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Host-pathogen interactions play a critical role in infectious diseases, and understanding the underlying mechanisms is vital for developing effective therapeutic strategies. The visualization and characterization of bacterial proteins within host cells is key to unraveling the dynamics of these interactions. Various protein labeling strategies have emerged as powerful tools for studying host-pathogen interactions, enabling the tracking, localization, and functional analysis of bacterial proteins in real-time. However, the labeling and localization of Salmonella secreted type III secretion system (T3SS) effectors in host cells poses technical challenges. Conventional methods disrupt effector stoichiometry and often result in non-specific staining. Bulky fluorescent protein fusions interfere with effector secretion, while other tagging systems such as 4Cys-FLaSH/Split-GFP suffer from low labeling specificity and a poor signal-to-noise ratio. Recent advances in state-of-the-art techniques have augmented the existing toolkit for monitoring the translocation and dynamics of bacterial effectors. This comprehensive review delves into the bacterial protein labeling strategies and their application in imaging host-pathogen interactions. Lastly, we explore the obstacles faced and potential pathways forward in the realm of protein labeling strategies for visualizing interactions between hosts and pathogens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Singh and Kenney.)

Purpose This study compares the dosimetry and dose sparing of cardiac substructures in single isocenter and dual isocenter RapidArc™ (Varian Medical Systems, Palo Alto, California, United States) radiotherapy planning for synchronous bilateral breast cancer. Methodology Six synchronous bilateral breast cancer (SBBC) patients received adjuvant radiation with the prescribed dose of 40.05 Gy in 15 fractions to the planning target volume (PTV) without local lymph nodal regions. PTVs and organs at risk (OARs), including both lungs, esophagus, spinal cord, heart, and left anterior descending coronary artery (LAD), both atria and ventricles were contoured. Single isocentric RapidArc (SIRA) and dual isocentric RapidArc (DIRA) plans were made for each patient and dosimetric differences between these two techniques were evaluated. Results There was no statistically significant difference in conformity index (CI) values between SIRA and DIRA plans, with 0.9681±0.01 and 0.9721±0.01 (p=0.505), respectively. SIRA planning showed superior homogeneity with homogeneity Index (HI) values of 0.0999±0.01 compared to DIRA planning with HI values of 0.1640±0.12 (p=0.230). The mean LAD dose of SIRA was valued higher than that of DIRA planning. Lower mean doses were obtained for both lungs in SIRA plans compared to DIRA plans. Meanwhile, doses to the right atrium, left atrium, left ventricle, right ventricle, and esophagus showed no statistical significance between these two techniques, except in the spinal cord. Conclusion Both SIRA and DIRA plans have satisfactory outcomes in sparing OARs. Meanwhile, SIRA techniques have less setup time and overall machine time., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Das et al.)

Purpose: Seroepidemiology and genomic surveillance are valuable tools to investigate infection transmission during a pandemic. North East (NE) India is a strategically important region being the gateway connecting the country with Southeast Asia. Here, we examined the spread of SARS-CoV-2 in NE India during the first and second waves of COVID-19 using serological and whole genome sequencing approaches., Methods: qRT-PCR analysis was performed on a selected population (n ​= ​16,295) from June 2020 to July 2021, and metadata was collected. Immunoassays were studied (n ​= ​2026) at three-time points (August 2020, February 2021, and June 2021) and in a cohort (n ​= ​35) for a year. SARS-CoV-2 whole genomes (n ​= ​914) were sequenced and analyzed with those obtained from the databases., Results: Test positivity rates (TPR) in the first and second waves were 6.34% and 6.64% in Assam, respectively, and a similar pattern was observed in other NE states. Seropositivity in the three time points was 10.63%, 40.3%, and 46.33%, respectively, and neutralizing antibody prevalence was 90.91%, 52.14%, and 69.30%, respectively. Persistence of pan-IgG-N SARS-CoV-2 antibody for over a year was observed among three subjects in the cohort group. Normal variants dominated the first wave, while B.1.617.2 and AY-sublineages dominated the second wave in the region. The prevalence of the variants co-related well with high TPR and seropositivity rate in the region and identified mostly among vaccinated individuals., Conclusion: The COVID-19 first wave in the region witnessed low transmission with the evolution of diverse variants. Seropositivity increased during the study period with over half of the individuals carrying neutralizing antibodies against SARS-CoV-2. High infection and seroprevalence in NE India during the second wave were associated with the dominant emergence of variants of concern., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Information flow among nodes in a complex network describes the overall cause-effect relationships among the nodes and provides a better understanding of the contributions of these nodes individually or collectively towards the underlying network dynamics. Variations in network topologies result in varying information flows among nodes. We integrate theories from information science with control network theory into a framework that enables us to quantify and control the information flows among the nodes in a complex network. The framework explicates the relationships between the network topology and the functional patterns, such as the information transfers in biological networks, information rerouting in sensor nodes, and influence patterns in social networks. We show that by designing or re-configuring the network topology, we can optimize the information transfer function between two chosen nodes. As a proof of concept, we apply our proposed methods in the context of brain networks, where we reconfigure neural circuits to optimize excitation levels among the excitatory neurons., (© 2023. The Author(s).)

Type three secretion systems (T3SSs) enable gram-negative bacteria to inject a battery of effector proteins directly into the cytosol of eukaryotic host cells. Upon entry, the injected effector proteins cooperatively modulate eukaryotic signaling pathways and reprogram cellular functions, enabling bacterial entry and survival. Monitoring and localizing these secreted effector proteins in the context of infections provides a footprint for defining the dynamic interface of host-pathogen interactions. However, labeling and imaging bacterial proteins in host cells without disrupting their structure/function is technically challenging. Constructing fluorescent fusion proteins does not resolve this problem, because the fusion proteins jam the secretory apparatus and thus are not secreted. To overcome these obstacles, we recently employed a method for site-specific fluorescent labeling of bacterial secreted effectors, as well as other difficult-to-label proteins, using genetic code expansion (GCE). This paper provides a complete step-by-step protocol to label Salmonella secreted effectors using GCE site-specifically, followed by directions for imaging the subcellular localization of secreted proteins in HeLa cells using direct stochastic optical reconstruction microscopy (dSTORM) Recent findings suggest that the incorporation of non-canonical amino acids (ncAAs) via GCE, followed by bio-orthogonal labeling with tetrazine-containing dyes, is a viable technique for selective labeling and visualization of bacterial secreted proteins and subsequent image analysis in the host. The goal of this article is to provide a straightforward and clear protocol that can be employed by investigators interested in conducting super-resolution imaging using GCE to study various biological processes in bacteria and viruses, as well as host-pathogen interactions.

Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex., (© 2022. The Author(s).)

Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the vaccine effectiveness. Asymptomatic breakthrough infections have been a major problem in assessing vaccine effectiveness in populations globally. Serological discrimination of vaccine response from infection has so far been limited to Spike protein vaccines since whole virion vaccines generate antibodies against all the viral proteins. Here, we show how a statistical and machine learning (ML) based approach can be used to discriminate between SARS-CoV-2 infection and immune response to an inactivated whole virion vaccine (BBV152, Covaxin). For this, we assessed serial data on antibodies against Spike and Nucleocapsid antigens, along with age, sex, number of doses taken, and days since last dose, for 1823 Covaxin recipients. An ensemble ML model, incorporating a consensus clustering approach alongside the support vector machine model, was built on 1063 samples where reliable qualifying data existed, and then applied to the entire dataset. Of 1448 self-reported negative subjects, our ensemble ML model classified 724 to be infected. For method validation, we determined the relative ability of a random subset of samples to neutralize Delta versus wild-type strain using a surrogate neutralization assay. We worked on the premise that antibodies generated by a whole virion vaccine would neutralize wild type more efficiently than delta strain. In 100 of 156 samples, where ML prediction differed from self-reported uninfected status, neutralization against Delta strain was more effective, indicating infection. We found 71.8% subjects predicted to be infected during the surge, which is concordant with the percentage of sequences classified as Delta (75.6%-80.2%) over the same period. Our approach will help in real-world vaccine effectiveness assessments where whole virion vaccines are commonly used., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

This paper deals with one of the key problems of e-healthcare which is the security. Patients are worried about the confidentiality of their electronic medical record (EMR) which could be used to expose their identities. It is high time to revisit the confidentiality and security issues of the existing telehealth system. Intruders can perform sniffing, spoofing, or phishing operations effortlessly during the online exchange of the EMR using a digital platform. The EMR must be transmitted anonymously with a high degree of hardness of encryption by protecting the authentication, confidentiality, and integrity criteria of the patient. These requirements recommend the security of the current system to be improved. In this paper, a neural synchronization-guided concatenation of header and secret shares with the ability to transmit the EMR with an end-to-end security protocol has been proposed. This proposed methodology breaks down the EMR into the n number of secret shares and transmits to the n number of recipients. The original EMR can be reconstructed after the amalgamation of a minimum k (threshold) number of secret shares. The novelty of the technique is that one share should come from a specific recipient to whom a special privilege is given to recreate the EMR among such a predefined number of shares. In the absence of this privileged share, the original EMR cannot be reconstructed. This proposed technique has passed various parametric tests. The results are compared with existing benchmark techniques. The results of the proposed technique have shown robust and effective potential., Competing Interests: Conflict of interestNo conflict of interest., (© King Fahd University of Petroleum & Minerals 2021.)

The antioxidant and growth stimulating properties of seeds of Achyranthes aspera were evaluated on UV-B irradiated Catla catla (catla) larvae. Catla larvae (initial weight: 1.2 ± 0.01 mg) were fed with four different diets--D1, D2 and D3 containing 0.1, 0.25 and 0.5% seeds of A. aspera and D4, control diet for 35 days. The larvae were then exposed to UV-B radiation (80 μW/cm2) on every alternate day for 20 days. Survival, growth, tissue glutamic oxaloacetic transminase (GOT), tissue glutamate pyruvate transminase (GPT), thiobarbituric acid reactive substances (TBARS) and nitric oxide synthase (NOS) were studied in larvae on day-21 of irradiation. Significantly (P < 0.05) higher survival and average weight were found in D3 diet fed fish compared to the other groups. Survival rate was 8-16% higher in seed enriched diet fed groups, compared to the control one. Higher levels of GOT and GPT found in control diet fed larvae showed the degree of tissue damage due to UV-B exposure. Significantly (P < 0.05) lower level of GPT in D3 indicated the UV-B protective effect of the seed of A. Aspera (earlier, the presence of ecdysterone, essential fatty acids and amino acids, polyphenolic compounds, steroids, etc. has been reported from seed). TBARS which indicated the level of tissue lipid peroxidation were significantly (P < 0.05) higher in control group, compared to the other feeding schemes. NOS level was significantly (P < 0.05) higher in D2 and D3, compared to the D1 and control groups. In conclusion, supplementation of A. aspera seed (0.5%) improved the physiological condition (in terms of reduce lipid oxidation and better immune system) and gave bioprotection to catla larvae challenged with UV-B stress.