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author:("Ullah, ilsan")
1.  Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes 
Journal of Experimental Botany  2015;66(21):6651-6663.
Highlight
We studied the genome-wide distribution characteristics of 5-Hydroxymethylcytosine (5hmC) modification in young panicles of a superhybrid rice combination.
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
doi:10.1093/jxb/erv372
PMCID: PMC4715260  PMID: 26272901
5-hydroxymethylcytosine; 5hmC profiles; heterochromatin; rice; transposable element.
2.  Mitochondrial damage contributes to Pseudomonas aeruginosa activation of the inflammasome and is downregulated by autophagy 
Autophagy  2015;11(1):166-182.
The nucleotide-binding domain, leucine-rich repeat containing family caspase recruitment domain containing 4 (NLRC4) inflammasome can be activated by pathogenic bacteria via products translocated through the microbial type III secretion apparatus (T3SS). Recent work has shown that activation of the NLRP3 inflammasome is downregulated by autophagy, but the influence of autophagy on NLRC4 activation is unclear. We set out to determine how autophagy might influence this process, using the bacterium Pseudomonas aeruginosa, which activates the NLRC4 inflammasome via its T3SS. Infection resulted in T3SS-dependent mitochondrial damage with increased production of reactive oxygen intermediates and release of mitochondrial DNA. Inhibiting mitochondrial reactive oxygen release or degrading intracellular mitochondrial DNA abrogated NLRC4 inflammasome activation. Moreover, macrophages lacking mitochondria failed to activate NLRC4 following infection. Removal of damaged mitochondria by autophagy significantly attenuated NLRC4 inflammasome activation. Mitochondrial DNA bound specifically to NLRC4 immunoprecipitates and transfection of mitochondrial DNA directly activated the NLRC4 inflammasome; oxidation of the DNA enhanced this effect. Manipulation of autophagy altered the degree of inflammasome activation and inflammation in an in vivo model of P. aeruginosa infection. Our results reveal a novel mechanism contributing to NLRC4 activation by P. aeruginosa via mitochondrial damage and release of mitochondrial DNA triggered by the bacterial T3SS that is downregulated by autophagy.
doi:10.4161/15548627.2014.981915
PMCID: PMC4502769  PMID: 25700738
DNA detection; infection; mitophagy; NLR proteins; type III secretion system; Three-MA, 3-methyladenine; AIM2, absent in melanoma 2; ATG, autophagy related; ATPIF1, ATPase inhibitory factor 1; BID, BH3 interacting domain death agonist; BMDM, bone marrow-derived macrophages; BrdU, 5-bromo-2-deoxyuridine; CASP, caspase; GFP, green fluorescent protein; IL1B, interleukin 1, β; LC3B, microtubule-associated protein 1 light chain 3 β; LDH, lactate dehydrogenase; LPS, lipopolysaccharide; Mito-TEMPO, (2-(2, 2, 6, 6-tetramethylpiperidin-1-oxyl-4-ylamino)-2-oxoethyl)triphenylphosphonium chloride; MT-CO1, mitochondrially encoded cytochrome c oxidase I; mtDNA, mitochondrial DNA; NAC, N-acetylcysteine; NAIP, NLR family apoptosis inhibitor; NGS, normal goat serum; NLR, nucleotide-binding domain, leucine-rich repeat containing; NLRC4, NLR family, CARD domain containing 4; NLRP3, NLR family, pyrin domain containing 3; PBS, phosphate-buffered saline; PINK1, PTEN induced putative kinase 1; Rn18s, 18S rRNA; T3SS, type III secretion system; TNF, tumor necrosis factor; TUBB5, tubulin, β 5 class I; Vav, vav 1 oncogene
3.  Beneficial effects of Bacopa monnieri extract on opioid induced toxicity 
Heliyon  2016;2(2):e00068.
The present study examined the hepatotoxicity and nephrotoxicity of morphine and illicit street heroin and their amelioration by a standardized methanolic extract of Bacopa monnieri (L.) (mBME) in rats. Morphine or street heroin was administered at a dose of 20 mg/kg for 14 and 21 days. mBME (40 mg/kg) or ascorbic acid (50 mg/kg) was administered two hours before morphine or street heroin. High performance liquid chromatography (HPLC) was used for the standardization of bacoside-A major components in mBME. The antioxidant potential of mBME was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay. Administration of morphine and street heroin resulted in marked elevation of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST) and creatinine. Histopathological changes induced by morphine and street heroin after 14 days were of reversible nature while treatment for 21 days was associated with irreversible changes. Pretreatment with mBME or ascorbic acid restored the elevation of serum ALT, AST and creatinine and protected liver and kidneys from the toxicological influence of morphine and street heroin. HPLC analysis showed that mBME contained bacoside-A major components i.e. bacoside-A3 (37.5 μg/mg), bacopaside-II (4.62 μg/mg) and bacopasaponin-C (1.91 μg/mg). The EC50 for the DPPH free radical scavenging assay revealed that mBME possessed strong antioxidant potential. These results concluded that as compared to morphine, street heroin was associated with severe biochemical and histopathological changes in the liver and kidneys. Bacopa monnieri having strong antioxidant potential may provide a beneficial herbal remedy for the efficient management of opioid related hepatotoxicity and nephrotoxicity.
doi:10.1016/j.heliyon.2016.e00068
PMCID: PMC4945900  PMID: 27441247
Pharmacotherapy; Biochemical pharmacology; Toxicology; Systemic pharmacology; Environmental toxicology; Substance management
4.  Mutualistic fungal endophytes produce phytohormones and organic acids that promote japonica rice plant growth under prolonged heat stress*  
This study identifies the potential role in heat-stress mitigation of phytohormones and other secondary metabolites produced by the endophytic fungus Paecilomyces formosus LWL1 in japonica rice cultivar Dongjin. The japonica rice was grown in controlled chamber conditions with and without P. formosus LWL1 under no stress (NS) and prolonged heat stress (HS) conditions. Endophytic association under NS and HS conditions significantly improved plant growth attributes, such as plant height, fresh weight, dry weight, and chlorophyll content. Furthermore, P. formosus LWL1 protected the rice plants from HS compared with controls, indicated by the lower endogenous level of stress-signaling compounds such as abscisic acid (25.71%) and jasmonic acid (34.57%) and the increase in total protein content (18.76%–33.22%). Such fungal endophytes may be helpful for sustainable crop production under high environmental temperatures.
doi:10.1631/jzus.B1500081
PMCID: PMC4686363  PMID: 26642184
Paecilomyces formosus LWL1; Plant-growth promotion; Heat-stress mitigation; Phytohormones; Organic acids; Endophytes
5.  Olanzapine induced biochemical and histopathological changes after its chronic administration in rats 
Objective: Olanzapine is a second generation antipsychotic acting mainly as a dopamine D2 and serotonine 5-HT2 receptors antagonist prescribed in the treatment of schizophrenia and various other psychiatric illnesses. Even though olanzapine is widely used in psychiatry, its effects on the architecture of pancreas, liver and kidneys are little known. The histology of pancreas especially has never been studied. For these reasons, the current study was designed to elucidate the toxic effects of chronic administration of olanzapine on pancreas, liver and kidneys and the enzymes released by these tissues in an escalating dose manner. Methods: Fourteen male rats were divided into two groups equally, the olanzapine group and the controls. Olanzapine was administered in a dose of 5 mg/kg/d for the first eight weeks, 10 mg/kg/d for next four weeks and 15 mg/kg/d through the last two week period of 14 weeks experiment. The controls received acidified saline only. Both the groups received restricted diet (20 g/12 h). The body weight and level of random blood sugar (RBS) were measured on a weekly basis. The levels of lipase, amylase, alanine transaminase (ALT) and aspartate transaminase (AST) were determined terminally. At the end of the experiment, the tissues were dissected out for histopathological evaluation. Results: Significant loss in body weight, change in the level of random blood sugar (∗∗P < 0.05, ∗∗∗P < 0.001) and significant rise in amylase and lipase levels (∗P < 0.05, ∗∗∗P < 0.001) were observed. However, the same treatment has shown no significant change in the levels of alanine and aspartate transaminases (P > 0.05). The pancreas has shown derangement of beta cells and fibrotic growth. A mild to moderate focal increase in glomerular cellularity, cellular proliferation and glomerular capsules with negligible basement membranes were observed in the kidneys. No changes were observed in the architecture of the liver. Conclusion: The findings of this study indicated that the incidence of adverse effects associated with olanzapine could be prevented/alleviated/delayed by allowing restricted diet.
doi:10.1016/j.jsps.2015.06.006
PMCID: PMC5094436  PMID: 27829813
Olanzapine; Antipsychotics; Rats; Hyperglycemia; Pancreas; Toxicity
6.  Sertraline enhances the activity of antimicrobial agents against pathogens of clinical relevance 
Background
Serotonin reuptake inhibitors were recently reported to possess antimicrobial potentials, potentiate activity of several antibiotics, reverse multidrug resistant phenotypes of bacteria and make them susceptible to previously resistant drugs. We investigated antimicrobial potentials of sertraline (SR) against ATCC strains, clinical isolates of Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa alone and in-combination with seven antibiotics. Antifungal activity was investigated against four fungal strains including Aspergillus niger, Aspergillus fumigatus, Aspergillus flavus, and Fusarium solani. Intrinsic antibacterial action and Minimum Inhibitory Concentrations (MICs) were determined using well assay, nutrient broth and agar dilution techniques. Disk diffusion and nutrient broth methods were used to study bacterial susceptibility to SR. Minimum Fungicidal Concentrations (MFCs) of SR were determined using Sabouraud dextrose Agar (SDA).
Results
Sertraline possesses strong intrinsic antibacterial, antifungal activities and has augmented the antibacterial activities of antibiotics. For S. aureus ATCC 6538, E. coli ATCC 8739 and P. aeruginosa ATCC 9027, the MICs of SR were 20, 40 and 60 μg ml−1, respectively, whereas 55.5% clinical isolates of S. aureus and 50% of E. coli strains were inhibited at 20 and 60 μg ml−1 of SR, respectively. Among the tested fungi, 60% of A. niger and A. fumigatus were inhibited at 40 and 80 μg ml−1, respectively. MFCs were 60 and 80 μg ml−1 for A. flavus and F. solani, respectively. Antibacterial activities of all antibiotics were significantly increased (p < 0.001) with the addition of SR 100 μg ml−1 against all tested bacteria.
Conclusion
Combination study revealed that SR had significantly increased the activity of antibiotics, and some previously resistant strains were made susceptible. Thus antidepressants are potential sources of resistance modifying agents when used in combination.
doi:10.1186/s40709-015-0028-1
PMCID: PMC4449573  PMID: 26029671
Sertraline; Well assay; Minimum fungicidal concentration; ATCC
7.  Anti-emetic mechanisms of zingiber officinale against cisplatin induced emesis in the pigeon; behavioral and neurochemical correlates 
Background
Zingiber officinale (ZO, family Zingiberaceae) has been reported for its antiemetic activity against cancer chemotherapy induced emesis in animal models and in clinics. Current study was designed to investigate ZO for potential usefulness against cisplatin induced vomiting in pigeon and its effects on central and peripheral neurotransmitters involved in the act of vomiting.
Methods
Zingiber officinale acetone fraction (ZO-ActFr) was investigated for attenuation of emesis induced by cisplatin in healthy pigeons. Neurotransmitters DA, 5HT and their metabolites DOPAC, HVA and 5HIAA were analyzed using High Performance Liquid Chromatography system coupled with electrochemical detector in area postrema, brain stem and intestine. Antiemetic effect of ZO-ActFr was correlated with central and intestinal neurotransmitters levels in pigeon.
Results
Cisplatin (7 mg/kg i.v.) induced emesis without lethality upto the observation period. ZO-ActFr (25, 50 & 100 mg/kg) attenuated cisplatin induced emesis ~ 44.18%, 58.13% (P < 0.05) and 27.9%, respectively; the reference drug, metoclopramide (MCP; 30 mg/kg), produced ~ 48.83% reduction (P < 0.05). ZO-ActFr reduced (P < 0.05 - 0.001) 5-hydroxytryptamine (5HT) concentration in the area postrema, brain stem and intestine at 3rd hour of cisplatin administration, while at the 18th hour ZO treatments attenuated the dopamine upsurge (P < 0.001) caused by cisplatin in the area postrema and 5HT concentration (P < 0.01 - 0.001) in the brain stem and intestine. ZO treatments alone did not altered the basal neurotransmitters and their metabolites in the brain areas and intestine.
Conclusion
The behavioral study verify the antiemetic profile of ZO against cisplatin induced emesis in the pigeon, where central and peripheral neural evidences advocate the involvement of serotonergic mechanism at initial time point (3rd hr), while the later time point (18th hr) is associated with serotonergic and dopaminergic component in the mediation of its antiemetic effect.
doi:10.1186/s12906-015-0556-0
PMCID: PMC4355376  PMID: 25888212
Cisplatin; Emesis; Zingiber officinale; Pigeon; Serotonin
8.  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
9.  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
10.  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
11.  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
12.  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
13.  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
14.  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 1-14 (14)