Subtractive proteomics-based vaccine targets annotation and reverse vaccinology approaches to identify multiepitope vaccine against Plesiomonas shigelloides.

Plesiomonas shigelloides, an aquatic bacterium belonging to the Enterobacteriaceae family, is a frequent cause of gastroenteritis with diarrhea and gastrointestinal severe disease. Despite decades of research, discovering a licensed and globally accessible vaccine is still years away. Developing a putative vaccine that can combat the Plesiomonas shigelloides infection by boosting population immunity against P. shigelloides is direly needed. In the framework of the current study, the entire proteome of P. shigelloides was explored using subtractive genomics integrated with the immunoinformatics approach for designing an effective vaccine construct against P. shigelloides. The overall stability of the vaccine construct was evaluated using molecular docking, which demonstrated that MEV showed higher binding affinities with toll-like receptors (TLR4: 51.5 ± 10.3, TLR2: 60.5 ± 9.2) and MHC receptors(MHCI: 79.7 ± 11.2 kcal/mol, MHCII: 70.4 ± 23.7). Further, the therapeutic efficacy of the vaccine construct for generating an efficient immune response was evaluated by computational immunological simulation. Finally, computer-based cloning and improvement in codon composition without altering amino acid sequence led to the development of a proposed vaccine. In a nutshell, the findings of this study add to the existing knowledge about the pathogenesis of this infection. The schemed MEV can be a possible prophylactic agent for individuals infected with P. shigelloides. Nevertheless, further authentication is required to guarantee its safeness and immunogenic potential.

Genome-based reclassification of Picrophilus torridus Zillig et al. 1996 as a later heterotypic synonym of Picrophilus oshimae Schleper et al. 1996.

In the present study, we attempt to clarify the taxonomic positions of Picrophilus oshimae and Picrophilus torridus. The 16S rRNA gene sequence similarity between P. oshimae DSM 9789T and P. torridus DSM9790T (99.4 %) was above the threshold value (98.6 %) for bacterial species delineation. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between P. oshimae DSM 9789T and P. torridus DSM9790T were higher than the threshold values (95-96 % for ANI and 70 % for dDDH) for bacterial species delineation. The present results indicate that Picrophilus torridus Zillig et al. 1996 is a later heterotypic synonym of Picrophilus oshimae Schleper et al. 1996.

Sphingosinicella terrae sp. nov. Isolated from a Desert Soil and Reclassification of Sphingomonas deserti as Sphingosinicella deserti comb. nov.

A motile, rod-shaped and yellow-coloured bacterium, designated strain SYSU D60001T, was isolated from a desert soil sample. Cells were Gram-stain-negative, catalase-negative and oxidase-positive. The major cellular fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0. The respiratory quinone was ubiquinone-10. The genomic DNA G+C content was 68%. The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and five unidentified polar lipids. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SYSU D60001T represents a novel species of the genus Sphingosinicella, with closely related strains Sphingosinicella ginsenosidimutans BS1T (95.81%), Sphingomonas deserti GL-C-18T (95.75%) and Sphingosinicella humi QZX222T (95.18%). Data from polyphasic taxonomy study suggest that the isolate represents a novel species in the genus Sphingosinicella, for which the name Sphingosinicella terrae sp. nov. is proposed. The type strain of the proposed new taxon is SYSU D60001T (= DSM 104938T = KCTC 52780T = NBRC 112955T). We also propose the reclassification of Sphingomonas deserti as Sphingosinicella deserti comb. nov.

Genome-based reclassification of Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii as later heterotypic synonyms of Caldicellulosiruptor acetigenus.

The present study was carried out to re-clarify the taxonomic relationship of Caldicellulosiruptor acetigenus, Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii. The 16S rRNA sequence similarities between these species of the genus Caldicellulosiruptor were above the threshold values (98.65%) for bacterial species delineation. Similarly, the digital DNA-DNA hybridization and average nucleotide and amino acid identity values were greater than the thresholds for bacterial species delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees Caldicellulosiruptor acetigenus, Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii clade together. The results of our analysis indicated that these three taxa are conspecific. Therefore, Caldicellulosiruptor lactoaceticus Mladenovska et al. 1997 and Caldicellulosiruptor kristjanssonii Bredholt et al. 1999 should be reclassified as later heterotypic synonyms of Caldicellulosiruptor acetigenus (Nielsen et al. 1994) Onyenwoke et al. 2006.

CRISPR-Cas technology based genome editing for modification of salinity stress tolerance responses in rice (Oryza sativa L.).

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) technology is an effective tool for site-specific genome editing, used to precisely induce mutagenesis in different plant species including rice. Salinity is one of the most stressful environmental constraints affecting agricultural productivity worldwide. As plant adaptation to salinity stress is under polygenic control therefore, 51 rice genes have been identified that play crucial role in response to salinity. This review offers an exclusive overview of genes identified in rice genome for salinity stress tolerance. This will provide an idea to produce rice varieties with enhanced salt tolerance using the potentially efficient CRISPR-Cas technology. Several undesirable off-target effects of CRISPR-Cas technology and their possible solutions have also been highlighted.

Exploring threatened traditional knowledge; ethnomedicinal studies of rare endemic flora from Lesser Himalayan region of Pakistan

ABSTRACT Himalayas are one among the world biodiversity hotspots harboring many endemic medicinal plants. Despite augmentation in the documentation of ethnopharmacological knowledge of medicinal plant species, information regarding endemic species is still underway. Current paper highlights the traditional medicinal uses of rare endemic and unexplored group of plants having potential for novel chemical constituents with effective pharmacological activities. In total, 142 informants (91 male and 51 female) including seventeen traditional healers were interviewed using semi-structured questionnaire, personal observations and group discussions. Interviews were taken in field or otherwise photographs were shown for identification. Females were interviewed indirectly through male family members. For data analysis, quantitative analytical approach was adopted using ethnopharmacological indices as Relative frequency of citations and Fidelity Level. In total, 38 endemic plant species belonging to nineteen families were utilized by the local inhabitants. Highest number of endemics was belonging to Ranunculaceae (7), followed by Gentianaceae and Rosaceae (4 each) with respect to number of species. Highest number of endemics was used in fever, wound healing, throat infection and tonic (4 species each). Root was the most widely used part (36.17%) in cure of diseases and the leading mode administered was decoction (25.49%). Highest use reports and RFC values were recorded for Pimpinella stewartii (58 citations, 0.41 RFC), Caltha alba var. alba (52 citations, 0.37 RFC). Endemic plant species considerably contribute toward ethnomedicinal knowledge and despite rarity, the communities prefer their utilization. Conservation of endemics is necessary for future availability to the local communities.

Solvent polarity mediates phytochemical yield and antioxidant capacity of Isatis tinctoria.

Secondary metabolites have been extensively used in the treatment of various health problems. The role of solvent polarity on the phytochemical isolation and antioxidant capacity of Isatis tinctoria (woad) is elusive. In the present study, 14 solvents with different polarity were used in the extraction and total phenolic and flavonoid content (TPC and TFC) investigation. Ferricyanide, phosphomolybdenum, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) methods were used to calculate and compare the antioxidant/free radical scavenging capacity. Our results showed that solvent polarity greatly affects TPC and TFC yield, which is mainly increasing with increasing solvent polarity index and suddenly decreasing at very high polarity. The comparative results showed that TPC is directly correlated with reducing power, antioxidant, and free radical scavenging capacity. Taken together, we conclude that different woad plant parts contain different level of secondary metabolites with a specific polarity that requires a particular solvent with an appropriate polarity index for the extraction. The identification of these biologically active crude extracts and fractions are very important for the basic biological sciences, pharmaceutical applications, and future research for HPLC based active compounds isolation.

Anticancer Plants: A Review of the Active Phytochemicals, Applications in Animal Models, and Regulatory Aspects.

The rising burden of cancer worldwide calls for an alternative treatment solution. Herbal medicine provides a very feasible alternative to western medicine against cancer. This article reviews the selected plant species with active phytochemicals, the animal models used for these studies, and their regulatory aspects. This study is based on a meticulous literature review conducted through the search of relevant keywords in databases, Web of Science, Scopus, PubMed, and Google Scholar. Twenty plants were selected based on defined selection criteria for their potent anticancer compounds. The detailed analysis of the research studies revealed that plants play an indispensable role in fighting different cancers such as breast, stomach, oral, colon, lung, hepatic, cervical, and blood cancer cell lines. The in vitro studies showed cancer cell inhibition through DNA damage and activation of apoptosis-inducing enzymes by the secondary metabolites in the plant extracts. Studies that reported in vivo activities of these plants showed remarkable results in the inhibition of cancer in animal models. Further studies should be performed on exploring more plants, their active compounds, and the mechanism of anticancer actions for use as standard herbal medicine.

An Era of CRISPR/ Cas9 Mediated Plant Genome Editing.

Recently the engineered nucleases have revolutionized genome editing to perturb gene expression at specific sites in complex eukaryotic genomes. Three important classes of these genome editing tools are Moreover, the more recent type II Clustered Regularly Inter-spaced Short Palindromic Repeats/Crispr associated protein (CRISPR/Cas9) system has become the most favorite plant genome editing tool for its precision and RNA based specificity unlike its counterparts which rely on protein based specificity. Plasmid-mediated co-delivery of multiple sgRNAs and Cas9 to the Plant cell can simultaneously alter more than one target loci which enable multiplex genome editing. In this review, we discuss recent advancements in the CRISPR/ Cas9 technology mechanism, theory and its applications in plants and agriculture. We also suggest that the CRISPR/ Cas9 as an effective genome editing tool, has vast potential for crop improvement and studying gene regulation mechanism and chromatin remodeling.

Exploring Durable Genetic Resistance against Leaf Rust through Phenotypic Characterization and Lr34Linked STS Marker in Wheat Germplasm / Explorando a resistência genética duradoura contra a ferrugem da folha através da caracterização fenotípica e do STS marker relacionado ao (GENE) LR34 do germoplasma do trigo

Present study was aimed to screening the population of 25 wheat genotypes from Baluchistan region of Pakistan along with five commercial cultivars for leaf rust adult plant resistance (APR) through gene postulation using natural inoculation of Puccinia triticina Erikss local pathotype. Infection severity was recorded on scale in comparison with susceptible control "Morroco" cultivar. On the basis of phenotypic score, seven accessions and four varieties (Zardana-89, Sariab-92, Zarlashta-99 and Raskoh-05) with AUDPC values up to 20% were characterized as resistant genotypes. Coefficient of infection (CI) score ranged from 0-10 for some accessions and cultivars showing high level of adult plant resistance. Furthermore, bi-allelic STS marker csLV34 having close linkage with Lr34 (0.4cM). This marker amplified one gene specific allele of 150bp in 21 genotypes, including 19 accessions and two commercial varieties (Sariab-92 and Zarghoon-79) which confirmed presence of Lr34 gene conferring adult plant resistance against leaf rust. The rust pathogenicity scale varied for accessions from resistant to moderately susceptible. However, beside Lr34, phenotypic gene postulation, in combination with marker assisted selection for leaf rust resistance, has revealed presence of some other unknown resistance genes in local wheat germplasm which signified its use in wheat improvement programs both locally and abroad.

O presente estudo teve como objetivo a triagem da população de 25 genótipos de trigo do Baluchistão, região do Paquistão, juntamente com cinco cultivares comerciais para o estudo da resistência à ferrugem da folha em plantas adultas (leaf rust adult plant resistance, APR, em inglês) através da postulação gênica usando a inoculação natural do patótipo local da Puccinia triticina Erikks. A gravidade da infecção foi registrada na escala em comparação ao cultivar de controle suscetível "Morroco". Com base na pontuação fenotípica, sete acessões e quatro variedades (Zardana-89, Sariab-92, Zarlashta-99 and Raskoh-05) com valores de AUDPC (area under the disease progress curve, em inglês) até 20% foram caracterizados como genótipos resistentes. A pontuação do coeficiente de infecção (CI) variou no intervalo de 0-10 para algumas acessões e cultivares evidenciando uma elevada resistência nas plantas adultas. Além disso, o STS marker para o csLV34 bi-alélico demonstrou uma ligação estreita com o Lr34 (0.4cM). Este marcador amplificou um alelo específico do gene do 150bp em 21 genótipos, incluindo 19 acessões e duas variedades comerciais (Sariab-92 and Zarghoon-79) o que confirmou a presença do gene Lr34 conferindo resistência às plantas adultas contra a ferrugem da folha. A escala de patogenicidade da ferrugem para as acessões de resistente a moderadamente suscetível. Contudo, além do Lr34, a postulação gênica fenotípica, em combinação com a seleção auxiliada (ou assistida) por marcadores para a resistência da ferrugem da folha, revelou a presença de outros genes resistentes desconhecidos no germoplasma do trigo local o que justifica a sua utilização em programas de melhoramento do trigo tanto a nível local quanto a nível internacional.