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author:("Ullah, hsan")
1.  Draft Genome Sequence and Annotation of the Insect Pathogenic Bacterium Xenorhabdus nematophila Strain C2-3, Isolated from Nematode Steinernema carpocapsae in the Republic of Korea 
Genome Announcements  2015;3(1):e01521-14.
Xenorhabdus nematophila strain C2-3, which belongs to the family Enterobacteriaceae, was isolated from entomopathogenic nematodes collected in the Republic of Korea. Herein, we report a 4.38-Mbp draft genome sequence of X. nematophila strain C2-3, with a 43.6% G+C content. The RAST annotation analysis revealed 4,994 protein-coding sequences in the draft genome.
doi:10.1128/genomeA.01521-14
PMCID: PMC4333654  PMID: 25676754
2.  Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste 
Genome Announcements  2014;2(6):e01237-14.
Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes.
doi:10.1128/genomeA.01237-14
PMCID: PMC4246171  PMID: 25428979
3.  Identification and Characterization of the Insecticidal Toxin “Makes Caterpillars Floppy” in Photorhabdus temperata M1021 Using a Cosmid Library 
Toxins  2014;6(7):2024-2040.
Photorhabdus temperata is an entomopathogenic enterobacterium; it is a nematode symbiont that possesses pathogenicity islands involved in insect virulence. Herein, we constructed a P. temperata M1021 cosmid library in Escherichia coli XL1-Blue MRF` and obtained 7.14 × 105 clones. However, only 1020 physiologically active clones were screened for insect virulence factors by injection of each E. coli cosmid clone into Galleria mellonella and Tenebrio molitor larvae. A single cosmid clone, PtC1015, was consequently selected due to its characteristic virulent properties, e.g., loss of body turgor followed by death of larvae when the clone was injected into the hemocoel. The sequence alignment against the available sequences in Swiss-Prot and NCBI databases, confirmed the presence of the mcf gene homolog in the genome of P. temperata M1021 showing 85% homology and 98% query coverage with the P. luminescens counterpart. Furthermore, a 2932 amino acid long Mcf protein revealed limited similarity with three protein domains. The N-terminus of the Mcf encompassed consensus sequence for a BH3 domain, the central region revealed similarity to toxin B, and the C-terminus of Mcf revealed similarity to the bacterial export domain of ApxIVA, an RTX-like toxin. In short, the Mcf toxin is likely to play a role in the elimination of insect pests, making it a promising model for use in the agricultural field.
doi:10.3390/toxins6072024
PMCID: PMC4113739  PMID: 25014195
insecticidal toxin; Galleria mellonella; makes caterpillar floppy; Photorhabdus temperata; Tenebrio molitor
4.  Ethnomedicine use in the war affected region of northwest Pakistan 
Background
North-West of Pakistan is bestowed with medicinal plant resources due to diverse geographical and habitat conditions. The traditional use of plants for curing various diseases forms an important part of the region’s cultural heritage. The study was carried out to document medicinal plants used in Frontier Region (FR) Bannu, an area affected by the “War on Terror”.
Methods
Fieldwork was carried out in four different seasons (spring, autumn, summer and winter) from March 2012 to February 2013. Data on medicinal plants was collected using structured and semi-structured questionnaires from 250 respondents. The voucher specimens were collected, processed and identified following standard methods.
Results
Of the 107 species of ethnomedicinal plants reported, fifty percent species are herbaceous. The majority of the reported species were wild (55%) but a substantial proportion are cultivated (29%). For most of the plant species (34%), leaves are the most commonly used part in the preparation of ethnomedicines. The most common use of species is for carminative purposes (14 species), with the next most common use being for blood purification (11 species). The main methods used in the preparation of ethnomedicinal recipes involves grinding and boiling, and nearly all the remedies are taken orally along with ingredients such as water, milk or honey for ease of ingestion. Traditional healers prepare plant remedies using one or more plants. There was a significant correlation (r2 = 0.95) between the age of local people and the number of plants known to them, which indicates that in the coming 20 years, an approximate decrease of 75% in the indigenous knowledge may be expected.
Conclusion
Traditional medicines are important to the livelihoods of rural communities in the region affected by the Global war on Terrorism. The medicinal recipes are indigenous; however, there is a threat to their future use on account of rapid modernization and terrorist activities. Documentation of medicinal plants and recipes may help in the conservation of the regional indigenous medicinal knowledge for future generations and to provide a baseline for further studies.
doi:10.1186/1746-4269-10-16
PMCID: PMC3932995  PMID: 24484608
Indigenous knowledge; Traditional medicines; Medicinal plants; Diseases
5.  Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA 
PLoS ONE  2013;8(12):e84620.
Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-2′-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5-HmdC, 5-formyl-2′-deoxycytidine (5-FodC), 5-carboxyl-2′-deoxycytidine (5-CadC), 5-hydroxymethyl-2′-deoxyuridine (5-HmdU), and the (5′S) diastereomer of 8,5′-cyclo-2′-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tet-family dioxygenase enzymes in Arabidopsis.
doi:10.1371/journal.pone.0084620
PMCID: PMC3877350  PMID: 24391970
6.  Draft Genome Sequence of Entomopathogenic Bacterium Photorhabdus temperata Strain M1021, Isolated from Nematodes 
Genome Announcements  2013;1(5):e00747-13.
Photorhabdus temperata strain M1021 is an entomopathogenic bacterium belonging to the family Enterobacteriaceae and is symbiotically associated with nematodes. The draft genome sequence of P. temperata strain M1021 consists of 5,598,253 bp with a G+C content of 43.7%, and it has 6,120 protein-coding genes.
doi:10.1128/genomeA.00747-13
PMCID: PMC3772151  PMID: 24029767
7.  Eco-geographically divergent diploids, Caucasian clover (Trifolium ambiguum) and western clover (T. occidentale), retain most requirements for hybridization 
Annals of Botany  2011;108(7):1269-1277.
Background and Aims
DNA sequence similarities and hybridization patterns in Trifolium (clovers) section Trifoliastrum suggest that rapid radiation from a common ancestral source led to this complex of diverse species distributed across Europe, western Asia and North Africa. Two of the most geographically and ecologically divergent of these species are the rhizomatous T. ambiguum from high altitudes in eastern Europe and western Asia and the stoloniferous T. occidentale from sea level in western Europe. Attempts were made to hybridize these species to ascertain whether, despite this separation, gene flow could be achieved, indicating the retention of the genetic factors necessary for hybridization.
Methods
Three F1 hybrids formed after embryo rescue were described, characterized by conventional and molecular cytogenetics, subjected to fertility tests and progeny generations were developed.
Results and Conclusions
Partially fertile hybrids between Trifolium ambiguum and T. occidentale were obtained for the first time. The F1 hybrids produced seeds after open-pollination, and also produced triploid progeny in backcrosses to T. occidentale from the functioning of unreduced gametes in the hybrids. These plants were fertile and produced progeny with T. occidentale and with T. repens. Meiotic chromosome pairing in the F1 showed six to eight bivalents per pollen mother cell, indicating pairing between the parental genomes. A chromosome-doubled form of one hybrid, produced using colchicine, showed some multivalents, indicative of interspecific chromosome pairing. The hybrid plants were robust and combined phenotypic characteristics of both species, having stolons, thick roots and a few rhizomes. Results show that despite separation by the entire breadth of Europe, the speciation process is incomplete, and these taxa have partially retained most of the genetic compatibilities needed for hybridization (possibly except for endosperm development, which was not tested). The fertile progeny populations could lead to new clover breeding strategies based on new hybrid forms.
doi:10.1093/aob/mcr226
PMCID: PMC3197454  PMID: 21880661
Trifolium ambiguum; T. occidentale; T. repens; interspecific hybridization; Caucasian clover; western clover; white clover; introgression; genetic bridge; unreduced gametes; speciation

Results 1-7 (7)