Sesame Genomic Web Resource (SesameGWR): a well-annotated data resource for transcriptomic signatures of abiotic and biotic stress responses in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is a globally cultivated oilseed crop renowned for its historical significance and widespread growth in tropical and subtropical regions. With notable nutritional and medicinal attributes, sesame has shown promising effects in combating malnutrition cancer, diabetes, and other diseases like cardiovascular problems. However, sesame production faces significant challenges from environmental threats such as charcoal rot, drought, salinity, and waterlogging stress, resulting in economic losses for farmers. The scarcity of information on stress-resistance genes and pathways exacerbates these challenges. Despite its immense importance, there is currently no platform available to provide comprehensive information on sesame, which significantly hinders the mining of various stress-associated genes and the molecular breeding of sesame. To address this gap, here a free, web-accessible, and user-friendly genomic web resource (SesameGWR, http://backlin.cabgrid.res.in/sesameGWR/) has been developed This platform provides key insights into differentially expressed genes, transcription factors, miRNAs, and molecular markers like simple sequence repeats, single nucleotide polymorphisms, and insertions and deletions associated with both biotic and abiotic stresses.. The functional genomics information and annotations embedded in this web resource were predicted through RNA-seq data analysis. Considering the impact of climate change and the nutritional and medicinal importance of sesame, this study is of utmost importance in understanding stress responses. SesameGWR will serve as a valuable tool for developing climate-resilient sesame varieties, thereby enhancing the productivity of this ancient oilseed crop.

Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat.

In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1-57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.

Development, characterization, and evaluation of Zn-SA-chitosan bionanoconjugates on wheat seed, experiencing chilling stress during germination.

This study aimed to develop and characterize the chitosan bionanoconjugates (BNCs) loaded with zinc (Zn) and salicylic acid (SA) and test their efficacy on wheat seed exposed to chilling stress. BNCs developed were spherical (480 ± 6.0 nm), porous, and positively charged (+25.2 ± 2.4 mV) with regulated nutrient release properties. They possessed complexation efficiency of 78.4 and 58.9 % for Zn, and SA respectively. BET analysis further confirmed a surface area of 12.04 m2/g. Release kinetics substantiated the release rates of Zn and SA, as 0.579 and 0.559 % per hour, along with a half-life of 119.7 and 124.0 h, respectively. BNCs positively affected the germination potential of wheat seeds under chilling stress as observed by significantly (p < 0.05) reduced mean emergence time (18 %), and increased germination rate (22 %), compared to the control. Higher activities of reserve mobilizing enzymes (α-amylase- 6.5 folds, protease -10.2 folds) as well as faster reserve mobilization of starch (64.4 %) and protein (63.5 %) molecules were also observed. The application further led to increased levels of the antioxidant enzymes (SOD and CAT) and reduced oxidative damage (MDA and H2O2). Thus, it is inferred that the developed BNCs could help substantially improve the germination and reserve mobilization potential, thereby increasing the crop yield.

Analysis of Hybrid Feature Optimization Techniques Based on the Classification Accuracy of Brain Tumor Regions Using Machine Learning and Further Evaluation Based on the Institute Test Data.

Aim: The goal of this study was to get optimal brain tumor features from magnetic resonance imaging (MRI) images and classify them based on the three groups of the tumor region: Peritumoral edema, enhancing-core, and necrotic tumor core, using machine learning classification models. Materials and Methods: This study's dataset was obtained from the multimodal brain tumor segmentation challenge. A total of 599 brain MRI studies were employed, all in neuroimaging informatics technology initiative format. The dataset was divided into training, validation, and testing subsets online test dataset (OTD). The dataset includes four types of MRI series, which were combined together and processed for intensity normalization using contrast limited adaptive histogram equalization methodology. To extract radiomics features, a python-based library called pyRadiomics was employed. Particle-swarm optimization (PSO) with varying inertia weights was used for feature optimization. Inertia weight with a linearly decreasing strategy (W1), inertia weight with a nonlinear coefficient decreasing strategy (W2), and inertia weight with a logarithmic strategy (W3) were different strategies used to vary the inertia weight for feature optimization in PSO. These selected features were further optimized using the principal component analysis (PCA) method to further reducing the dimensionality and removing the noise and improve the performance and efficiency of subsequent algorithms. Support vector machine (SVM), light gradient boosting (LGB), and extreme gradient boosting (XGB) machine learning classification algorithms were utilized for the classification of images into different tumor regions using optimized features. The proposed method was also tested on institute test data (ITD) for a total of 30 patient images. Results: For OTD test dataset, the classification accuracy of SVM was 0.989, for the LGB model (LGBM) was 0.992, and for the XGB model (XGBM) was 0.994, using the varying inertia weight-PSO optimization method and the classification accuracy of SVM was 0.996 for the LGBM was 0.998, and for the XGBM was 0.994, using PSO and PCA-a hybrid optimization technique. For ITD test dataset, the classification accuracy of SVM was 0.994 for the LGBM was 0.993, and for the XGBM was 0.997, using the hybrid optimization technique. Conclusion: The results suggest that the proposed method can be used to classify a brain tumor as used in this study to classify the tumor region into three groups: Peritumoral edema, enhancing-core, and necrotic tumor core. This was done by extracting the different features of the tumor, such as its shape, grey level, gray-level co-occurrence matrix, etc., and then choosing the best features using hybrid optimal feature selection techniques. This was done without much human expertise and in much less time than it would take a person.

Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain.

INTRODUCTION: Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DRC). METHODOLOGY: A cross-sectional, observational, cohort study was performed among patients of all ages admitted to the Kamituga Hospital with Mpox infection symptoms between late September 2023 and late January 2024. DNA was isolated from Mpox swabbed lesions and sequenced followed by phylogenetic analysis, genome annotation, and mutational profiling. RESULTS: We describe an ongoing Clade I Mpox outbreak in the city of Kamituga, South Kivu Province, Democratic Republic of Congo. Whole-genome sequencing of the viral RNA samples revealed, on average, 201.5 snps, 28 insertions, 81 deletions, 2 indels, 312.5 total variants, 158.3 amino acid changes, 81.66 intergenic variants, 72.16 synonymous mutations, 106 missense variants, 41.16 frameshift variants, and 3.33 inframe deletions across six samples. By assigning mutations at the proteome level for Kamituga MPXV sequences, we observed that seven proteins, namely, C9L (OPG047), I4L (OPG080), L6R (OPG105), A17L (OPG143), A25R (OPG151), A28L (OPG153), and B21R (OPG210) have emerged as hot spot mutations based on the consensuses inframe deletions, frameshift variants, synonymous variants, and amino acids substitutions. Based on the outcome of the annotation, we found a deletion of the D14L (OPG032) gene in all six samples. Following phylogenetic analysis and whole genome assembly, we determined that this cluster of Mpox infections is genetically distinct from previously reported Clade I outbreaks, and thus propose that the Kamituga Mpox outbreak represents a novel subgroup (subgroup VI) of Clade I MPXV. CONCLUSIONS: Here we report the complete viral genome for the ongoing Clade I Mpox Kamituga outbreak for the first time. This outbreak presents a distinct mutational profile from previously sequenced Clade I MPXV oubtreaks, suggesting that this cluster of infections is a novel subgroup (we term this subgroup VI). These findings underscore the need for ongoing vigilance and continued sequencing of novel Mpox threats in endemic regions.

Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility.

Exitrons are exonic introns. This subclass of intron retention alternative splicing does not contain a Pre-Terminating stop Codon. Therefore, when retained, they are always a part of a protein. Intron retention is a frequent phenomenon predominantly found in plants, which results in either the degradation of the transcripts or can serve as a stable intermediate to be processed upon induction by specific signals or the cell status. Interestingly, exitrons have coding ability and may confer additional attributes to the proteins that retain them. Therefore, exitron-containing and exitron-spliced isoforms will be a driving force for creating protein diversity in the proteome of an organism. This review establishes a basic understanding of exitron, discussing its genesis, key features, identification methods and functions. We also try to depict its other potential roles. The present review also aims to provide a fundamental background to those who found such exitronic sequences in their gene(s) and to speculate the future course of studies.

Fluoride export is required for the competitive fitness of pathogenic microorganisms in dental biofilm models.

Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas oral commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with the genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of oral commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time. Biochemical purification of the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms and that S. mutans is especially susceptible to fluoride toxicity. IMPORTANCE: Dental caries is a globally prevalent condition that occurs when pathogenic species, including Streptococcus mutans and Candida albicans, outcompete beneficial species, such as Streptococcus gordonii, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species S. mutans and C. albicans to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpaste and mouth rinses. This is a novel strategy to treat dental caries.

Regression modelling strategies for projected and sustainable kraft pulping of wheat straw.

The demand for paper and paper-based packaging has seen a massive increase in past years, resulting in accelerated deforestation to meet the rising demand, negatively impacting the environment, and there is a need to look towards different non-woody raw materials. Kraft pulping (KP) is widely used in paper making, for which the chemical dose, temperature, time, and energy required must be optimized, for which many insignificant experimental trials are performed. An effort is made to solve this problem by developing the regression equations with the help of Excel using One Factor at a Time Analysis (OFAT), followed by carrying out design of experiments (DoE) using orthogonal approach and regression analysis in Minitab software. Life cycle Assessment (LCA) using the Open-LCA software estimates the effect of chemicals and energy required during pulping on human health, ecosystem quality, and resource depletion. Using regression analysis, the equations for predicting kappa number, yield (%), total energy consumed, and mechanical properties of the paper sheet showed a good fit with an R2 value in the range of 0.90-0.99. Apart from that, the mechanical properties, namely tensile index (41.43 Nm/g), tear index (6.96 mN m2/g), bending stiffness (0.5 mN m), and burst index (3.92 kPa m2/g) of the unbeaten sheet, were determined experimentally at optimized conditions. Based on the Open-LCA result, the optimized pulping conditions had less impact on human health, ecosystem quality, and resource depletion. Industries can use the model to predict the values of kappa number, yield, mechanical properties, and energy consumption without performing optimization experiments that may impact the industry's economy to a greater extent.

Multivalent Sulfur Vacancy-Rich NiCo2 S4 @MnO2 Urchin-Like Heterostructures for Ambient Electrochemical N2 Reduction to NH3.

Innovative advances in the exploitation of effective electrocatalytic materials for the reduction of nitrogen (N2 ) to ammonia (NH3 ) are highly required for the sustainable production of fertilizers and zero-carbon emission fuel. In order to achieve zero-carbon footprints and renewable NH3 production, electrochemical N2 reduction reaction (NRR) provides a favorable energy-saving alternative but it requires more active, efficient, and selective catalysts. In current work, sulfur vacancy (Sv)-rich NiCo2 S4 @MnO2 heterostructures are efficaciously fabricated via a facile hydrothermal approach followed by heat treatment. The urchin-like Sv-NiCo2 S4 @MnO2 heterostructures serve as cathodes, which demonstrate an optimal NH3 yield of 57.31 µg h-1  mgcat -1 and Faradaic efficiency of 20.55% at -0.2 V versus reversible hydrogen electrode (RHE) in basic electrolyte owing to the synergistic interactions between Sv-NiCo2 S4 and MnO2 . Density functional theory (DFT) simulation further verifies that Co-sites of urchin-like Sv-NiCo2 S4 @MnO2 heterostructures are beneficial to lowering the energy threshold for N2 adsorption and successive protonation. Distinctive micro/nano-architectures exhibit high NRR electrocatalytic activities that might motivate researchers to explore and concentrate on the development of heterostructures for ambient electrocatalytic NH3 generation.

Expanding a peptide-covalent probe hybrid for PET imaging of S. aureus driven focal infections.

BACKGROUND: The urgent demand for innovative theranostic strategies to combat bacterial resistance to antibiotics is evident, with substantial implications for global health. Rapid diagnosis of life-threatening infections can expedite treatment, improving patient outcomes. Leveraging diagnostic modalities i.e., positron emission tomography (PET) and single photon emission computed tomography (SPECT) for detecting focal infections has yielded promising results. Augmenting the sensitivity of current PET and SPECT tracers could enable effective imaging of pathogenic bacteria, including drug-resistant strains.UBI (29-41), an antimicrobial peptide (AMP) fragment recognizes the S. aureus membrane through electrostatic binding. Radiolabeled UBI (29-41) is a promising SPECT and PET-based tracer for detecting focal infections. 2-APBA (2-acetyl-phenyl-boronic acid), a non-natural amino acid, specifically targets lysyl-phosphatidyl-glycerol (lysyl-PG) on the S. aureus membranes, particularly in AMP-resistant strains. We propose that combining UBI with 2-APBA could enhance the diagnostic potential of radiolabeled UBI. RESULTS: Present work aimed to compare the diagnostic potential of two radiolabeled peptides, namely UBI (29-41) and 2-APBA modified UBI (29-41), referred to as UBI and UBI-APBA. APBA modification imparted antibacterial activity to the initially non-bactericidal UBI against S. aureus by inducing a loss of membrane potential. The antibacterial activity demonstrated by UBI-APBA can be ascribed to the synergistic interaction of both UBI and UBI-APBA on the bacterial membrane. To enable PET imaging, we attached the chelator 1,4,7-triazacyclononane 1-glutaric acid 4,7-acetic acid (NODAGA) to the peptides for complexation with the positron emitter Gallium-68 (68Ga). Both NODAGA conjugates were radiolabeled with 68Ga with high radiochemical purity. The resultant 68Ga complexes were stable in phosphate-buffered saline and human serum. Uptake of these complexes was observed in S. aureus but not in mice splenocytes, indicating the selective nature of their interaction. Additionally, the APBA conjugate exhibited superior uptake in S. aureus while preserving the selectivity of the parent peptide. Furthermore, [68Ga]Ga-UBI-APBA demonstrated accumulation at the site of infection in rats, with an improved target-to-non-target ratio, as evidenced by ex-vivo biodistribution and PET imaging. CONCLUSIONS: Our findings suggest that linking UBI, as well as AMPs in general, with APBA shows promise as a strategy to augment the theranostic potential of these molecules.

Postharvest handling of ethylene with oxidative and absorptive means.

Fruit ripening is an unfolding of a series of genetically-programmed modifications and tend to be highly orchestrated irrevocable phenomenon mediated by ethylene. Phytohormone ethylene also leads to over-ripening, senescence, loss of texture, microbial attack, reduced post-harvest life and other associated problems during storage and transportation of fruits. Its harmful impacts on fresh fruits, vegetables, and ornamentals result in substantial product losses even up to 80%. Curbing of this inevitable menace is therefore need of the hour. Accrual of ethylene in packaging system should fundamentally be ducked to extend the shelf-life and uphold an adequate superiority of perishables in visual and organoleptic terms. The current review discusses about properties, factors affecting and impact of ethylene, intimidation of its impact at gene vis-à-vis activity level using gene-modification/inhibition techniques, chemical/physical in conjunction with other suitable approaches. It also entails the most commercially cultivated approaches worldwide viz. KMnO4-based oxidation together with adsorption-based scrubbing of ethylene in thorough details. Future ethylene removal strategies should focus on systematic evaluation of KMnO4-based scavenging, exploring the mechanism of adsorption, adsorbent(s) behavior in the presence of other gases and their partial pressures, volatiles, temperature, relative humidity, development of hydrophobic adsorbents to turn-up under high RH, regeneration of adsorbent by desorption, improvement in photocatalytic oxidation etc. and further improvements thereof. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-023-05777-1.

Uniting Synergistic Effect of Single-Ni Site and Electric Field of B- Bridged-N for Boosted Electrocatalytic Nitrate Reduction to Ammonia.

Electrochemical conversion of nitrate, a prevalent water pollutant, to ammonia (NH3 ) is a delocalized and green path for NH3 production. Despite the existence of different nitrate reduction pathways, selectively directing the reaction pathway on the road to NH3 is now hindered by the absence of efficient catalysts. Single-atom catalysts (SACs) are extensively investigated in a wide range of catalytic processes. However, their application in electrocatalytic nitrate reduction reaction (NO3 - RR) to NH3 is infrequent, mostly due to their pronounced inclination toward hydrogen evolution reaction (HER). Here, Ni single atoms on the electrochemically active carrier boron, nitrogen doped-graphene (BNG) matrix to modulate the atomic coordination structure through a boron-spanning strategy to enhance the performance of NO3 - RR is designed. Density functional theory (DFT) study proposes that BNG supports with ionic characteristics, offer a surplus electric field effect as compared to N-doped graphene, which can ease the nitrate adsorption. Consistent with the theoretical studies, the as-obtained NiSA@BNG shows higher catalytic activity with a maximal NH3 yield rate of 168 µg h-1  cm-2 along with Faradaic efficiency of 95% and promising electrochemical stability. This study reveals novel ways to rationally fabricate SACs' atomic coordination structure with tunable electronic properties to enhance electrocatalytic performance.

AMR Threat Perception Assessment of Heterotrophic Bacteria From Shrimp Aquaculture Through Epidemiological Cut off Values.

BACKGROUND: Emergence and dissemination of antibiotic resistance is one of the major risks associated with the rampant usage of antibiotics in food-producing animals including aquaculture. OBJECTIVE: To determine Epidemiological Cut-OFF (ECOFF) values of heterotrophic bacterial populations from shrimp culture environments against five different antibiotics. METHODS: In this present study, bacterial samples were isolated from Penaeus vannamei culture environment in different locations of Andhra Pradesh, which is the aquaculture hub of India. The bacterial isolates were assessed for antibiotic resistance towards five antibiotics belonging to different classes (oxytetracycline, chloramphenicol, erythromycin, ciprofloxacin, and co-trimoxazole) by the disc diffusion method. Determination of Epidemiological Cut-OFF (ECOFF) values and analysis by employing normalized resistance interpretation (NRI) was carried out. RESULTS: The most dominant bacterial populations from shrimp culture were Vibrio spp. (pathogenic bacteria) followed by Bacillus spp. (probiotic bacteria). The bacterial isolates showed highest resistance towards oxytetracycline (overall 23.38%) and in location L6 (59.4%) followed by co-trimoxazole (31.1%). ECOFF values calculated by employing NRI showed that the disc diffusion data were distributed in a normalized manner. The maximum ECOFF value was obtained for ciprofloxacin (23.32 mm), while the minimum value was observed for oxytetracycline (9.05 mm). The antibiotic resistant phenotypes showed that the majority of the heterotrophic bacterial isolates (>60%) belonged to the non-wild type phenotype and primarily towards oxytetracycline (90%). CONCLUSION: The presence of non-wild antibiotic-resistant phenotypes of heterotrophic bacterial populations (which include not only pathogenic bacteria but also probiotic bacteria) indicates that shrimp culture ponds may be a reservoir for drug-resistant bacteria and there is a greater risk associated with transmission of resistant genes across bacterial flora. HIGHLIGHTS: NRI analysis of antibiotic disc diffusion data of heterotrophic bacterial populations in shrimp aquaculture environments revealed that majority of them belonged to non-wild type (90%) paticularly to oxytetracycline in comparison to other studied antibiotics (chloramphenicol, erythromycin, ciprofloxacin and co-trimoxazole).

CDBProm: the Comprehensive Directory of Bacterial Promoters.

The decreasing cost of whole genome sequencing has produced high volumes of genomic information that require annotation. The experimental identification of promoter sequences, pivotal for regulating gene expression, is a laborious and cost-prohibitive task. To expedite this, we introduce the Comprehensive Directory of Bacterial Promoters (CDBProm), a directory of in-silico predicted bacterial promoter sequences. We first identified that an Extreme Gradient Boosting (XGBoost) algorithm would distinguish promoters from random downstream regions with an accuracy of 87%. To capture distinctive promoter signals, we generated a second XGBoost classifier trained on the instances misclassified in our first classifier. The predictor of CDBProm is then fed with over 55 million upstream regions from more than 6000 bacterial genomes. Upon finding potential promoter sequences in upstream regions, each promoter is mapped to the genomic data of the organism, linking the predicted promoter with its coding DNA sequence, and identifying the function of the gene regulated by the promoter. The collection of bacterial promoters available in CDBProm enables the quantitative analysis of a plethora of bacterial promoters. Our collection with over 24 million promoters is publicly available at https://aw.iimas.unam.mx/cdbprom/.

PoxiPred: An Artificial-Intelligence-Based Method for the Prediction of Potential Antigens and Epitopes to Accelerate Vaccine Development Efforts against Poxviruses.

Poxviridae is a family of large, complex, enveloped, and double-stranded DNA viruses. The members of this family are ubiquitous and well known to cause contagious diseases in humans and other types of animals as well. Taxonomically, the poxviridae family is classified into two subfamilies, namely Chordopoxvirinae (affecting vertebrates) and Entomopoxvirinae (affecting insects). The members of the Chordopoxvirinae subfamily are further divided into 18 genera based on the genome architecture and evolutionary relationship. Of these 18 genera, four genera, namely Molluscipoxvirus, Orthopoxvirus, Parapoxvirus, and Yatapoxvirus, are known for infecting humans. Some of the popular members of poxviridae are variola virus, vaccine virus, Mpox (formerly known as monkeypox), cowpox, etc. There is still a pressing demand for the development of effective vaccines against poxviruses. Integrated immunoinformatics and artificial-intelligence (AI)-based methods have emerged as important approaches to design multi-epitope vaccines against contagious emerging infectious diseases. Despite significant progress in immunoinformatics and AI-based techniques, limited methods are available to predict the epitopes. In this study, we have proposed a unique method to predict the potential antigens and T-cell epitopes for multiple poxviruses. With PoxiPred, we developed an AI-based tool that was trained and tested with the antigens and epitopes of poxviruses. Our tool was able to locate 3191 antigen proteins from 25 distinct poxviruses. From these antigenic proteins, PoxiPred redundantly located up to five epitopes per protein, resulting in 16,817 potential T-cell epitopes which were mostly (i.e., 92%) predicted as being reactive to CD8+ T-cells. PoxiPred is able to, on a single run, identify antigens and T-cell epitopes for poxviruses with one single input, i.e., the proteome file of any poxvirus.

A Metal Coordination Number Determined Catalytic Performance in Manganese Borides for Ambient Electrolysis of Nitrogen to Ammonia.

A new strategy that can effectively increase the nitrogen reduction reaction performance of catalysts is proposed and verified by tuning the coordination number of metal atoms. It is found that the intrinsic activity of Mn atoms in the manganese borides (MnBx) increases in tandem with their coordination number with B atoms. Electron-deficient boron atoms are capable of accepting electrons from Mn atoms, which enhances the adsorption of N2 on the Mn catalytic sites (*) and the hydrogenation of N2 to form *NNH intermediates. Furthermore, the increase in coordination number reduces the charge density of Mn atoms at the Fermi level, which facilitates the desorption of ammonia from the catalyst surface. Notably, the MnB4 compound with a Mn coordination number of up to 12 exhibits a high ammonia yield rate (74.9 ± 2.1 µg h-1 mgcat -1) and Faradaic efficiency (38.5 ± 2.7%) at -0.3 V versus reversible hydrogen electrode (RHE) in a 0.1 m Li2SO4 electrolyte, exceeding those reported for other boron-related catalysts.

Evaluation of 177Lu-Labeled Pertuzumab F(ab')2 Fragments for HER2-Positive Cancer Targeting: A Comparative In Vitro and In Vivo Study.

Background: Radiolabeled antibody fragments present a promising opportunity as theranostic agents, offering distinct advantages over whole antibodies. In this study, the authors investigate the potential of [177Lu]Lu-DTPA-F(ab')2-pertuzumab as a theranostic agent for precise targeting of human epidermal growth factor receptor 2 (HER2)-positive cancers. Additionally, the authors aim to quantitatively assess the binding synergism in the presence of cold trastuzumab. Materials and Methods: F(ab')2-pertuzumab was prepared by pepsin digestion and conjugated with a bifunctional chelator. The immunoconjugate was radiolabeled with 177Lu and characterized by chromatography techniques. Binding parameters (affinity, specificity, and immunoreactivity) and cellular binding enhancement studies were evaluated in HER2-overexpressing and triple-negative cell lines. The in vivo enhancement in tumor uptake of the radiolabeled immunoformulation was assessed in severe combined immunodeficient (SCID) mice bearing tumors, both in the presence and absence of unlabeled trastuzumab. Results: The formulation of [177Lu]Lu-DTPA-F(ab')2-pertuzumab could be prepared in high yields and with consistent radiochemical purity, ensuring reproducibility. Comprehensive in vitro and in vivo evaluation studies confirmed high specificity and immunoreactivity of the formulation toward HER2 receptors. Binding synergism of radiolabeled pertuzumab fragments in the presence of trastuzumab to HER2 receptors was observed. Conclusions: The radioformulation of [177Lu]Lu-DTPA-F(ab')2-pertuzumab holds great promise as a targeted approach for addressing HER2-positive cancers. A potentially effective strategy to amplify therapeutic efficacy involves dual epitope targeting by combining radiolabeled pertuzumab with cold trastuzumab.

Valorizing Assorted Logging Residues: Response Surface Methodology in the Extraction Optimization of a Green Norway Spruce Needle-Rich Fraction To Obtain Valuable Bioactive Compounds.

During stemwood harvesting, substantial volumes of logging residues are produced as a side stream. Nevertheless, industrially feasible processing methods supporting their use for other than energy generation purposes are scarce. Thus, the present study focuses on biorefinery processing, employing response surface methodology to optimize the pressurized extraction of industrially assorted needle-rich spruce logging residues with four solvents. Eighteen experimental points, including eight center point replicates, were used to optimize the extraction temperature (40-135 °C) and time (10-70 min). The extraction optimization for water, water with Na2CO3 + NaHSO3 addition, and aqueous ethanol was performed using yield, total dissolved solids (TDS), antioxidant activity (FRAP, ORAC), antibacterial properties (E. coli, S. aureus), total phenolic content (TPC), condensed tannin content, and degree of polymerization. For limonene, evaluated responses were yield, TDS, antioxidant activity (CUPRAC, DPPH), and TPC. Desirability surfaces were created using the responses showing a coefficient of determination (R2) > 0.7, statistical significance (p ≤ 0.05), precision > 4, and statistically insignificant lack-of-fit (p > 0.1). The optimal extraction conditions were 125 °C and 68 min for aqueous ethanol, 120 °C and 10 min for water, 111 °C and 49 min for water with Na2CO3 + NaHSO3 addition, and 134 °C and 41 min for limonene. The outcomes contribute insights to industrial logging residue utilization for value-added purposes.

Laser-Synthesized Co-Doped CuO Electrocatalyst: Unveiling Boosted Methanol Oxidation Kinetics for Enhanced Hydrogen Production Efficiency by In Situ/Operando Raman and Theoretical Analyses.

The present study details the strategic development of Co-doped CuO nanostructures via sophisticated and expedited pulsed laser ablation in liquids (PLAL) technique. Subsequently, these structures are employed as potent electrocatalysts for the anodic methanol oxidation reaction (MOR), offering an alternative to the sluggish oxygen evolution reaction (OER). Electrochemical assessments indicate that the Co-CuO catalyst exhibits exceptional MOR activity, requiring a reduced potential of 1.42 V at 10 mA cm-2 compared to that of pure CuO catalyst (1.57 V at 10 mA cm-2 ). Impressively, the Co-CuO catalyst achieved a nearly 180 mV potential reduction in MOR compared to its OER performance (1.60 V at 10 mA cm-2 ). Furthermore, when pairing Co-CuO(+)ǀǀPt/C(-) in methanol electrolysis, the cell voltage required is only 1.51 V at 10 mA cm-2 , maintaining remarkable stability over 12 h. This represents a substantial voltage reduction of ≈160 mV relative to conventional water electrolysis (1.67 V at 10 mA cm-2 ). Additionally, both in situ/operando Raman spectroscopy studies and theoretical calculations have confirmed that Co-doping plays a crucial role in enhancing the activity of the Co-CuO catalyst. This research introduces a novel synthetic approach for fabricating high-efficiency electrocatalysts for large-scale hydrogen production while co-synthesizing value-added formic acid.