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21.
Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) encodes a functional type II restriction-modification (R-M) system designated PamI. Homologous systems were identified in the genomes of distinct taxonomic groups of Bacteria and Archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of R-M modules - even between domains. Analysis of the cleavage specificity of the R.PamI endonuclease revealed that this protein is an isoschizomer of restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest that R.PamI and NcoI are accompanied by methyltransferases of different methylation specificities (C5-methylcytosine and N4-methylcytosine methyltransferases, respectively), which possibly exemplifies recombinational shuffling of genes coding for individual components of R-M systems. The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level. Therefore, it functions in an analogous manner to plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of pAMI7 is nonfunctional, it is highly probable that this lack is compensated by the stabilizing activity of PamI. This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria. 相似文献
22.
Aysha H Khan Muniba Aban Jamal Raza Naeem ul Haq Abdul Jabbar Tariq Moatter 《BMC endocrine disorders》2011,11(1):1-6
Background
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH.Methods
A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay.Results
Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females representing all the major ethnic groups of Pakistan. Parental consanguinity was reported in 65% cases and was equally distributed in the major ethnic groups. Among 58 chromosomes analyzed, mutations were identified in 45 (78.6%) chromosomes. The most frequent mutation was I2 splice (27%) followed by Ile173Asn (26%), Arg 357 Trp (19%), Gln319stop, 16% and Leu308InsT (12%), whereas Val282Leu was not observed in this study. Homozygosity was seen in 44% and heterozygosity in 34% cases. I2 splice mutation was found to be associated with SW in the homozygous. The Ile173Asn mutation was identified in both SW and SV forms. Moreover, Arg357Trp manifested SW in compound heterozygous state.Conclusion
Our study showed that CAH exists in our population with ethnic difference in the prevalence of mutations examined. 相似文献23.
Gagui S. Meradji H. Ghemid S. Naeem S. Haq Bakhtiar Ul Ahmed R. Kushwaha A. K. 《Journal of molecular modeling》2023,29(1):1-13
Journal of Molecular Modeling - The recent advances in the application of machine learning to drug discovery have made it a ‘hot topic’ for research, with hundreds of academic groups... 相似文献
24.
Ibrar Ahmed Peter J. Matthews Patrick J. Biggs Muhammad Naeem Patricia A. McLenachan Peter J. Lockhart 《Molecular ecology resources》2013,13(5):929-937
Recently, we reported the chloroplast genome‐wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra‐specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra‐specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high‐resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups. 相似文献
25.
Tauqeer Ahmad Yasir Sobia Aslam Muhammad Shahid Rizwan Allah Wasaya Muhammad Ateeq Muhammad Naeem Khan Sikander Khan Tanveer Walid Soufan Basharat Ali Allah Ditta Arpna Kumari Ayman EL Sabagh 《Phyton》2022,91(11):2491-2504
In soil biota, higher and enduring concentration of heavy metals like cadmium (Cd) is hazardous and associated
with great loss in growth, yield, and quality parameters of most of the crop plants. Recently, in-situ applications of
eco-friendly stabilizing agents in the form of organic modifications have been utilized to mitigate the adverse
effects of Cd-toxicity. This controlled experiment was laid down to appraise the imprints of various applied
organic amendments namely poultry manure (PM), farmyard manure (FYM), and sugarcane press mud (PS)
to immobilize Cd in polluted soil. Moreover, phytoavailability of Cd in wheat was also accessed under an alkaline
environment. Results revealed that the addition of FYM (5–10 ton ha-1
) in Cd-contaminated soil significantly
increased germination rate, leaf chlorophyll content, plant height, spike length, biological and grain yield amongst
all applied organic amendments. Moreover, the addition of FYM (5–10 ton ha-1
) also reduced the phytoavailability of Cd by 73–85% in the roots, 57–83% in the shoots, and 81–90% in grains of wheat crop. Thus, it is affirmed
that incorporation of FYM (5–10 ton ha-1
) performed better to enhance wheat growth and yield by remediating
Cd. Thus, the application of FYM (5–10 ton ha-1
) reduced the toxicity induced by Cd to plants by declining its
uptake and translocation as compared to all other applied organic amendments to immobilize Cd under sandy
alkaline polluted soil. 相似文献
26.
Saghir Abbas Muhammad Tariq Javed Qasim Ali Muhammad Sohail Akram Kashif Tanwir Shafaqat Ali Hassan Javed Chaudhary Naeem Iqbal 《Physiology and Molecular Biology of Plants》2021,27(2):297
Cadmium (Cd) in soil–plant system can abridge plant growth by initiating alterations in root zones. Hydroponics and rhizoboxes are useful techniques to monitor plant responses against various natural and/or induced metal stresses. However, soil based studies are considered more appropriate in order to devise efficient food safety and remediation strategies. The present research evaluated the Cd-mediated variations in elemental dynamics of rhizospheric soil together with in planta ionomics and morpho-physio-biochemical traits of two differentially Cd responsive maize cultivars. Cd-sensitive (31P41) and Cd-tolerant (3062) cultivars were grown in pots filled with 0, 20, 40, 60 and 80 µg/kg CdCl2 supplemented soil. The results depicted that the maize cultivars significantly influenced the elemental dynamics of rhizosphere as well as in planta mineral accumulation under applied Cd stress. The uptake and translocation of N, P, K, Ca, Mg, Zn and Fe from rhizosphere and root cell sap was significantly higher in Cd stressed cv. 3062 as compared to cv. 31P41. In sensitive cultivar (31P41), Cd toxicity resulted in significantly prominent reduction of biomass, leaf area, chlorophyll, carotenoids, protein contents as well as catalase activity in comparison to tolerant one (3062). Analysis of tolerance indexes (TIs) validated that cv. 3062 exhibited advantageous growth and efficient Cd tolerance due to elevated proline, phenolics and activity of antioxidative machinery as compared to cv. 31P41. The cv. 3062 exhibited 54% and 37% less Cd bio-concentration (BCF) and translocation factors (TF), respectively in comparison to cv. 31P41 under highest Cd stress regime. Lower BCF and TF designated a higher Cd stabilization by tolerant cultivar (3062) in rhizospheric zone and its potential use in future remediation plans. 相似文献
27.
A Gram-negative bacterium was previously isolated from an oil field in Shizuoka, Japan, and designated strain HD-1. Here we have performed detailed characterization of the strain, and have found that it represents a novel genus. The 16S rRNA sequence of strain HD-1 displayed highest similarity to various uncultured species (86.7-99.7%), along with 86.2-88.2% similarity to sequences from Azospirillum, Methylobacterium, Rhizobium, and Hyphomicrobium, all members of the alpha-Proteobacteria. Phylogenetic analysis revealed that HD-1 represented a deep-branched lineage among the alpha-Proteobacteria. DNA-DNA hybridization analysis with Azospirillum lipoferum and Hyphomicrobium vulgare revealed low levels of similarity among the strains. We further examined the biochemical properties of the strain under aerobic conditions. Among carbon sources, ethanol, n-propanol, n-butanol, and n-tetradecanol were the most preferred, while acetate, propionate, and pyruvate also supported high levels of growth. The strain could also grow on aromatic compounds such as toluene, benzene and phenol, and aliphatic hydrocarbons such as n-octane and n-tetradecane. In contrast, glycerol and various sugars, including glucose, fructose, maltose, and lactose, failed to support growth of HD-1. Under an anaerobic gas phase with butanol as the carbon source, little increase in cell weight was observed with the addition of several possible electron acceptors. As strain HD-1 represents a novel genus in the alpha-Proteobacteria, we designated the strain as Oleomonas sagaranensis gen. nov., sp. nov., strain HD-1. 相似文献
28.
Frédérique Le Roux Yannick Labreuche Brigid M. Davis Naeem Iqbal Sophie Mangenot Cyrille Goarant Didier Mazel Matthew K. Waldor 《Environmental microbiology》2011,13(2):296-306
Vibrioses are the predominant bacterial infections in marine shrimp farms. Vibrio nigripulchritudo is an emerging pathogen of the cultured shrimp Litopenaeus stylirostris in New Caledonia and other regions in the Indo‐Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have revealed that recent pathogenic V. nigripulchritudo isolates from New Caledonia all cluster into a monophyletic clade and contain a small plasmid, pB1067. Here, we report that a large plasmid, pA1066 (247 kb), can also serve as a marker for virulent V. nigripulchritudo, and that an ancestral version of this plasmid was likely acquired prior to other virulence‐linked markers. Additionally, we demonstrate that pA1066 is critical for the full virulence of V. nigripulchritudo in several newly developed experimental models of infection. Plasmid pB1067 also contributes to virulence; only strains containing both plasmids induced the highest level of shrimp mortality. Thus, it appears that these plasmids, which are absent from non‐pathogenic isolates, may be driving forces, as well as markers, for the emergence of a pathogenic lineage of V. nigripulchritudo. 相似文献
29.
Protoplasma - Recently, a promising technique has come forward in field of radiation-agriculture in which the natural polysaccharides are modified into useful oligomers after depolymerization.... 相似文献
30.
Muhammad Waseem Abbasi Naeem Ahmed Muhammad Javed Zaki S. Shahid Shuakat D. Khan 《Plant and Soil》2014,375(1-2):159-173