasks, or capabilities, and assesses the quality of user stories based on the user story framework. Additionally, it endorse the importance of process innovation in shaping the requirements gathering process and subsequently influencing the quality of user stories. Keywords: User story, Agile Software Development, Requirements Elicitation, Stakeholder, Domain Knowledge, Process Innovation

Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view.

Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.

Professional skateboarding trousers design: according to the three-dimensional kinematic analysis for varied skateboarding manoeuvres

The popularity of skateboarding has caused an expansion of enthusiasts worldwide. Moreover, skateboarding is becoming increasingly professional at an international level. Professional skateboarding trousers are regarded as critical equipment and their design research should not be overlooked. This research aims to use motion capture to measure the angular changes characteristics of critical lower limb joints in skaters during sports activities, measure the length of the knee joint during actions, and establish a formula that describes the change characteristics between the angle and the length. The formula would allow for a data reference when designing the elasticity at the knee joints of skateboarding trousers. Thus, the initial step in this research methodology was to use a Vicon motion capture system to test and analyse the kinematic characteristics of seven skaters in the squat, jump, ollie, pop shove it, heel flip, kickflip, and 180° ollie. Based on the kinematic characteristics, the dynamic movements were broken down into static postures at 0°, 45°, 90°, 112.5°, and 135°. The body surface drawing method was then employed to measure changes in the knee joint body surface dimensions of the subjects. Next, the experimental data were analysed to explore the relationship between angle and length changes. Finally, the design was developed based on the data. Analysis and processing of the experimental data yielded the following conclusions: (1) The most significant knee joint change characteristics during skateboarding was the angle change observed during an ollie. (2) Knee joint skin stretch deformation is most evident in the anterior mid-leg line y2. (3) The relationship between kinematics and the structural design of skateboarding trousers was derived from the experimental data. Specifically, the equation for the relationship between angle change and length change is given by y2 = 0.0442x + 23.906. (4) The results show that the extreme range of skin stretching in the anterior midline is between –0.7 and 6.3 cm. Therefore, the loose design of the knee part of professional skateboarding trousers should not exceed 6.3 cm. This research approach can offer an effective design solution for professional skateboard trousers and can also be applied to other types of trousers.

Principle and practice of hydraulic softening top-cutting and pressure relief technology in weakly cemented strata

Extremely thick and hard roofs are difficult to break in the mining of a working face, and the large area of the suspended roof easily induces a strong ground pressure or dynamic impact disasters. The roof control of a coal mining face in a mine in western China was taken as a case study. The mineral composition, microstructure, and hydrophysical properties of the hard roof overlying the coal seam were analyzed. The characteristics of the weak-cementation strata that are prone to mud and collapse when encountering water were targeted to investigate the hydraulic softening roof-cutting and pressure relief technology. It was found that the clay mineral composition in the roof plate accounts for 60.6%. After 24 h of natural immersion, the rock strength decreased by approximately 10.3%–49%, and further immersion caused disintegration. By arranging high and low double-row water injection softening drilling holes in the cutting hole and roadway of the working face, the strength of roof rock strata in the target area was reduced, and the initial weighting step distance and weighting strength of the working face were reduced. The hydraulic softening roof-cutting pressure relief technology effectively regulated the weighting step distance of the hard roof and the peak weighting of the working face.

The Single Toxin Origin of Alzheimer's Disease and Other Neurodegenerative Disorders Enables Targeted Approach to Treatment and Prevention.

New data suggest that the aggregation of misfolded native proteins initiates and drives the pathogenic cascade that leads to Alzheimer's disease (AD) and other age-related neurodegenerative disorders. We propose a unifying single toxin theory of brain neurodegeneration that identifies new targets and approaches to the development of disease-modifying treatments. An extensive body of genetic evidence suggests soluble aggregates of beta-amyloid (Aβ) as the primary neurotoxin in the pathogenesis of AD. New insights from fluid biomarkers, imaging, and clinical studies provide further evidence for the decisive impact of toxic Aβ species in the initiation and progression of AD. Understanding the distinct roles of soluble and insoluble amyloid aggregates on AD pathogenesis has been the key missing piece of the Alzheimer's puzzle. Data from clinical trials with anti-amyloid agents and recent advances in the diagnosis of AD demonstrate that the driving insult in biologically defined AD is the neurotoxicity of soluble Aβ aggregates, called oligomers and protofibrils, rather than the relatively inert insoluble mature fibrils and amyloid plaques. Amyloid oligomers appear to be the primary factor causing the synaptic impairment, neuronal stress, spreading of tau pathology, and eventual cell death that lead to the clinical syndrome of AD dementia. All other biochemical effects and neurodegenerative changes in the brain that are observed in AD are a response to or a downstream effect of this initial toxic insult by oligomers. Other neurodegenerative disorders follow a similar pattern of pathogenesis, in which normal brain proteins with important biological functions become trapped in the aging brain due to impaired clearance and then misfold and aggregate into neurotoxic species that exhibit prion-like behavior. These aggregates then spread through the brain and cause disease-specific neurodegeneration. Targeting the inhibition of this initial step in neurodegeneration by blocking the misfolding and aggregation of healthy proteins has the potential to slow or arrest disease progression, and if treatment is administered early in the course of AD and other neurodegenerative disorders, it may delay or prevent the onset of clinical symptoms.

Arctigenin from Arctium lappa L. inhibits chikungunya virus by affecting its entry and replication

BackgroundDengue and chikungunya, caused by dengue virus (DENV) and chikungunya virus (CHIKV) respectively, are the most common arthropod-borne viral diseases worldwide, for which there are no FDA-approved antivirals or effective vaccines. Arctigenin, a phenylpropanoid lignan from the seeds of Arctium lappa L. is known for its anti-inflammatory, anti-cancer, antibacterial, and immunomodulatory properties. Arctigenin's antimicrobial and immunomodulatory capabilities make it a promising candidate for investigating its potential as an anti-DENV and anti-CHIKV agent. PurposeThe aim of the study was to explore the anti-DENV and anti-CHIKV effects of arctigenin and identify the possible mechanisms of action. MethodsThe anti-DENV or anti-CHIKV effects of arctigenin was assessed using various in vitro and in silico approaches. Vero CCL-81 cells were infected with DENV or CHIKV and treated with arctigenin at different concentrations, temperature, and time points to ascertain the effect of the compound on virus entry or replication. In silico molecular docking was performed to identify the interactions of the compound with viral proteins. ResultsArctigenin had no effects on DENV. Various time- and temperature-dependent assays revealed that arctigenin significantly reduced CHIKV RNA copy number and infectious virus particles and affected viral entry. Entry bypass assay revealed that arctigenin inhibited the initial steps of viral replication. In silico docking results revealed the high binding affinity of the compound with the E1 protein and the nsp3 macrodomain of CHIKV. ConclusionThis study demonstrates the in-vitro anti-CHIKV potential of arctigenin and suggests that the compound might affect CHIKV entry and replication. Further preclinical and clinical studies are needed to identify its safety and efficacy as an anti-CHIKV drug.

Observation of Large, Charged Droplet Signatures within the High-Vacuum Region of a Commercial Electrospray TOF-MS.

Electrospray ionization (ESI) is one of the most prominent atmospheric pressure ionization techniques in modern mass spectrometry. It generates charged droplets from an analyte-containing solution as an initial step in the ionization process. Textbooks and the majority of the articles assume the entire droplet evaporation and release of bare analyte ions within the ionization chamber. However, non-mass-spectrometry-related literature and recent reports demonstrate droplet observation in regions of the vacuum systems of a variety of mass spectrometers. In this work, we report on the observation of large droplet fragments within the orthogonal acceleration stage of a Bruker micrOTOF by connecting an oscilloscope to an auxiliary ion current detector downstream of the acceleration stage. Moreover, we detected fragment debris even with the MCP TOF detector by evaluating individual TOF spectra. Droplet fragments appear as pronounced and intensive pulses of the ion current. This observation is clearly connected to ESI, as other atmospheric pressure ionization methods do not show this behavior. The recorded droplet signatures show clear dependencies on the ion source and transfer stage parameters. The existence of large and highly charged droplets may adversely affect or at least impact the analytical performance of the instrument due to space charge or complex heterogeneous chemical reactions. Furthermore, the penetration of large charged aggregates into the vacuum system explains the reported surface contamination after multipole stages. This contamination of critical components leads to substantially higher maintenance efforts.

Edman Degradation Reveals Unequivocal Analysis of the Disulfide Connectivity in Peptides and Proteins.

Disulfide bridges in peptides and proteins play an essential role in maintaining their conformation, structural integrity, and consequently function. Despite ongoing efforts, it is still not possible to detect disulfide bonds and the connectivity of multiply bridged peptides directly through a simple and sufficiently validated protein sequencing or peptide mapping method. Partial or complete reduction and chemical cysteine modification are required as initial steps, followed by the application of a proper detection method. Edman degradation (ED) has been used for primary sequence determination but is largely neglected since the establishment of mass spectrometry (MS)-based protein sequencing. Here, we evaluated and thoroughly characterized the phenyl thiohydantoin (PTH) cysteine derivatives PTH-S-methyl cysteine and PTH-S-carbamidomethyl cysteine as bioanalytical standards for cysteine detection and quantification as well as for the elucidation of the disulfide connectivity in peptides by ED. Validation of the established derivatives was performed according to the guidelines of the International Committee of Harmonization on bioanalytical method validation, and their analytical properties were confirmed as reference standards. A series of model peptides was sequenced to test the usability of the PTH-Cys-derivatives as standards, whereas the native disulfide-bonded peptides CCAP-vil, μ-conotoxin KIIIA, and human insulin were used as case studies to determine their disulfide bond connectivity completely independent of MS analysis.

Addressing the Environmental Concerns: Statistical Approach for Mg2+ and Mn2+ Mitigation in Water System Sustainability in Indonesia

This research aimed to determine the most effective adsorbent for reducing Mg2+ and Mn2+ levels in residential water near the oil and gas industry in the Tambun area, Bekasi, Indonesia. Bentonite was tested with varying temperature conditions. The study further compared activated charcoal and bentonite as potential adsorbents, examining their efficacy under different contact times (10, 20, and 30 minutes). Thus, sampling followed the SNI 6989.57:2008 method for surface water sampling, with bentonite conditioning and activation as initial steps. Next, the adsorption experiments utilized a separating funnel, varying the contact time between adsorbent and sample. Hence, the filtrates were analyzed quantitatively for Mn2+ using atomic absorption spectroscopy and for Mg2+ through complexometric titration.

Study on CO2 and CH4 Competitive Adsorption in Shale Organic and Clay Porous Media from Molecular- to Pore-Scale Simulation

Summary The elucidation of the competitive adsorption behaviors between CO2 and CH4 holds great importance in the context of improving natural gas recovery in shale reservoirs. Shale rock, as a complex porous medium, exhibits a highly interconnected multiscale pore network with pore size spanning from several to tens of nanometers. Nevertheless, accurately capturing the adsorption effects and studying the CO2/CH4 competitive adsorption within a large-scale, realistic, 3D nanoporous matrix remains a significant challenge. In this paper, we proposed a novel lattice Boltzmann method (LBM) coupled molecular simulation to investigate CO2/CH4 competitive adsorption in 3D shale nanoporous media. The initial step involves conducting Grand Canonical Monte Carlo (GCMC) simulations to simulate the competitive adsorption behaviors of CO2 and CH4 in kerogen and illite slit pores, with the aim of obtaining the atomic density distribution. Subsequently, a Shan-Chen-based lattice Boltzmann (LB) simulation is used under identical conditions. By coupling the molecular simulation results, the fluid-solid interaction parameters are determined. Finally, LB simulations are performed in designed 3D porous media, utilizing the fluid-solid interaction parameters. The effects of mineral type, CO2 concentration, and pore structure on competitive adsorption behaviors are discussed carefully. Our research offers significant contributions to the improvement of gas recovery and carbon geological sequestration through the examination of CO2/CH4 competitive adsorption in nanoporous media. Additionally, it serves as a link between molecular and pore-scale phenomena by leveraging the benefits of both molecular simulations and pore-scale simulations.

Perspectives on the role of nutrition in influencing academy soccer player development and performance: A qualitative case study of key stakeholders from an English category one soccer academy

ABSTRACT This study aimed to explore player and stakeholder perceptions of the role of nutrition in influencing the development of male academy soccer players. Semi-structured interviews (28 ± 13 mins in length) were conducted with 31 participants from an English category one academy, including players (Youth Development Phase, YDP: n = 6; Professional Development Phase, PDP: n = 4), parents/guardians (n = 10), coaches (n = 3), sport scientists (n = 3), physiotherapists (n = 3), and catering (n = 2). Via reflexive thematic analysis, data demonstrate an apparent lack of understanding and awareness on the role of nutrition in influencing player development, especially in relation to growth, maturation and reducing injury risk. Players highlighted the influence of their parents on their dietary behaviours, whilst parents also called for education to better support their sons. Notably, players and stakeholders perceived that the daily schedule of an academy soccer player presents as “too busy to eat”, especially in relation to before school, and before and after training. The results demonstrate the necessity for the co-creation of player and stakeholder specific nutrition education programmes as an initial step towards positively impacting the nutrition culture associated with the academy soccer environment.

Maintaining the gap: women’s early career experiences of entry into the UK graduate labour market

ABSTRACT Gender inequality in the workplace remains a persistent issue that impacts upon women from their first point of entry into the labour market. In this paper, we explore the experiences, of 20 women in the UK as they take their initial steps onto the career ladder upon graduation. Adopting an interpretive methodology that uses a Bourdieusian framework based on habitus, capital, and field, we highlight that women continue to face structural and individual barriers that influence, and in many cases limit, available career opportunities. By intersecting gender with social class and ethnicity, intra-gender differences are identified that demonstrate the deep-seated nature of disadvantage faced by working class and ethnic minority female graduates in securing employment in comparison to their white, middle-class peers. We conclude by recommending that careers support and guidance should be introduced earlier in the education system to raise aspirations and challenge the perpetuation of gender inequality.

Chemo-enzymatic synthesis of tetrasaccharide linker peptides to study the divergent step in glycosaminoglycan biosynthesis.

Glycosaminoglycans are extended linear polysaccharides present on cell surfaces and within the extracellular matrix that play crucial roles in various biological processes. Two prominent glycosaminoglycans, heparan sulfate and chondroitin sulfate, are covalently linked to proteoglycan core proteins through a common tetrasaccharide linker comprising glucuronic acid, galactose, galactose, and xylose moities. This tetrasaccharide linker is meticulously assembled step by step by four Golgi-localized glycosyltransferases. The addition of the fifth sugar moiety, either N-acetylglucosamine or N-acetylgalactosamine, initiates further chain elongation, resulting in the formation of heparan sulfate or chondroitin sulfate, respectively. Despite the fundamental significance of this step in glycosaminoglycan biosynthesis, its regulatory mechanisms have remained elusive. In this study, we detail the expression and purification of the four linker-synthesizing glycosyltransferases and their utilization in the production of fluorescent peptides carrying the native tetrasaccharide linker. We generated five tetrasaccharide peptides, mimicking the core proteins of either heparan sulfate or chondroitin sulfate proteoglycans. These peptides were readily accepted as substrates by the EXTL3 enzyme, which adds an N-acetylglucosamine moiety, thereby initiating heparan sulfate biosynthesis. Importantly, EXTL3 showed a preference towards peptides mimicking the core proteins of heparan sulfate proteoglycans over the ones from chondroitin sulfate proteoglycans. This suggests that EXTL3 could play a role in the decision-making step during glycosaminoglycan biosynthesis. The innovative strategy for chemo-enzymatic synthesis of fluorescent-labeled linker-peptides promises to be instrumental in advancing future investigations into the initial steps and the divergent step of glycosaminoglycan biosynthesis.

Intrapreneurs, high performers, or hybrid stars? How individual entrepreneurial orientation affects employee performance

Recently, scholars have extended the concept of entrepreneurial orientation to the individual level. Yet, how individual entrepreneurial orientation (IEO) contributes to employee performance is not well understood. Building on role theory, we develop a novel typology of employee performance that distinguishes between employee behavior aimed at achieving in-role performance and employee engagement in intrapreneurial activities. To test how IEO affects the different performance prototypes of this typology, we collected survey and archival data on IEO, entrepreneurial self-efficacy (ESE), employee in-role performance, and engagement in intrapreneurship in a Dutch subsidiary of an international consultancy firm. Our results show that IEO is positively associated with in-role performance and intrapreneurship. ESE is also positively associated with in-role performance and intrapreneurship, albeit indirectly via IEO. These results mark an initial step in unraveling the impact of IEO on employee and firm performance, as well as why different outcomes occur as a result of IEO.

Bi-stage feature selection for crop mapping using grey wolf metaheuristic optimization

Machine learning classifiers have been widely used for crop mapping; however, employing numerous features can reduce classifier accuracy. Feature selection is a widely recognized technique that addresses the issue of high dimensionality by choosing the most relevant subset of features with the highest degree of relevance and practicality. Therefore, the optimal combination of feature selection methods and classifiers for high-precision crop mapping remains an open problem. In this study, we introduce a novel hybrid feature selection approach to obtain the optimal subset of features for effective crop mapping. Initially, spectro-temporal remote sensing features from the dataset were ranked using two distinct feature selection techniques: Mutual Information (MI) and ReliefF filter. The most relevant features from each filter-based approach were combined into a union subset. Subsequently, the Gray Wolf Optimization (GWO), a metaheuristic optimization technique, was applied to enhance the feature set generated in the initial step. In the final stage, a random forest classifier leveraged the optimized feature subset for accurate crop type prediction. The effectiveness of the proposed approach was evaluated in Behiera governorate, Egypt. Comparative analysis against existing crop mapping methods demonstrated the superior performance of the proposed approach, achieving an accuracy rate of 82%. Furthermore, this approach showcased a significant reduction in the feature count, streamlining the set from 308 down to only 26 features.

A dataset of genetic diversity studies in the China Seas

Genetic diversity, a fundamental aspect of biodiversity, greatly influences the ecological and evolutionary characteristics of populations and species. Compiling genetic data is crucial as the initial step in comprehending and applying genetic resources; however, regional collating work is still insufficient, especially in marine ecosystems. Here, by conducting a thorough literature search and quality-control procedures, we provide a dataset of genetic diversity studies on marine species in the China Seas. The final dataset comprised a total of 746 studies (encompassing 840 data sets and 3658 populations) across 343 species from 1998 to 2022. For each data set, information including publication year, publication language, studied species, belonged taxonomic group, applied molecular markers, and sampling strategies (number of populations, total number of individuals, etc.) was collated to analyse the scope, strengths, and omissions of these works. This dataset offers a comprehensive overview of genetic diversity studies in the China Seas, which may help to adjust future research focuses, promote conservation and macrogenetics studies in this region, and also facilitate regional cooperation.

The Diverse Nature of the Molecular Interactions That Govern the COV-2 Variants' Cell Receptor Affinity Ranking and Its Experimental Variability.

A critical determinant of infectivity and virulence of the most infectious and or lethal variants of concern (VOCs): Wild Type, Delta and Omicron is related to the binding interactions between the receptor-binding domain of the spike and its host receptor, the initial step in cell infection. It is of the utmost importance to understand how mutations of a viral strain, especially those that are in the viral spike, affect the resulting infectivity of the emerging VOC, knowledge that could help us understand the variant virulence and inform the therapies applied or the vaccines developed. For this sake, we have applied a battery of computational protocols of increasing complexity to the calculation of the spike binding affinity for three variants of concern to the ACE2 cell receptor. The results clearly illustrate that the attachment of the spikes of the Delta and Omicron variants to the receptor originates through different molecular interaction mechanisms. All our protocols unanimously predict that the Delta variant has the highest receptor-binding affinity, while the Omicron variant displays a substantial variability in the binding affinity of the spike that relates to the structural plasticity of the Omicron spike-receptor complex. We suggest that the latter result could explain (at least in part) the variability of the in vitro binding results for this VOC and has led us to suggest a reason for the lower virulence of the Omicron variant as compared to earlier strains. Several hypotheses have been developed around this subject.

Deficiency of polypeptide N-acetylgalactosamine transferase 9 contributes to a risk for Parkinson's disease via mitochondrial dysfunctions

Polypeptide N-acetylgalactosamine transferase 9 (GALNT9) catalyzes the initial step of mucin-type O-glycosylation via linking N-acetylgalactosamine (GalNAc) to serine/threonine in a protein. To unravel the association of GALNT9 with Parkinson's disease (PD), a progressive neurodegenerative disorder, GALNT9 levels were evaluated in the patients with PD and mice treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, and statistically analyzed based on the GEO datasets of GSE114918 and GSE216281. Glycoproteins with exposing GalNAc were purified using lectin affinity chromatography and identified by LC-MS/MS. The influence of GALNT9 on cells was evaluated via introducing a GALNT9-specific siRNA into SH-SY5Y cells. Consequently, GALNT9 deficiency was found to occur under PD conditions. GALNT9 silencing contributed to a causative factor in PD pathogenesis via reducing the levels of intracellular dopamine, tyrosine hydroxylase and soluble α-synuclein, and promoting α-synuclein aggregates. MS identification revealed 14 glycoproteins. 5 glycoproteins, including ACO2, ATP5B, CKB, CKMT1A, ALDOC, were associated with energy metabolism. GALNT9 silencing resulted in mitochondrial dysfunctions via increasing ROS accumulation, mitochondrial membrane depolarization, mPTPs opening, Ca2+ releasing and activation of the CytC-related apoptotic pathway. The dysfunctional mitochondria then triggered mitophagy, possibly intermediated by adenine nucleotide translocase 1. Our study suggests that GALNT9 is potentially developed into an auxiliary diagnostic index and therapeutic target of PD.

NINJ1 induces plasma membrane rupture and release of damage-associated molecular pattern molecules during ferroptosis.

Ferroptosis is a regulated form of necrotic cell death caused by iron-dependent accumulation of oxidized phospholipids in cellular membranes, culminating in plasma membrane rupture (PMR) and cell lysis. PMR is also a hallmark of other types of programmed necrosis, such as pyroptosis and necroptosis, where it is initiated by dedicated pore-forming cell death-executing factors. However, whether ferroptosis-associated PMR is also actively executed by proteins or driven by osmotic pressure remains unknown. Here, we investigate a potential ferroptosis role of ninjurin-1 (NINJ1), a recently identified executor of pyroptosis-associated PMR. We report that NINJ1 oligomerizes during ferroptosis, and that Ninj1-deficiency protects macrophages and fibroblasts from ferroptosis-associated PMR. Mechanistically, we find that NINJ1 is dispensable for the initial steps of ferroptosis, such as lipid peroxidation, channel-mediated calcium influx, and cell swelling. In contrast, NINJ1 is required for early loss of plasma membrane integrity, which precedes complete PMR. Furthermore, NINJ1 mediates the release of cytosolic proteins and danger-associated molecular pattern (DAMP) molecules from ferroptotic cells, suggesting that targeting NINJ1 could be a therapeutic option to reduce ferroptosis-associated inflammation.