Browsing by Author "Ahmed I"

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    Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential.
    (Springer Nature Limited, 2023-06-20) Sattar S; Bailie M; Yaqoob A; Khanum S; Fatima K; Altaf AURB; Ahmed I; Shah STA; Munawar J; Zehra QA; Daud S; Arshad A; Imdad K; Javed S; Tariq A; Bostan N; Altermann E
    Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.
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    Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia
    (John Wiley and Sons Ltd, 2020-12) Ahmed I; Lockhart PJ; Agoo EMG; Naing KW; Nguyen DV; Medhi DK; Matthews PJ
    As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).
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    Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae.
    (MDPI (Basel, Switzerland), 2022-01-25) Sattar S; Ullah I; Khanum S; Bailie M; Shamsi B; Ahmed I; Abbas Shah T; Javed S; Ghafoor A; Pervaiz A; Sohail F; Imdad K; Tariq A; Bostan N; Ali I; Altermann E; Griffiths M; Anany H
    Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.
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    Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes.
    (Springer Nature Limited, 2022-04-06) Sattar S; Ullah I; Khanum S; Bailie M; Shamsi B; Ahmed I; Shah STA; Javed S; Ghafoor A; Pervaiz A; Sohail F; Shah NA; Imdad K; Bostan N; Altermann E
    Salmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.
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    Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV.
    (AMER PHYSICAL SOC, 9/07/2010) Khachatryan V; Sirunyan AM; Tumasyan A; Adam W; Bergauer T; Dragicevic M; Erö J; Fabjan C; Friedl M; Frühwirth R; Ghete VM; Hammer J; Hänsel S; Hoch M; Hörmann N; Hrubec J; Jeitler M; Kasieczka G; Kiesenhofer W; Krammer M; Liko D; Mikulec I; Pernicka M; Rohringer H; Schöfbeck R; Strauss J; Taurok A; Teischinger F; Waltenberger W; Walzel G; Widl E; Wulz C-E; Mossolov V; Shumeiko N; Suarez Gonzalez J; Benucci L; Ceard L; De Wolf EA; Hashemi M; Janssen X; Maes T; Mucibello L; Ochesanu S; Roland B; Rougny R; Selvaggi M; Van Haevermaet H; Van Mechelen P; Van Remortel N; Adler V; Beauceron S; Blyweert S; D'Hondt J; Devroede O; Kalogeropoulos A; Maes J; Maes M; Tavernier S; Van Doninck W; Van Mulders P; Villella I; Chabert EC; Charaf O; Clerbaux B; De Lentdecker G; Dero V; Gay APR; Hammad GH; Marage PE; Vander Velde C; Vanlaer P; Wickens J; Costantini S; Grunewald M; Klein B; Marinov A; Ryckbosch D; Thyssen F; Tytgat M; Vanelderen L; Verwilligen P; Walsh S; 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CMS Collaboration
    Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.
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    Yeast as a Model to Understand Actin-Mediated Cellular Functions in Mammals-Illustrated with Four Actin Cytoskeleton Proteins
    (MDPI (Basel, Switzerland), 2020-03-10) Akram Z; Ahmed I; Mack H; Kaur R; Silva RC; Castilho BA; Friant S; Sattlegger E; Munn AL
    The budding yeast Saccharomyces cerevisiae has an actin cytoskeleton that comprises a set of protein components analogous to those found in the actin cytoskeletons of higher eukaryotes. Furthermore, the actin cytoskeletons of S. cerevisiae and of higher eukaryotes have some similar physiological roles. The genetic tractability of budding yeast and the availability of a stable haploid cell type facilitates the application of molecular genetic approaches to assign functions to the various actin cytoskeleton components. This has provided information that is in general complementary to that provided by studies of the equivalent proteins of higher eukaryotes and hence has enabled a more complete view of the role of these proteins. Several human functional homologues of yeast actin effectors are implicated in diseases. A better understanding of the molecular mechanisms underpinning the functions of these proteins is critical to develop improved therapeutic strategies. In this article we chose as examples four evolutionarily conserved proteins that associate with the actin cytoskeleton: 1) yeast Hof1p/mammalian PSTPIP1, 2) yeast Rvs167p/mammalian BIN1, 3) yeast eEF1A/eEF1A1 and eEF1A2 and 4) yeast Yih1p/mammalian IMPACT. We compare the knowledge on the functions of these actin cytoskeleton-associated proteins that has arisen from studies of their homologues in yeast with information that has been obtained from in vivo studies using live animals or in vitro studies using cultured animal cell lines.