Search Results (215)

Biotechnological research increasingly focuses on developing new drugs to counter the rise of antibiotic-resistant strains in hospitals. This study aimed to create bacterial lysates from antibiotic-resistant pathogens isolated from patients and medical instruments across hospital departments. Identification was performed based on morphological, cultural, and biochemical characteristics, as well as 16S rRNA gene sequencing using the BLAST algorithm. Strain viability was assessed using the Miles and Misra method, while sensitivity to eight antibacterial drug groups and biosafety between cultures were evaluated using agar diffusion. From 15 clinical sources, 25 pure isolates were obtained, and their phenotypic and genotypic properties were studied. Carbohydrate fermentation testing confirmed that the isolates belonged to the genera Escherichia, Citrobacter, Klebsiella, Acinetobacter, Pseudomonas, Staphylococcus, Haemophilus, and Streptococcus. The cultures exhibited good viability (10⁹–10¹⁰ CFU/mL) and compatibility with each other. Based on prevalence and clinical significance, three predominant hospital pathogens (Klebsiella pneumoniae 12 BL, Pseudomonas aeruginosa 3 BL, and Acinetobacter baumannii 24 BL) were selected to develop a bacterial lysate consortium. Lysates were prepared with physical disruption using a French press homogenizer. The resulting product holds industrial value and may stimulate the immune system to combat respiratory pathogens prevalent in Kazakhstan’s healthcare settings. Full article

(1) Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder driven by the BCR::ABL oncoprotein. During the chronic phase, Philadelphia chromosome-positive hematopoietic stem cells generate proliferative myeloid cells with various stages of maturation. Despite this expansion, leukemic stem cells (LSCs) retain self-renewal capacity via asymmetric cell divisions, sustaining the stem cell pool. Quiescent LSCs are known to be resistant to tyrosine kinase inhibitors (TKIs), potentially through BCR::ABL-independent signaling pathways. We hypothesize that dysregulation of genes governing asymmetric division in LSCs contributes to disease progression, and that their expression pattern may serve as a prognostic marker during the chronic phase of CML. (2) Methods: Genes related to asymmetric cell division in the context of hematopoietic stem cells were extracted from the PubMed database with the keyword “asymmetric hematopoietic stem cell”. The collected relative gene set was tested on two independent bulk transcriptome cohorts and the results were confirmed by single-cell RNA sequencing. (3) Results: The expression of genes involved in asymmetric hematopoietic stem cell division was found to discriminate disease phases during CML progression in the two independent transcriptome cohorts. Concordance between cohorts was observed on asymmetric molecules downregulated during blast crisis (BC) as compared to the chronic phase (CP). This downregulation during the BC phase was confirmed at single-cell level for SELL, CD63, NUMB, HK2, and LAMP2 genes. Single-cell analysis during the CP found that CD63 is associated with a poor prognosis phenotype, with the opposite prediction revealed by HK2 and NUMB expression. The single-cell trajectory reconstitution analysis in CP samples showed CD63 regulation highlighting a trajectory cluster implicating HSPB1, PIM2, ANXA5, LAMTOR1, CFL1, CD52, RAD52, MEIS1, and PDIA3, known to be implicated in hematopoietic malignancies. (4) Conclusion: Regulation of CD63, a tetraspanin involved in the asymmetric division of hematopoietic stem cells, was found to be associated with poor prognosis during CML progression and could be a potential new therapeutic target. Full article

Morkhor 60-3 is an upland rice variety primarily cultivated in northeastern Thailand. This glutinous rice is valued for its adaptability and rich aroma but remains susceptible to significant diseases, particularly blast and bacterial blight. Using resistant varieties represents the most cost-effective approach to address this limitation. This study incorporated the QTLs/genetic markers qBl1, qBl2, and xa5 from Morkhor 60-1 through marker-assisted backcrossing. From the BC₁F₃ population, ten lines were selected based on their parentage and evaluated for blast resistance using a spray inoculation method with 12 isolates of Pyricularia oryzae, and for bacterial blight (BB) resistance using a leaf-clipping method with nine isolates of Xanthomonas oryzae pv. oryzae. Broad-spectrum resistance (BSR) was also assessed in the lines for both diseases. Subsequently, BC₁F₄ lines were evaluated for field performance, including agronomic traits and aroma. Results identified three superior lines, BC₁F₄ 22-7-140-4, BC₁F₄ 22-7-322-5, and BC₁F₄ 22-7-311-9, that demonstrated resistance to both BB and blast pathogens with average BSR values of 0.61 and 1.00, 0.66 and 1.00, and 0.55 and 0.87, respectively. These lines also exhibited enhanced performance in flowering date, plant height, panicle number per plant, grain number per plant, and grain weight. These findings demonstrate the effectiveness of marker-assisted selection (MAS) for gene pyramiding in rice improvement. Full article

Background: Antimicrobial resistance (AMR) is a critical global health threat, with AMR Salmonella enterica serovar Typhimurium strains being a major foodborne pathogen. Integrons, a type of mobile genetic element, capture and transfer resistance genes, thereby playing a role in the spread of AMR. Objectives: This study aimed to characterize the locations of integrons carrying AMR genes within the whole genomes of 32 Salmonella Typhimurium isolates collected from dairy cattle by two U.S. Veterinary Diagnostic Laboratories between 2009 and 2012. Methods: Class I integrons were sequenced from PCR-amplified products. DNA was extracted, quantified, barcoded, and sequenced on the Illumina MiSeq platform. Whole genome sequences were trimmed and assembled using the SPAdes assembler in Geneious Prime^®, and plasmids were identified with the PlasmidFinder pipeline in Linux. Integron locations were determined by aligning their sequences with whole genome contigs and plasmids, while AMR genes were identified through BLAST with the MEGARes 3.0 database and confirmed by alignment with isolate, plasmid, and integron sequences. Statistical analysis was applied to compare the proportions of isolates harboring integrons on their chromosome versus plasmids and also to examine the associations between integron presence and AMR gene presence. Results: Seven plasmid types were identified from all isolates: IncFII(S) (n = 14), IncFIB(S) (n = 13), IncC (n = 7), Inc1-I(Alpha) (n = 3), and ColpVC, Col(pAHAD28), and Col8282 (1 isolate each). Of the 32 isolates, 16 (50%) carried at least one size of integron. Twelve of them carried both 1000 and 1200 bp; 3 carried only 1000 bp and 1 carried 1800 bp integrons. Of the 15 isolates that carried 1000 bp integron, 12 harbored it on IncFIB(S) plasmids, 2 on IncC plasmids, and 1 on the chromosome. The 1200 bp integrons from all 12 isolates were located on chromosomes. There were significant positive associations between the presence of integrons and the presence of several AMR genes including sul1, aadA2, blaCARB-2, qacEdelta1, tet(G), and floR (p < 0.05). AMR genes were located as follows: aadA2 on IncFIB(S) and IncC plasmids; bla_CMY-2 on IncC plasmid; qacEdelta1 on IncFIB(S), IncC, and chromosome; bla_CARB-2, floR, tet(A) and tet(G) on the chromosome. Conclusions: The findings highlight the genomic and plasmid complexity of Salmonella Typhimurium which is impacted by the presence and location of integrons, and this study provides genomic insights that can inform efforts to enhance food safety and protect both animal and public health. Full article

The Yangtze River Delta (YRD) is one of the most important japonica rice planting areas in China. Balancing the resistance, yield, and quality has always been a core issue in rice breeding due to the negative correlation among these three factors, while the broad-spectrum blast resistance gene Piz is closely linked with Hd1, the major gene regulating days to heading (DTH), and a precise combination of their beneficial alleles plays a key role in synchronously improving blast resistance and the regional adaptability of japonica rice in YRD. In this study, using the backcross progeny population derived from backbone parent ZD9471 and W1063, two alleles of Hd1 were identified. Then, through molecular marker-assisted selection combined with Green Super Rice 40K (GSR40K) chip-based screening, six introgression lines (ILs) with two different alleles combinations of Hd1 and Pigm were obtained. An evaluation of the blast resistance, yield, and quality traits showed that compared with the recipient parent, the panicle blast resistance of ILs was significantly enhanced; the grain number per panicle increased consistently with the delaying of the growth period, leading to higher yield in the ILs; the grain quality were synchronously improved. Two representative lines with similar genetic backgrounds but a significantly different regional adaptability, exhibiting a good blast resistance, high yield, and prominent quality were approved and demonstrated promising application prospects. Full article

Diseases and weeds occupy a leading place among the factors limiting the yield of agricultural crops, including rice. These factors can be overcome through the use of chemical protective agents, as well as through the creation and introduction into agricultural production of rice varieties resistant to these stressors. The use of DNA marking technologies for target genes of economically valuable traits in the creation of promising varieties allows not only for the identification of genes but also the monitoring of their transmission during crosses and the selection of breeding-valuable genotypes with genes of interest. In addition, this ensures a reduction in the volume of breeding nurseries, as well as time and material costs during variety modeling, and rapid rotation of new high-yield varieties with specified characteristics. We have selected effective marker systems based on the use of DNA marking technologies for target genes for resistance to blast (Pi) and submergence tolerance (Sub1A). These systems allow for precise targeted selection of hybrid plants with these genes in the breeding process. In addition, we have automated the detection of transferred Pi-ta and Pi-b genes, which greatly relieves the DNA analysis during mass screening of breeding material. The final result of this work is the created rice varieties Al’yans, Lenaris and Kapitan with the Pi-ta blast resistance gene and the Pirouette rice variety with the Pi-1, Pi-2, and Pi-33 genes. These varieties exceed the standards by 0.64–2.2 t/ha, and their involvement in production makes it possible to obtain additional products by increasing yields in the amount of about RUB 80 thousand/ha. Full article

Rice (Oryza sativa) is a globally important crop that plays a central role in maintaining food security. This scientific review examines the critical role of genetic disease resistance in protecting rice yields, dissecting at the molecular level how rice plants detect and respond to pathogen attacks while evaluating modern approaches to developing improved resistant varieties. The analysis covers single-gene-mediated and multi-gene resistance systems, detailing how on one hand specific resistance proteins, defense signaling components, and clustered loci work together to provide comprehensive protection against a wide range of pathogens and yet their production is severely impacted by pathogens such as Xanthomonas oryzae (bacterial blight) and Magnaporthe oryzae (rice blast). The discussion extends to breakthrough breeding technologies currently revolutionizing rice improvement programs, including DNA marker-assisted selection for accelerating traditional breeding, gene conversion methods for introducing new resistance traits, and precision genome editing tools such as CRISPR/Cas9 for enabling targeted genetic modifications. By integrating advances in molecular biology and genomics, these approaches offer sustainable solutions to safeguard rice yields against evolving pathogens. Full article

Leaf rust (LR) is a devastating foliar disease that impacts common wheat (Triticum aestivum L.) globally. For optimal disease protection, wheat cultivars should possess adult plant resistance (APR) to leaf rust. In the current study, the objective was to map quantitative trait loci (QTL) related to leaf rust resistance. This was achieved by using 193 recombinant inbred line (RIL) populations which were developed from the cross between N. Strampelli and Huixianhong. Four trials were conducted in China (three in Baoding, Hebei province, and one in Zhoukou, Henan province) to assesses the leaf rust response of the RILs and parental lines. The wheat 660K SNP array and additional SSR markers were used to genotype the RIL populations. Through inclusive composite interval mapping (ICIM), three QTL related to leaf rust (LR) resistance were detected. ICIM was also employed to reevaluate previously published data in order to identify QTL with pleiotropic effects. To determine the physical positions, the flanking sequences of all SNP probes were compared against the Chinese Spring wheat reference sequence through BLAST searches. Three leaf rust resistance loci, two on chromosome 2A and 5B, were contributed by N. Strampelli. QLr.hbau-2AL.1 was detected in three leaf rust environments with phenotypic variance explained (PVE of 12.2–17%); QLr.hbau-2AL.2 was detected in two environments with 12.5–13.2% of the PVE; and QLr.hbau-5BL was detected in all leaf rust environments with phenotypic variance explained (PVE) of 17.8–19.1%. QLr.hbau-5BL exhibited potentially pleiotropic responses to multiple diseases. The QTL and the associated flanking markers discovered in this study could prove valuable for purposes such as fine mapping, the exploration of candidate genes, and marker-assisted selection (MAS). Full article

Rice blast disease is a major threat to rice yields. Sustainable control relies on resistant varieties, where plant immunity is triggered by pattern recognition receptors like receptor-like proteins (RLPs). The rice RLP chitin-elicitor binding protin (CEBiP) recognizes fungal chitin and confers blast resistance to pathogen Magnaporthe oryzae. However, understanding of the broader signaling and metabolomic pathways associated with CEBiP activation remains limited. Here, we performed an integrated transcriptomic and metabolomic analysis of the rice Zhonghua 11 genotype and CEBiP knockout plants. Both plants were infected with M. oryzae, and infected leaves were harvested at 24, 48, and 72 hpi for RNA sequencing and Liquid Chromatography-Tandem Mass Spectrometry analysis. Transcriptomics identified a total of 655 genes that were differentially regulated upon knockout of CEBiP; they were mainly related to diterpenoid/phenylpropanoid biosynthesis, nitrogen metabolism, the mitogen-activated protein kinasesignaling pathway, plant–pathogen interaction, and plant hormone signal transduction. The presence of a large number of pathogenesis-related protein 1 family genes indicates the key role of salicylic acid (SA) in CEBiP immunity. Metabolomics detected a total of 962 differentially accumulated metabolites and highlights the roles of caffeine and glutathione metabolism in CEBiP-mediated immunity. Since caffeine and glutathione metabolism can regulate SA signaling, we propose that SA signaling plays a central role in the CEBiP immune function. Full article

Brucella intermedia, a gram-negative, non-lactose-fermenting, aerobic, rod-shaped bacterium, is found in environmental sources (e.g., soil and water). In 2020, Ochrobactrum was reclassified as Brucella. We conducted a genomic analysis of B. intermedia from hospital wastewater samples in western Ghana. A hybrid genome assembly was constructed integrating short-read data from DNA Nanoball sequencing with long-read sequences generated by Oxford Nanopore MinION technology. Identification and antimicrobial susceptibility profiles were determined using MicroScan autoSCAN-4 based on Clinical and Laboratory Standard Institute documents. ResFinder and CARD Resistance Gene Identifier (RGI) were used to identify antimicrobial resistance (AMR) genes, and BLAST and VFDB datasets were used to identify virulence factor genes. The complete genome had two chromosomes, no plasmid, and a high average nucleotide identity value (98.05%) with B. intermedia. Resistance to trimethoprim-sulfamethoxazole was revealed, the first report in this species. CARD RGI revealed the presence of AMR genes, including ANT(9)-Ic and adeF. Local BLAST analysis revealed Cgs, a B. melitensis virulence factor. B. intermedia is an opportunistic human pathogen clinically isolated several times, suggesting the importance of accurately identifying multidrug resistance. B. intermedia may possess virulence factors similar to those of B. melitensis. Further study is needed to fully elucidate its pathogenesis. Full article

The virus-induced gene silencing (VIGS) technique can effectively inhibit systemic viral infection by down-regulating plant endogenous gene expression, and it has become an important tool to study plant gene function. However, few studies have reported that wheat dwarf virus (WDV), which enables high-throughput gene silencing, could be used in a rice VIGS system. In this study, a VIGS vector system was constructed based on WDV, and successfully silenced the Phytoene desaturase gene and the rice blast resistance gene Pi21 in rice. Pi21-silenced plants showed significantly increased resistance to rice blast, significantly reduced lesion area, and did not show high disease symptoms (grade 8–9). In addition, the WDV vector has the advantages of rapid infection, high proliferation, and an unconformity genome, and has little influence on rice growth and development. This study validates the effectiveness of the WDV-VIGS system in rice gene function studies and provides a new gene silencing tool for blast resistance breeding. Full article

Rice blast caused by the ascomycete fungus Magnaporthe oryzea is one of the most widespread and destructive rice diseases worldwide. The most economical and effective strategy for controlling rice blast is the rational use and promotion of disease-resistant varieties. To enhance disease resistance, it is essential to analyze the resistance levels of rice varieties and the role of resistance (R) genes. To investigate blast resistance, R gene distribution, and their contributions in japonica rice, 287 varieties were evaluated through artificial inoculation. PCR detection was also performed using specific primers for eleven R genes. The results showed that 24.4% of the varieties exhibited moderate resistance (MR), indicating an overall moderate resistance level. The frequency of R genes varied significantly: Pib was the most prevalent (89.2%), followed by Pi5 (73.5%), Pita (62.4%), Pia (54.4%), Pikh (48.4%), Pik (41.1%), Pi9 (35.5%), Pizt (23.7%), Pit (10.8%), and Pi1 (10.5%). No Pigm was detected. Among these, Pik, Pi9, Pizt, and Pita contributed most significantly to disease resistance, with contributions of 42.4%, 38.2%, 38.2%, and 33.5%, respectively. The number of R genes detected in the tested varieties ranged from 0 to 9, with most varieties containing more than three genes. The highest proportion of resistant varieties was observed in those carrying six genes. The most common R gene combinations in resistant varieties were ‘Pib + Pita + Pi5 + Pikh + Pik + Pi9’ and ‘Pizt + Pib + Pita + Pia + Pi5 + Pik + Pi9’. In conclusion, these findings provide valuable insights into the breeding and utilizing blast-resistant japonica rice varieties in Anhui Province. Full article

Although lactic acid bacteria (LABs) possess unique metabolic and physiological characteristics that have crucial effects on the transport of substances both into and out of the cell, there is still a lack of systematic research on membrane transporters in LABs and their roles in material transport. In this study, genomic data for the species Lactobacillus delbrueckii, Streptococcus thermophilus, Leuconostoc lactis, Pediococcus lactis, Lactococcus garvieae, and Bifidobacterium lactis were analyzed to identify the associated transport systems, including what kind of substances are transported. As part of a comparative genomics approach, we used the G-BLAST and AveHAS programs in the TCDB database to screen for transport proteins and clarify the distribution of these proteins in different Lactobacillus strains, allowing for further prediction of their transport substrates. Studies have shown that the distributions of these transporters differ among the selected LAB strains. Through screening and tabulation, we found that the content of transporters in the six LAB proteomes was greater than 20%, with the dominance of the large transporter group indicating complex metabolic and probiotic effects. Furthermore, it was found that the LAB strains contain a variety of homologs of drug-efflux proteins, which may make them resistant to antibiotics, as well as a large number of toxin-related transporters. This study allowed for reasonable predictions of the roles of toxin-related proteins in LABs, and further research on these proteins may be valuable for understanding the probiotic effects of LABs that arise through competition. The study of LAB transporters and the prediction of their functions might support a better understanding of the metabolic and physiological activities of these bacteria. In the future, we aim to extract DNA from laboratory strains and perform PCR amplification using suitable primers designed by us. Through comparison of the obtained gene sequences with those reported in this study, we can explore the differences among them. Full article

The avirulence (AVR) genes of the filamentous ascomycete fungus Magnaporthe oryzae (M. oryzae) are known to mutate rapidly under a higher selection pressure, allowing the pathogen to evade recognition by rice resistance (R) genes. Understanding the geographic distribution and natural variation of AVR genes is critical for the rational utilization and prolonging of the effectiveness of R genes. In this study, a total of 1060 M. oryzae strains collected from 19 rice blast nurseries in 13 provinces across southern China were subjected to presence/absence variation (PAV), genetic variation, and virulence analyses of the AVR-Pita1 gene. PCR amplification results indicated that AVR-Pita1 was present in only 57.45% of the blast strains, with significant geographic variation in distribution frequency. Specifically, the highest frequency (100%) was observed in strains from Chengmai, Hainan, while the lowest (1.79%) was observed in strains from Baoshan, Yunnan. A sequencing analysis identified 29 haplotypes of AVR-Pita1, characterized by insertions, deletions, and base substitutions. A phylogenetic analysis indicated that haplotypes of AVR-Pita1 identified in this study were clustered into one clade. A further amino acid sequence analysis of these haplotypes led to the identification of 25 protein variants. Notably, four haplotypes of AVR-Pita1 exhibited pathogenicity toward its corresponding rice R gene, PtrA. Additionally, we performed allele profiling of Ptr in a collection of elite parental lines that are widely used in rice breeding in southern China and found that the functional Ptr alleles (PtrA, PtrB, and PtrC) accounted for over 70%. Full article

The cultivation of jujube (Ziziphus jujuba) in China is threatened by jujube witches’ broom (JWB) disease, a devastating infectious disease associated with JWB phytoplasma (‘Candidatus Phytoplasma ziziphi’). In many plants, proteins in the Argonaute (AGO) family, as main components of the RNA-induced silencing complex (RISC), play important roles in RNA silencing and pathogen resistance. The jujube telomere-to-telomere genome was searched by BLAST using Arabidopsis AGOs as probes. A total of nine jujube AGO gene members were identified, with each containing the conserved N-terminal, PZA, and PIWI domains. Phylogenetic analysis revealed that the nine jujube AGOs scattered into all three Arabidopsis AGO clades. Expression patterns of the ZjAGO genes were analyzed in response to phytoplasma in transcriptome data and by qRT–PCR. The jujube–phytoplasma interaction altered the expression of jujube AGO genes. ZjAGO1 and ZjAGO8 were up-regulated in the majority of the eight sampling periods subjected to qRT–PCR analysis. In the transcriptome data, ZjAGO1 and ZjAGO8 were also up-regulated during the key stages 37 and 39 weeks after grafting (WAG) with phytoplasma-infected material. These two jujube Argonaute genes may play important roles in response to JWB phytoplasma infection. Full article