Introduction: What could be an ideal raw material for developing a drug or a vaccine? In line with the research on different biomolecules like DNA, RNA, protein, and peptide, we explore the potential use of non-coding DNA in designing lifesaving vaccines and drugs.

Methods: Using computational approaches, a multi-parametric virtual library of novel peptides from the intergenic regions of the Escherichia coli genome was generated, and their therapeutic potential was studied. The potential antigens from the peptides were analyzed for their B cell epitopes and MHC binding T cell epitopes, which find application in epitope-based vaccine design. Alzheimer's disease (AD) immunotherapy was selected as an example to demonstrate the possible application of the non-coding DNA-derived peptides as promising candidates for Synthetic Peptide Vaccine Design.

Results: Sequence and structure comparison studies between toxic amyloid beta (Aβ₄₂) peptides and the non-coding DNA-derived peptides revealed promising matches. The structural mimics of Aβ₄₂ with potential mimotopes were further studied through mimotope-antibody docking and molecular dynamic simulation for their affinity towards the antibody's antigen-binding fragment (Fab).

Conclusion: Our study put forward a novel method to identify therapeutic peptides from non-coding DNA, which offers a non-obvious source of potential mimotope candidates for designing novel synthetic vaccines against Alzheimer’s Disease.

Introduction: In recent years, there has been growing interest in tick-borne infections, particularly tick-borne rickettsioses (TBRs). Assessing the genospecies composition and regional distribution of spotted fever group rickettsiae (SFGR) is crucial for optimizing risk-based surveillance of TBR. However, the genospecies diversity of SFGR populations in the Russian Federation remains understudied. To address this, we studied ticks collected from vegetation, humans, and animals in eight regions of Russia to identify the SFGR genospecies, which may have significance for human morbidity.

Materials and Methods: From 2020 to 2024, we collected 2,431 ticks from eight regions of Russia, representing Western Siberia (Altai Krai), North Caucasus (Karachay-Cherkessia), Southern Russia (Astrakhan Oblast), the Volga region (Samara Oblast), Central Russia (Moscow, Tula Oblast, Oryol Oblast), and Central Europe (Kaliningrad Oblast). We utilized commercial qPCR kits for SFGR screening and identified genospecies by Sanger sequencing partial genes for citrate synthase (gltA) and outer-membrane protein A (ompA), comparing the results with the GenBank database.

Results: Our findings revealed six distinct genospecies of SFGR across the eight regions of Russia; however, the diversity of these genospecies varied by region. The highest diversity (five genospecies: R. raoultii, R. slovaca, R. helvetica, R. monacensis, and R. aeschlimannii) was found in North Caucasus in ticks from three genera. In Western Siberia, we detected three genospecies—R. sibirica, R. raoultii, and R. helvetica—in two genera of ticks. In the Volga region, the genospecies R. slovaca and R. raoultii were found in Dermacentor ticks, while in Southern Russia, R. raoultii and R. aeschlimannii were identified in two different genera of ticks. Central Russia (three regions) and Europe showed a similar pattern, with R. raoultii in Dermacentor and R. helvetica in Ixodes.

Conclusions: Our study highlights significant regional variations in SFGR genospecies diversity in Russia, underscoring the necessity for ongoing research and monitoring for public health.

Polyploidy is a key factor influencing traits such as chloroplast number, stomatal size, and leaf yield. In mulberry (Morus spp.), triploids are well known to be superior over other ploidies in terms of yield traits. However, the cellular and molecular processes driving these benefits remain unclear. Transcriptome analysis is a powerful tool used to understand the molecular mechanisms underlying various plant traits, which requires coding skills and high-performance computers that hinder the utilization of publicly available huge RNA-Seq datasets. To address this issue, repository RNA-Seq datasets were analyzed using Galaxy to decode the genetic basis of the superior functionality of triploid mulberry. Leaf transcriptome datasets of diploids and triploids were retrieved and analyzed in Galaxy, where the genome of M. indica K2 was used as a reference. A variety of tools, including Trimmomatic, HISAT2, Stringtie, StringtieMerge, Featurecount, DEseq2, and WGCNA, were employed to identify differentially expressed genes, which were further analyzed using iDEP tools. For data interpretation, a PCA, volcano plot, heatmap, dendrogram, and bubble diagram were generated. The analysis revealed that triploid mulberry germplasm yielded a considerable number of up- and downregulated genes compared to diploids. Notably, the upregulated genes were associated with photosynthesis, chlorophyll biosynthesis, and carbon fixation, which in turn relay the molecular basis of the advantageous effect of triploids over diploids. These transcriptome studies indicate that polyploidization enhances photosynthetic capacity and other metabolic attributes. Therefore, this methodology helps to decipher the molecular basis of the advantageous effect of triploids over diploids without coding skills and high-performance computers.

The increasing prevalence of antibiotic-resistant bacteria, especially Klebsiella spp., represents a major threat to both human and veterinary medicine. This study aimed to isolate and characterize the antimicrobial resistance profiles of Klebsiella spp. from broilers and broiler bursitis.

A total of 210 samples were collected, including 70 from hens, 40 from free-range chickens, 40 from bursitis, 20 from males, 20 from roosters, and 20 from young chickens. Antimicrobial susceptibility testing was conducted using the disc diffusion method, as recommended by EUCAST and CLSI guidelines, against 14 antibiotics. Additionally, PCR analysis revealed the presence of several resistance genes.

From the 210 samples, 51 isolates of Klebsiella spp. were obtained, including 20 from hens, 10 from young chickens, 8 from bursitis, 6 from free-range chickens, 4 from roosters, and 3 from males. Regarding the antimicrobial resistance, 57% of the isolates were classified as multidrug-resistant. The highest levels of resistance were observed for ampicillin (98.04%) and amoxicillin-clavulanic acid (86.27%). Resistance to nalidixic acid, trimethoprim-sulfamethoxazole, ciprofloxacin, gentamicin, and tetracycline was detected in 52.94%, 50.98%, 47.06%, 45.10%, and 23.53% of the isolates, respectively. None of the isolates showed resistance to imipenem, cefotaxime, or ceftazidime. The sul2 gene was detected in 65.39% of isolates resistant to trimethoprim-sulfamethoxazole, while sul3 was found in only 3.85%. The bla_TEM gene, associated with beta-lactam resistance, was present in 78% of isolates, while bla_SHV was detected in 4%. For tetracycline resistance, the tetA and tetB genes were found in 58.33% and 41.67% of the isolates, respectively.

This study highlights the significant antimicrobial resistance found in Klebsiella spp. isolated from poultry, underscoring the public health risks associated with the consumption of poultry products. More than half of the isolates were multidrug-resistant, which calls for ongoing surveillance and responsible antibiotic use in animal production to mitigate the spread of resistant strains.

Introduction: Leprosy, caused by Mycobacterium leprae, shows variations in individual susceptibility, which may be linked to genetic differences in the exome. Exonic single-nucleotide polymorphisms (SNPs) can influence immune response and disease progression. This study aimed to analyze, in silico, the functional and structural impact of exonic SNPs associated with leprosy susceptibility. Methods: Data from the literature on leprosy-risk SNPs were retrieved from PubMed and SciELO. Analyses were conducted on synonymous (sSNP) and non-synonymous SNPs (nsSNP). For sSNPs, predictions included effects on mRNA structure (RNAfold, CycleFold, Kinefold), splicing (MaxEnt Scan, Ex Skip), and miRNA binding (TargetScan Score). For nsSNPs, protein damage was assessed using SIFT, PolyPhen 2, PhD-SNP, SNPs and GO, and Predict SNP 2. Pathogenicity filters identified 11 nsSNPs for further analysis of stability (CUPSAT), functionality (MutPred), and evolutionary conservation (ConSurf). Results: A total of 35 exonic SNPs were analyzed (6 sSNPs, 29 nsSNPs). The sSNP rs2230365 (NFKBIL1) showed the highest potential for impacting miRNA regulation and mRNA structure, while no significant changes were observed in splicing. The nsSNP rs5743708 (TLR2) was predicted as deleterious by all tools used. SNP rs145562243 (NCKIPSD) was shown to be destabilizing with an unfavorable ΔΔG (-5.53 kcal/mol). The molecular, structural and evolutionary impacts of each SNP were reported. Highly conserved and exposed SNPs like rs5743708 suggest that they are critical for protein function. Conclusion: This study identified 12 exonic SNPs (1 sSNP and 11 nsSNPs) as potential candidates for further in vivo studies on leprosy. These SNPs reveal complex interactions between genetic variations and their functional consequences, contributing to the understanding of disease mechanisms.

Introduction: Inherited retinal diseases (IRDs) are clinically complex and genetically heterogeneous visual impairment disorders with varying penetrance and severity. Disease-causing variants in at least 289 nuclear and mitochondrial genes have been implicated in their pathogenesis. Methods: Genomic DNA was isolated from peripheral blood lymphocytes. Exome sequencing was performed on an Illumina platform, and splicing analysis was performed using a pET01 minigene plasmid in Hela cells. Results: In the current study, we performed exome sequencing on a 51 year-old Ashkenazi Jewish patient with non-syndromic retinitis pigmentosa (RP) and identified compound heterozygous variants in the CLRN1 gene: a known pathogenic missense [p.(N48K)] and a novel deep intronic variant, c.254- 643G>T. A minigene splicing assay was performed, aiming to study the effect of the c.254- 643G>T variant on CLRN1 pre-mRNA splicing, and this revealed the inclusion of a pseudo-exon that was also reported to be included in the transcript due to an adjacent variant, c.254-649T>G. However, unlike the reported c.254-649T>G variant, c.254-643G>T showed aberrant splicing in a leaky manner, implying that the identified variant is not totally penetrant. Conclusion: The non-syndromic phenotype observed in this index case may be attributed to the leaky nature of this variant, which causes some normal transcripts to be produced. To conclude, we report on a novel deep intronic variant in CLRN1 causing non-syndromic RP due to the leaky nature of the identified variant.

Secondary metabolite production in Artemisia has been studied for its anti-parasitic, anti-tumor, and anti-inflammatory actions. Artemisia californica is a drought resilient plant with medicinal value used traditionally as a topical for severe pain relief; flavonoids, stilbenes, sesquiterpene lactones, and terpenes are main therapeutic components.

We aimed to create novel genomic resources, including a leaf & flower transcriptome and soil WGS metagenomics from the A. californica rootzone. Snap frozen plant tissues and rhizosphere soil were collected from the field and sent to BGIA for extraction, library preparation, and sequencing. Following QC, de novo assembly and quantification, transcripts were annotated with the best SPROT BLASTX and BLASTP hits. The completeness of the assemblies was assessed using BUSCO. Transcripts with TPM>10 and length>1000 were examined for evidence of candidate genes related to production of the expected bioactive compounds.

Assembly summary statistics were computed. There were 212,818 total sequences with a total length of 2.07*10^8. The average sequence length was 908; the length ranged between 193-13,630. L50 value was 41,357, N50 was 1,591, and N80 was 647. The Artemisia californica transcriptome was 91.4% complete. In the transcripts, there was evidence of sesquiterpene production, sesquiterpene lactones, and flavonoids. Beta-caryophyllene synthase was related to Artemisia, however with low similarity (62.70% ID, TPM= 14.86, length=2889). Multiple sesquiterpenoids and triterpenoids appeared to be elevated. Chalcone synthase transcripts were 96.23% similar to Australasian lineages of Asteraceae.

There was evidence of a distinct rootzone microbial community. Geodermatophilus from Actinomycetes was well-represented. The Biobakery metagenomics output indicated that there are differences in taxonomy in soil samples from different plant species, although there were few differences in function.

Future studies should focus on Nanopore sequencing of plant RNA and mining for novel bacterial species in the Artemisia rootzone using WGS data. Further studies should include biochemical analysis to confirm genomic findings.

Ribes malvaceum is commonly known as Chaparral Currant. This pilot project aimed to create genomic resources for R. malvaceum for phylogenomic studies of secondary metabolite production. The Ribes sp. are of interest in this study due to production of bioactive compounds for human health. R. malvaceum is of interest due to its desirable climate resiliency traits. Based on known characteristics of closely related cultivated species Ribes nigrum and the best BLASTX results, we hypothesize that we will find transcriptomic evidence of similar secondary metabolites produced by R. malvaceum in the transcripts.

Ribes malvaceum tissue was collected on the Red Trail at Gold Creek Preserve, Angeles National Forest. Leaf and fruit tissue was snap frozen in the field and sent to BGI Americas for extraction, library preparation, and sequencing. The data pipeline for plant RNAseq consisted of QC, de novo assembly, BUSCO evaluation, quantification, and annotation. The shell script find_transcript_ids.sh was used to find lant transcripts with TPM>10 (Transcripts Per Million) and length>1000. The downstream analysis was performed in order to narrow down interesting secondary metabolite genes which had high length and high TPM. The BUSCO results showed that the transcriptome was 90.63% complete.

Delta (8)-fatty-acid desaturase sequences were closely related to Helianthus (70.43% similar), TPM=42.85, length= 2115. Transcripts closely matched Chalcone synthase from Humulus, with 90.69% similarity and length of 1506, and were elevated (TPM= 644.85). A transcript related to Flavonoid 3’-monooxygenase in Petunia was identified (77.57% similar), length 2075, TPM=132.70. Anthocyanidin reductase ((2S)-flavan-3-ol-forming) was highly similar to Vitis (84.57%), TPM=39.75, length=1249. Monothiol glutaredoxin was related to the sequence Arabidopsis (70.67% similar, TPM=49.77, effective length=3616). Transcripts related to 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2 were identified that were 87.69% similar to Vitis (TPM=231.54, effective length= 1029).

These results are a starting point for further investigation into the species’ resiliency and natural products.

Introduction: Individual host susceptibility to coronavirus disease 2019 (COVID-19) can be attributed in part to single-nucleotide polymorphisms (SNPs), which may be exist at exonic sites of the genome. The objective of this work was to analyze, in silico, the functional and structural impact of exonic SNPs that are related to susceptibility to COVID-19 in the literature. Methods: Literature data were retrieved from PubMed and Science Direct in relation to COVID-19 risk-associated SNPs, and a separate analysis was performed between synonymous (sSNP) and non-synonymous (nsSNP) SNPs. To characterize the sSNPs, the following predictions were made: effects on mRNA structure (with RNAfold; CycleFold; Kinefold); splicing effects on mRNA (MaxEnt Scan; Ex Skip); and effects on miRNA binding (TargetScan Score). Regarding the nsSNPs, a functional analysis of protein damage (with SIFT, PolyPhen 2, PhD-SNP, SNPs&GO, Predict SNP 2) was performed. After passing the pathogenicity criteria, 8 nsSNPs were selected to predict their impacts on stability (CUPSAT), functionality, and residual evolution (MutPred, ConSurf). Results: The sample consisted of 16 exonic SNPs, 4 sSNP, and 12 nsSNP. Among the sSNPs, the SNP rs12252 of IFITM3 had the greatest potential impact on mRNA structure, alternative splicing, and miRNA binding and indicated a moderate impact on post-transcriptional regulation. Regarding the nsSNPs, the TYK2 SNP rs34536443 was predicted to be deleterious/damaging by all the tools used. The SNPs predicted to be destabilizing by CUPSAT, such as the PLSCR1 SNP rs343320, appear to have a greater negative impact on protein stability. The molecular, structural, and evolutionary impacts of each SNP were described. Conclusion: A total of nine exonic SNPs (one sSNP and eight nsSNPs) were indicated here as potential candidates for further in vivo studies for COVID-19, as they may alter protein stability, interactions, and functional motifs that may be associated with antiviral response pathways.

Surfactin is a highly effective biosurfactant with broad potential applications in the medical and environmental technology sectors. Its biosynthesis in Bacillus subtilis is orchestrated by intricate genetic networks responsive to environmental stimuli. This study explores the enhancement of surfactin production in Bacillus subtilis ATCC 21332 through targeted genetic modifications, particularly under nitrate-enriched conditions, resulting in a significant boost in production. Comprehensive systems-level analysis identified pivotal genetic components governing nitrogen metabolism, fatty acid biosynthesis, and membrane transport, which were experimentally validated as key to facilitating increased surfactin output. Specifically, the upregulation of genes including nitrate reductase subunit genes narG and NarH, long-chain fatty acid β-hydroxylase gene cypC, preprotein translocase subunit gene secA, and the ATPase involved in cell division, gene ftsE, proved critical in optimizing surfactin synthesis. Through systematic engineering and the combination of these gene targets, the engineered strain SURb8 exhibited remarkable improvements in surfactin yield and production efficiency. Furthermore, a tailored feeding regime, designed to align with surfactin biosynthesis pathways, elevated the final production to 14.41 g/L, a 41.4-fold increase over that of the wild-type strain. This research offers valuable insights into the genetic and metabolic regulation of surfactin biosynthesis, highlighting the potential of microbial genetic engineering to enhance biosurfactant production for industrial applications.