Publications by authors named "Raees Khan"

33 Publications

Morpho-anatomical affinities and evolutionary relationships of three paleoendemic podocarp genera based on seed cone traits.

Ann Bot 2021 Sep 2. Epub 2021 Sep 2.

School of Biological Sciences, The University of Adelaide, SA 5005, Australia.

Background And Aims: The three relict genera Pherosphaera, Microcachrys and Saxegothaea in Podocarpaceae produce quite distinct seed cone types in comparison to other genera and does not form a clade along with Acmopyle. The detailed seed cone morpho-anatomy of these three relict genera and affinities with other podocarps are poorly known. This study aims to understand the seed cone morpho-anatomy and affinities among these three disjunct relict genera and with other podocarps.

Methods: We comparatively analysed the seed cone morpho-anatomical traits of the three podocarps genera and used ancestral state reconstruction to understand the evolution of these traits.

Key Results: We described the seed cone morpho-anatomical structures of the three relict genera in detail. The three genera produce aggregated multiovulate cones. Both Microcachrys and Saxegothaea has an asymmetrical free cup-like epimatium. Both species of Pherosphaera lack epimatium. The ancestral state reconstruction implies that the presence of epimatium is an ancestral trait in podocarps and independently lost in Pherosphaera and Phyllocladus. The seed cones are fleshy in Microcachrys and non-fleshy in Saxegothaea and Pherosphaera. The seed cone macrofossils of both extinct and living podocarps also show the presence of epimatium and fleshiness in podocarps.

Conclusions: Altogether, the morpho-anatomy suggests Pherosphaera, Microcachrys and Saxegothaea present affinities with each other and other podocarps but the reconstruction of ancestral seed cone in Podcarpaceae is quite complex due to multiple convergent evolutions of several structures. These structures (e.g. epimatium, aril, receptaculum) are of low taxonomic value but of great evolutionary and ecologically significance and are responsive adaptations to ever-changing environmental conditions.
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http://dx.doi.org/10.1093/aob/mcab113DOI Listing
September 2021

In vitro anticancer activity of extracted oil from Parrotiopsis jacquemontiana (Decne) Rehder.

Phytomedicine 2021 Aug 5;91:153697. Epub 2021 Aug 5.

Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. Electronic address:

Background: Parrotiopsis jacquemontiana, commonly referred to as "Beranj" in the local community, is widely used traditionally and has numerous health benefits. However, no studies have been conducted to investigate its anticancer potential, particularly its extracted oil.

Purpose: The present study was put forth to appraise the anticancer potential of Parrotiopsis jacquemontiana extracted oil against liver (hcclm3 and hepg2) and breast cancer (mda-mb 231 and mcf-7) cell lines relative to normal cell lines (lo2 and mcf-10a) via MTT assay.

Methods: Flow cytometry indicated the apoptotic effect whereas invasion and migration capabilities of oil against cancer cells were determined by Matrigel invasion chamber and wound-scratch assays.

Results: The results of oil revealed a time and dose-dependent increase in cell proliferation inhibition, conferring to least IC50 shown against hcclm3 (144.9 ± 0.75 μg/ml) and mda-mb 231 (145.7 ± 0.32 μg/ml) cell line at 72 h, whereas no cytotoxic effect on normal cells was observed. In addition, the oil significantly (p < 0.001) suppressed the migration and invasion of hcclm3 and mda-mb 231 cells, showing noteworthy anti-metastatic potential. Furthermore, cell death was confirmed by Annexin‒V/PI staining where the maximum apoptotic percentage was calculated for oil (200 μg/ml) alongside mda-mb 231 conferring to 15.36 ± 1.22, 26.7 ± 1.2, and 36.43 ± 1.65 at 24, 48, and 72 h whereas 12.33 ± 1.05, 19.36 ± 1.62, and 29.3 ± 0.79 was recorded alongside hcclm3 at similar time intervals, respectively.

Conclusion: In conclusion, the extracted oil exhibited strong anti-proliferative, anti-metastatic, and apoptotic effects and therefore may have potential applications in cancer treatment, however, further studies of oil regarding the action mechanisms and compounds involved in anticancer therapy are necessary.
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http://dx.doi.org/10.1016/j.phymed.2021.153697DOI Listing
August 2021

Green synthesized silver nanoparticles (AgNPs) from Parrotiopsis jacquemontiana (Decne) Rehder leaf extract and its biological activities.

Microsc Res Tech 2021 Jul 30. Epub 2021 Jul 30.

Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

Parrotiopsis jacquemontiana (Decne) Rehder aqueous extract of leaf was used for biosynthesis of AgNPs and characterized through UV-Visible spectroscopy, X-ray diffraction, Fourier-transform-infrared, diffraction light scattering, and scanning electron microscope analysis. Moderate to strong antioxidant activity during in vitro antioxidant assays for scavenging of 2,2-diphenyl-1-picryl hydrazyl (DPPH), hydroxyl (OH), nitric oxide (NO) radicals, iron chelation, and inhibition of β-carotene bleaching was recorded with minimum IC value (27.70 ± 2.67 μg/ml) calculated for OH radicals. The AgNPs were evaluated against six multidrug resistant human bacterial strains and minimum inhibitory concentration (MIC) along with minimum bactericidal concentration (MBC) values was determined and all were found remarkably susceptible. The bacterial strain Staphylococcus aureus was the most susceptible with MIC = 5 μg/ml and MBC = 10 μg/ml. Among six fungal strains, Fumigatus esculentum was the most susceptible with MIC and MBC of 10 μg/ml. 3-(4,5-Dimethylthiazol-2 yl)-2,5-diphenyltetrazolium bromide (MTT) screening assay against cancer cell lines (HCCLM3, HEPG2, MDA-MB 231, and MCF-7) revealed the least IC values against HCCLM3 (74.20 ± 5.04) and MCF-7 (91.90 ± 1.17). While no cytotoxicity against normal cell lines; LO2 and MCF-10a was recorded. Parrotiopsis jacquemontiana silver nanoparticles (PJAgNPs) significantly (p > .001) prevented the migration of HCCLM3 cells in a dose-dependent style, relative to control. The wound healing potential of AgNPs in rat was found higher (p < .05) for wound contraction rates, hydroxyproline content, hemostatic and re-epithelization and regeneration efficiency in comparison to the reference group.
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http://dx.doi.org/10.1002/jemt.23882DOI Listing
July 2021

Ethnoveterinary botanical survey of medicinal plants used in Pashto, Punjabi and Saraiki communities of Southwest Pakistan.

Vet Med Sci 2021 Jul 22. Epub 2021 Jul 22.

Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan.

Medicinal plants are highly used in the ethnoveterinary practice as considerable livestock resources in remote areas. The aim of the present study is to explore the ethnoveterinary medicinal practices in three different communities and discuss the cross-cultural consensus on the usage of medicinal plants for the treatment of animals. The field survey was conducted by the animal healers of the area during the different seasons of plant growth. A total of 83 informants were interviewed through Semi-structured interview involving experts of traditional knowledge in 21 localities of the three regions (Zhob, D. I. Khan and Mianwali) were conducted. Findings of the study were quantitatively analyzed through the informant consensus factors to identify the homogeneity information provided by the informants. Furthermore, cross-culture consensuses were analyzed and recorded data were represented in a tabulated and Venn diagrams. In particularly, 59 species of plants were documented in the comparative analysis. Among them, 32 plant species were recorded in Pashto community, while Punjabi and Sarakai communities exhibited nine and four plant species, respectively. Whereas cross-cultural analysis showed 14 medicinal plants that were commonly utilized by three different ethnic communities, that indicated low interregional consensus in regard to ethnoveterinary practices of medicinal plants. The current study showed that different communities and ethnic groups sharing some traditional knowledge and cross-culturally approaches have been reported from traditional uses of plants against livestock's diseases. Therefore, current findings are the opportunities to scrutinize the plants for the discovery of new drug sources for humans and animals.
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http://dx.doi.org/10.1002/vms3.582DOI Listing
July 2021

Ensuring data integrity of healthcare information in the era of digital health.

Healthc Technol Lett 2021 Jun 16;8(3):66-77. Epub 2021 Apr 16.

Department of Information Technology Babasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India.

Data integrity continues to be a persistent problem in the current healthcare sector. It ensures that the data is correct and has not even in any manner been improperly changed. Incorrect data might become significant health threats for patients and a big responsibility for clinicians, resulting in problems such as scam, misconduct, inadequate treatment and data theft. This sort of endangering scenario causes tremendous difficulty in handling healthcare data. This research intends to describe the threat plot of data integrity in healthcare through numerous attack statistics from around the world and Saudi Arabia and identify the criticality in Saudi Arabia in particular. A literature review by descriptive analysis, unit analysis and rating analysis to achieve the planned systematic literature review goal is outlined. The outcome of ranking analysis using a fuzzy analytical hierarchy process methodology offers a route for Saudi Arabian researchers to promote medical records or data security in Arabic healthcare. It is suggested that blockchain is the most prioritized method for regular use and adaptation across Saudi Arabia in all data integrity management techniques. To address the challenges of data integrity and future path, the authors critically examine the challenges posed by data integrity in the healthcare sector.
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http://dx.doi.org/10.1049/htl2.12008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136763PMC
June 2021

Green synthesized AgNPs from Periploca hydaspidis Falc. and its biological activities.

Microsc Res Tech 2021 Oct 21;84(10):2268-2285. Epub 2021 Apr 21.

Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

Characterization of bio-synthesized silver nanoparticles (AgNPs) using Periploca hydaspidis (PHAgNPs) whole plant extract for the first time via UV-Visible spectroscopy, XRD, FTIR, DLS, and SEM analysis techniques was done. A rich variety of phytochemicals in P. hydaspidis aqueous extract (PHA) functioned as possible reducing and capping agents for AgNPs synthesis. In vitro antioxidant activities (DPPH, Iron chelating, Hydroxyl ion, Nitric oxide, and β-carotene bleaching assays) of PHAgNPs revealed least IC values especially in hydroxyl ion (39.08 ± 0.88 μg/mL) and nitric oxide (37.53 ± 2.24 μg/mL) scavenging assays relative to standard controls (ascorbic acid, rutin, and gallic acid) and PHA. In addition, visible inhibition zone diameters were formed around discs against all pathogenic microbial strains including multi-drug resistant strains (MDR's). MIC and MBC/MFC were depicted least in PHAgNPs with maximum bactericidal/fungicidal effects. MTT assay displayed a significant antiproliferative potential of PHAgNPs against HCCLM3, MCF-7, MDA-MB 231, and HEPG2 cancer cell lines, where least IC values were recorded against HEPG2 (12.97 ± 0.04 μg/mL) and MCF-7 (5.73 ± 0.22 μg/mL). Furthermore, PHAgNPs considerably (p > 0.001) prevented the migration of MCF-7 cancer cells in vitro whereas in in vivo wound healing assay, faster skin regeneration, and epithelization in wound biopsies was observed via histological analysis. PHAgNPs treated group rats significantly increased (p < 0.05) the wound contraction rate, hydroxyproline content and hemostatic potential compared to control and PHA-treated groups.
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http://dx.doi.org/10.1002/jemt.23780DOI Listing
October 2021

Dissection of plant microbiota and plant-microbiome interactions.

J Microbiol 2021 Mar 23;59(3):281-291. Epub 2021 Feb 23.

Department of Applied Bioscience, Dong-A University, Busan, 49315, Republic of Korea.

Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.
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http://dx.doi.org/10.1007/s12275-021-0619-5DOI Listing
March 2021

Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant.

Front Plant Sci 2020 7;11:1186. Epub 2020 Aug 7.

Department of Applied Bioscience, Dong-A University, Busan, South Korea.

Plant-associated microbiota plays an important role in plant disease resistance. Bacterial wilt resistance of tomato is a function of the quantitative trait of tomato plants; however, the mechanism underlying quantitative resistance is unexplored. In this study, we hypothesized that rhizosphere microbiota affects the resistance of tomato plants against soil-borne bacterial wilt caused by . This hypothesis was tested using a tomato cultivar grown in a defined soil with various microbiota transplants. The bacterial wilt-resistant Hawaii 7996 tomato cultivar exhibited marked suppression and induction of disease severity after treatment with upland soil-derived and forest soil-derived microbiotas, respectively, whereas the transplants did not affect the disease severity in the susceptible tomato cultivar Moneymaker. The differential resistance of Hawaii 7996 to bacterial wilt was abolished by diluted or heat-killed microbiota transplantation. Microbial community analysis revealed the transplant-specific distinct community structure in the tomato rhizosphere and the significant enrichment of specific microbial operational taxonomic units (OTUs) in the rhizosphere of the upland soil microbiota-treated Hawaii 7996. These results suggest that the specific transplanted microbiota alters the bacterial wilt resistance in the resistant cultivar potentially through a priority effect.
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http://dx.doi.org/10.3389/fpls.2020.01186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427413PMC
August 2020

Security Risk Assessment of Healthcare Web Application Through Adaptive Neuro-Fuzzy Inference System: A Design Perspective.

Risk Manag Healthc Policy 2020 28;13:355-371. Epub 2020 Apr 28.

Department of Information Technology, Babasaheb Bhimrao Ambedkar University, Lucknow, UP, India.

Introduction: The imperative need for ensuring optimal security of healthcare web applications cannot be overstated. Security practitioners are consistently working at improvising on techniques to maximise security along with the longevity of healthcare web applications. In this league, it has been observed that assessment of security risks through soft computing techniques during the development of web application can enhance the security of healthcare web applications to a great extent.

Methods: This study proposes the identification of security risks and their assessment during the development of the web application through adaptive neuro-fuzzy inference system (ANFIS). In this article, firstly, the security risk factors involved during healthcare web application development have been identified. Thereafter, these security risks have been evaluated by using the ANFIS technique. This research also proposes a fuzzy regression model.

Results: The results have been compared with those of ANFIS, and the ANFIS model is found to be more acceptable for the estimation of security risks during the healthcare web application development.

Conclusion: The proposed approach can be applied by the healthcare web application developers and experts to avoid the security risk factors during healthcare web application development for enhancing the healthcare data security.
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http://dx.doi.org/10.2147/RMHP.S233706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196436PMC
April 2020

Healthcare Data Breaches: Insights and Implications.

Healthcare (Basel) 2020 May 13;8(2). Epub 2020 May 13.

Department of Information Technology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India.

The Internet of Medical Things, Smart Devices, Information Systems, and Cloud Services have led to a digital transformation of the healthcare industry. Digital healthcare services have paved the way for easier and more accessible treatment, thus making our lives far more comfortable. However, the present day healthcare industry has also become the main victim of external as well as internal attacks. Data breaches are not just a concern and complication for security experts; they also affect clients, stakeholders, organizations, and businesses. Though the data breaches are of different types, their impact is almost always the same. This study provides insights into the various categories of data breaches faced by different organizations. The main objective is to do an in-depth analysis of healthcare data breaches and draw inferences from them, thereby using the findings to improve healthcare data confidentiality. The study found that hacking/IT incidents are the most prevalent forms of attack behind healthcare data breaches, followed by unauthorized internal disclosures. The frequency of healthcare data breaches, magnitude of exposed records, and financial losses due to breached records are increasing rapidly. Data from the healthcare industry is regarded as being highly valuable. This has become a major lure for the misappropriation and pilferage of healthcare data. Addressing this anomaly, the present study employs the simple moving average method and the simple exponential soothing method of time series analysis to examine the trend of healthcare data breaches and their cost. Of the two methods, the simple moving average method provided more reliable forecasting results.
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http://dx.doi.org/10.3390/healthcare8020133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349636PMC
May 2020

A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis.

FEBS J 2020 11 15;287(21):4710-4728. Epub 2020 Mar 15.

Department of Agricultural Biotechnology, Seoul National University, Korea.

The synthetic biocide triclosan targets enoyl-acyl carrier protein reductase(s) (ENR) in bacterial type II fatty acid biosynthesis. Screening and sequence analyses of the triclosan resistome from the soil metagenome identified a variety of triclosan-resistance ENRs. Interestingly, the mode of triclosan resistance by one hypothetical protein was elusive, mainly due to a lack of sequence similarity with other proteins that mediate triclosan resistance. Here, we carried out a structure-based function prediction of the hypothetical protein, herein referred to as FabMG, and in vivo and in vitro functional analyses. The crystal structure of FabMG showed limited structural homology with FabG and FabI, which are also involved in type II fatty acid synthesis. In vivo complementation and in vitro activity assays indicated that FabMG is functionally a FabI-type ENR that employs NADH as a coenzyme. Variations in the sequence and structure of FabMG are likely responsible for inefficient binding of triclosan, resulting in triclosan resistance. These data unravel a previously uncharacterized FabMG, which is prevalent in various microbes in triclosan-contaminated environments and provide mechanistic insight into triclosan resistance.
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http://dx.doi.org/10.1111/febs.15267DOI Listing
November 2020

Attribute based honey encryption algorithm for securing big data: Hadoop distributed file system perspective.

PeerJ Comput Sci 2020 17;6:e259. Epub 2020 Feb 17.

Information Technology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India.

Hadoop has become a promising platform to reliably process and store big data. It provides flexible and low cost services to huge data through Hadoop Distributed File System (HDFS) storage. Unfortunately, absence of any inherent security mechanism in Hadoop increases the possibility of malicious attacks on the data processed or stored through Hadoop. In this scenario, securing the data stored in HDFS becomes a challenging task. Hence, researchers and practitioners have intensified their efforts in working on mechanisms that would protect user's information collated in HDFS. This has led to the development of numerous encryption-decryption algorithms but their performance decreases as the file size increases. In the present study, the authors have enlisted a methodology to solve the issue of data security in Hadoop storage. The authors have integrated Attribute Based Encryption with the honey encryption on Hadoop, i.e., Attribute Based Honey Encryption (ABHE). This approach works on files that are encoded inside the HDFS and decoded inside the Mapper. In addition, the authors have evaluated the proposed ABHE algorithm by performing encryption-decryption on different sizes of files and have compared the same with existing ones including AES and AES with OTP algorithms. The ABHE algorithm shows considerable improvement in performance during the encryption-decryption of files.
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http://dx.doi.org/10.7717/peerj-cs.259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924543PMC
February 2020

Light microscopy of Pakistani Berberis leaf cuticles and its taxonomic implications.

Microsc Res Tech 2020 May 25;83(5):541-550. Epub 2020 Jan 25.

Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.

Taxonomy of the genus Berberis is quite complex, due to overlapping morphological characters, making it very difficult to differentiate the species within the genus. In order to resolve this taxonomic complexity, the foliar anatomy of 10 Berberis L. species was carried out, for the first time from Pakistan, using light microscopy (LM). Significant variation in terms of epidermal cells shape, size, cell wall pattern, and stomata type was observed. B. baluchistanica has the largest epidermal cells, Adaxial: length = 45-(53.9 ± 3.6)-62.5 μm; and width = 22.5-(26.3 ± 1.3)-30 μm; Abaxial: length = 37.5-(43.25 ± 2.5)-50 μm; and width = 20-(22.6 ± 0.8)-25. The highest number of stomata was observed in B. glaucocarpa as 62 on the abaxial surface while the lowest number of stomata was recorded in B. baluchistanica as 8 on the adaxial surface. Of 10 investigated species, 6 possess anomocytic type stomata, while 2 species that is, B. aitchisonii and B. parkeriana have both anomocytic and anisocytic stomata while B. baluchistanica and B. calliobotrys have only paracytic type stomata. The highest number of cells per unit area was present on the adaxial surface of B. calliobotrys ranging from 245-(252.4)-260 followed by B. parkeriana with 209-(227.8)-250 on the abaxial surface. Stomatal index (SI) also varied considerably and was the lowest (2.6) percentage in B. baluchistanica and highest (31.9) percentage in B. kunawurensis. A taxonomic key based on micro-morphological characters is provided for species identification.
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http://dx.doi.org/10.1002/jemt.23443DOI Listing
May 2020

Biochemical and Structural Insights Concerning Triclosan Resistance in a Novel YXK Type Enoyl-Acyl Carrier Protein Reductase from Soil Metagenome.

Sci Rep 2019 10 28;9(1):15401. Epub 2019 Oct 28.

Department of Applied Bioscience, Dong-A University, Busan, 49315, Republic of Korea.

Enoyl-acyl carrier protein reductase (ENR) catalyzes the last reduction step in the bacterial type II fatty acid biosynthesis cycle. ENRs include FabI, FabL, FabL2, FabK, and FabV. Previously, we reported a unique triclosan (TCL) resistant ENR homolog that was predominant in obligate intracellular pathogenic bacteria and Apicomplexa. Herein, we report the biochemical and structural basis of TCL resistance in this novel ENR. The purified protein revealed NADH-dependent ENR activity and shared similarity to prototypic FabI. Thus, this metagenome-derived ENR was designated FabI2. Unlike other prototypic bacterial ENRs with the YXK type catalytic domain, FabI2 possessed a unique YXK type catalytic domain. Computational modeling followed by site-directed mutagenesis revealed that mild resistance (20 µg/ml of minimum inhibitory concentration) of FabI2 to TCL was confined to the relatively less bulky side chain of A128. Substitution of A128 in FabI2 with bulky valine (V128) elevated TCL resistance. Phylogenetic analysis further suggested that the novel FabI2 and prototypical FabI evolved from a common short-chain dehydrogenase reductase family. To our best knowledge, FabI2 is the only known ENR shared by intracellular pathogenic prokaryotes, intracellular pathogenic lower eukaryotes, and a few higher eukaryotes. This suggests that the ENRs of prokaryotes and eukaryotes diverged from a common ancestral ENR of FabI2.
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http://dx.doi.org/10.1038/s41598-019-51895-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817880PMC
October 2019

Culturing Simpler and Bacterial Wilt Suppressive Microbial Communities from Tomato Rhizosphere.

Plant Pathol J 2019 Aug 1;35(4):362-371. Epub 2019 Aug 1.

Department of Applied Bioscience, Dong-A University, Busan 49315, Korea.

Plant phenotype is affected by a community of associated microorganisms which requires dissection of the functional fraction. In this study, we aimed to culture the functionally active fraction of an upland soil microbiome, which can suppress tomato bacterial wilt. The microbiome fraction (MF) from the rhizosphere of Hawaii 7996 treated with an upland soil or forest soil MF was successively cultured in a designed modified M9 (MM9) medium partially mimicking the nutrient composition of tomato root exudates. Bacterial cells were harvested to amplify V3 and V4 regions of 16S rRNA gene for QIIME based sequence analysis and were also treated to Hawaii 7996 prior to inoculation. The disease progress indicated that the upland MM9 1 transfer suppressed the bacterial wilt. Community analysis revealed that species richness was declined by successive cultivation of the MF. The upland MM9 1 transfer harbored population of phylum Proteobacteria (98.12%), Bacteriodetes (0.69%), Firmicutes (0.51%), Actinobacteria (0.08%), unidentified (0.54%), Cyanobacteria (0.01%), FBP (0.001%), OD1 (0.001%), Acidobacteria (0.005%). The family of Proteobacteria was the dominant member (86.76%) of the total population of which genus composed 86.76% making it a potential candidate to suppress bacterial wilt. The results suggest that this mixed culture approach is feasible to harvest microorganisms which may function as biocontrol agents.
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http://dx.doi.org/10.5423/PPJ.FT.07.2019.0180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706014PMC
August 2019

Security durability assessment through fuzzy analytic hierarchy process.

PeerJ Comput Sci 2019 2;5:e215. Epub 2019 Sep 2.

Information Technology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India.

Background: Security is an integral aspect of the development of quality software. Furthermore, security durability is even more imperative and in persistent demand due to high investment in recent years. To achieve the desired target of efficacious and viable durability of security services, there needs to be nodal focus on durability along with security. Unfortunately, the highly secure design of software becomes worthless because the durability of security services is not as it should be.

Methods: Security durability attributes have their own impact while integrating security with durability and assessment of security durability plays a crucial role during software development. Within this context, this paper estimates the security durability of the two alternatives versions of a locally developed software called version 1 and version 2. To assess the security durability, authors are using the hybrid fuzzy analytic hierarchy process decision analysis approach.

Results: The impact of the security durability on other attributes has been evaluated quantitatively. The result obtained contains the assessment of security durability. The study posits conclusions which are based on this result and are useful for practitioners to assess and improve the security life span of software services.
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http://dx.doi.org/10.7717/peerj-cs.215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924713PMC
September 2019

Pollen morphological variation of Berberis L. from Pakistan and its systematic importance.

Microsc Res Tech 2019 Sep 27;82(9):1593-1600. Epub 2019 Jun 27.

Joint International Research Laboratory of Metabolic & Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.

Due to overlapping and diverse morphological characters, Berberis is among the most taxonomically complex genera. Palynology is one of the taxonomic tools for delimitation and identification of complex species. In this study, pollens of 10 Berberis species were analyzed through light and scanning electron microscopy. Qualitative as well as quantitative features (pollen shape, size, presence or absence of colpi, colpi length and width, exine thickness, ornamentation, pollen class, aperture, and polar-equatorial ratio) were measured. Five species were observed to have colpate (pantocolpate) with elongated ends, radially symmetrical, isopolar, monads, and psilate-regulate pollens. In polar view, six pollen were spheroidal, two were ovoid, one spherical, and one oblate. Similarly, variation in pollen length was prominent and the largest pollen on polar view was recorded for B. psodoumbellata 60-65 μm (62.4 ± 0.9), while the smallest one was observed for B. lycium 29-35 μm (32.2 ± 1). The observed variation in both quantitative and qualitative features were important in taxonomic identification. This shows that palynological characters are helpful in identification of Berberis genus at the species level.
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http://dx.doi.org/10.1002/jemt.23325DOI Listing
September 2019

Utilization of foliar cuticle morphology for the identification of weedy grasses.

Microsc Res Tech 2019 Jul 1;82(7):1231-1239. Epub 2019 Apr 1.

Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

For the robust identification of weeds of taxonomically complex families like Poaceae, scanning electron microscopy (SEM) and light microscopy (LM) are of significant implications. In this study, SEM and LM methods were used by investigating 12 Pakistani weedy grass species as an example for foliar epidermal micromorphological characters for its role in the identification of grasses species. Qualitative and quantitative foliar micromorphological variations in stomatal type, number, guard cells, subsidiary cells, silica bodies and trichomes were studied. Significant variation was observed in both qualitative and quantitative features and based on this diversity in epidermal characters, a key was drawn to delimitate the species. Variations in stomata, silica bodies (SiO ·nH O), macrohairs, microhairs, hooks, papillae, prickles, and other epidermal structures were used in establishing the taxonomic key. The data were also statistically evaluated by determining its mean, standard deviation, variance, the coefficient of variance, and standard error. Foliar epidermal characters such as silica bodies shape and trichomes were taxonomically more useful than stomatal types, subsidiary, and guard cells. SEM and LM micromorphological characters were of substantial importance in the delimitation of closely related species.
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http://dx.doi.org/10.1002/jemt.23272DOI Listing
July 2019

Mapping human health risk from exposure to potential toxic metal contamination in groundwater of Lower Dir, Pakistan: Application of multivariate and geographical information system.

Chemosphere 2019 Jun 12;225:785-795. Epub 2019 Mar 12.

Department of Chemistry, Quaid-i-Azam University, Islamabad, PO 45320, Pakistan.

The study aimed to assess the physicochemical parameters (pH, electrical conductivity (EC), total dissolve solid (TDS), oxidation reduction potential (ORP), Temperature) and potential toxic metals (PTMs), including Ni, Mn, Cr, Cu, Cd, Pb, Co, Fe and Zn in the groundwater of Lower Dir, Pakistan. Furthermore, the pollution sources and spatial distribution pattern of PTMs were also investigated via principal component analysis (PCA) and geographic information system (GIS) application to understand the changing behaviors of PTMs in groundwater. The average concentrations of physicochemical parameters such as pH, EC, TDS, ORP and Temperature were 7.1, 418 μS/cm, 251 mg/L, 193 mV and 25.7 C, while the concentrations of PTMs; Ni, Mn, Cr, Cu, Cd, Pb, Co, Fe and Zn were 0.25, 0.34, 0.09, 0.29, 0.10, 0.08, 0.10, 0.83 and 0.25  mg/L, respectively. Among the selected metals, Mn, Cr, Cd, Pb, Co and Fe were exceeded the WHO guidelines and their percentage contribution were 43%, 57%, 45%, 70%, 70% and 62%, respectively. The increasing order of PTMs were; Pb > Co > Fe > Cr > Cd > Mn > Cu > Ni > Zn in the study area. PCA represented three significant factors, which explained 76% variability in the groundwater. Whereas, clustering analysis (CA) grouped groundwater into three distinct clusters less polluted (C1), moderate polluted (C2) and highly polluted (C3). Human health risk assessment was carried out to check the suitability of groundwater for drinking and domestic uses. The HQ and HRIs values of Cd were >1, suggested that the groundwater sources are unfit for drinking and domestic purposes and may be caused potential health risk after long term ingestion.
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http://dx.doi.org/10.1016/j.chemosphere.2019.03.066DOI Listing
June 2019

Biochemical and Structural Basis of Triclosan Resistance in a Novel Enoyl-Acyl Carrier Protein Reductase.

Antimicrob Agents Chemother 2018 08 27;62(8). Epub 2018 Jul 27.

Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea

Enoyl-acyl carrier protein reductases (ENR), such as FabI, FabL, FabK, and FabV, catalyze the last reduction step in bacterial type II fatty acid biosynthesis. Previously, we reported metagenome-derived ENR homologs resistant to triclosan (TCL) and highly similar to 7-α hydroxysteroid dehydrogenase (7-AHSDH). These homologs are commonly found in , a class that contains several human-pathogenic bacteria, including the genera and Here we report the biochemical and predicted structural basis of TCL resistance in a novel 7-AHSDH-like ENR. The purified protein exhibited NADPH-dependent ENR activity but no 7-AHSDH activity, despite its high homology with 7-AHSDH (69% to 96%). Because this ENR was similar to FabL (41%), we propose that this metagenome-derived ENR be referred to as FabL2. Homology modeling, molecular docking, and molecular dynamic simulation analyses revealed the presence of an extrapolated six-amino-acid loop specific to FabL2 ENR, which prevented the entry of TCL into the active site of FabL2 and was likely responsible for TCL resistance. Elimination of this extrapolated loop via site-directed mutagenesis resulted in the complete loss of TCL resistance but not enzyme activity. Phylogenetic analysis suggested that FabL, FabL2, and 7-AHSDH diverged from a common short-chain dehydrogenase reductase family. This study is the first to report the role of the extrapolated loop of FabL2-type ENRs in conferring TCL resistance. Thus, the FabL2 ENR represents a new drug target specific for pathogenic .
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http://dx.doi.org/10.1128/AAC.00648-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105837PMC
August 2018

Fluoride prevalence in groundwater around a fluorite mining area in the flood plain of the River Swat, Pakistan.

Sci Total Environ 2018 Sep 24;635:203-215. Epub 2018 Apr 24.

Hydrogeochemistry Laboratory, Department of Environmental Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, PO 45320, Pakistan.

This study investigated the fluoride (F) concentrations and physicochemical parameters of the groundwater in a fluorite mining area of the flood plain region of the River Swat, with particular emphasis on the fate and distribution of F and the hydrogeochemistry. To better understand the groundwater hydrochemical profile and F enrichment, groundwater samples (n=53) were collected from shallow (24-40m), mid-depth (48-65m) and deep (85-120m) aquifers, and then analysed using an ion-selective electrode. The lowest F concentration (0.7mg/L) was recorded in the deep-aquifer groundwater, while the highest (6.4mg/L) was recorded in shallow groundwater. Most groundwater samples (62.2%) exceeded the guideline (1.5mg/L) set by the World Health Organization (WHO); while for individual sources, 73% of shallow-groundwater samples (F concentration up to 6.4mg/L), 42% of mid-depth-groundwater samples, and 17% of deep-groundwater samples had F concentrations that exceeded this permissible limit. Assessment of the overall quality of the groundwater revealed influences of the weathering of granite and gneisses rocks, along with silicate minerals and ion exchange processes. Hydrogeochemical analysis of the groundwater showed that Na is the dominant cation and HCO the major anion. The anionic and cationic concentrations across the entire study area increased in the following order: HCO>SO>Cl>NO>F>PO and Na>Ca>Mg>K, respectively. Relatively higher F toxicity levels were associated with the NaHCO water type, and the chemical facies were found to change from the CaHCO to (NaHCO) type in calcium-poor aquifers. Thermodynamic considerations of saturation indices indicated that fluorite minerals play a vital role in the prevalence of fluorosis, while under-saturation revealed that - besides fluorite minerals - other F minerals that are also present in the region further increase the F concentrations in the groundwater. Finally, a health risk assessment via Dean's classification method identified that the groundwater with relatively higher F concentrations is unfit for drinking purposes.
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http://dx.doi.org/10.1016/j.scitotenv.2018.04.064DOI Listing
September 2018

Comparative SEM and LM foliar epidermal and palyno-morphological studies of Amaranthaceae and its taxonomic implications.

Microsc Res Tech 2018 May 27;81(5):474-485. Epub 2018 Feb 27.

Lahore College for Women University, Lahore, Pakistan.

Palynological features as well as comparative foliar epidermal using light and scanning electron microscope (SEM) of 17 species (10genera) of Amaranthaceae have been studied for its taxonomic significance. Different foliar and palynological micro-morphological characters were examined to explain their value in resolving the difficulty in identification. All species were amphistomatic but stomata on abaxial surface were more abundant. Taxonomically significant epidermal character including stomata type, trichomes (unicellular, multicellular, and capitate) and epidermal cells shapes (polygonal and irregular) were also observed. Pollens of this family are Polypantoporate, pores large, spheroidal, mesoporous region is sparsely to scabrate, densely psilate, and spinulose. All these characters can be active at species level for identification purpose. This study indicates that at different taxonomic levels, LM and SEM pollen and epidermal morphology is explanatory and significant to identify species and genera.
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http://dx.doi.org/10.1002/jemt.23001DOI Listing
May 2018

Exploration and local utilization of medicinal vegetation naturally grown in the Deusai plateau of Gilgit, Pakistan.

Saudi J Biol Sci 2018 Feb 28;25(2):326-331. Epub 2017 Jul 28.

Department of Plant Production, Faculty of Food & Agricultural Sciences, P.O. Box 2460, Riyadh 11451, Saudi Arabia.

In the study area, the traditional knowledge regarding the uses of local wild medicinal plants for the health care of human and domestic animals is totally in hold of old people. The young ones are unaware about such an indispensable practices. The objective of the current study was to transfer this sort of precious knowledge from old members of the community to young generations in documented form.
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http://dx.doi.org/10.1016/j.sjbs.2017.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815990PMC
February 2018

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis.

PLoS One 2018 8;13(2):e0192277. Epub 2018 Feb 8.

Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea.

The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192277PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805296PMC
April 2018

Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum.

J Biotechnol 2018 Mar 3;270:30-38. Epub 2018 Feb 3.

Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea. Electronic address:

Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized. Phylogenetic analysis revealed that metagenomic enzymes were novel esterase/lipase candidates as they clustered as novel subfamilies of family I, V, X, and family XI. The purified enzymes displayed various levels of hydrolytic activities towards 3-OH PAME with optimum activity at 40-50 °C and pH 7-10. Interestingly, ELP104 also displayed N-(3-oxohexanoyl)-L-homoserine lactone hydrolysis activity. Heterologous expression of the gene encoding 3-OH PAME hydrolase in R. solanacearum significantly decreased exopolysaccharide production without affecting bacterial growth. mRNA transcription analysis revealed that genes regulated by quorum-sensing, such as phcA and xpsR, were significantly down-regulated in the stationary growth phase of R. solanacearum. Therefore, metagenomic enzymes are capable of quorum-quenching by hydrolyzing the autoinducer 3-OH PAME, which could be used as a biocontrol strategy against bacterial wilt.
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http://dx.doi.org/10.1016/j.jbiotec.2018.01.023DOI Listing
March 2018

Describing one generic and two new species record to the flora of Pakistan using LM and SEM methods.

Microsc Res Tech 2018 May 31;81(5):469-473. Epub 2018 Jan 31.

Qarshi University, Lahore, Pakistan.

Common mulberry weed (Fatoua villosa (Thunb.) Nakai) and creeping amaranth (Amaranthus crassipes Schlecht) are reported for the first time in Pakistan's flora as these were not listed in any other literature nor identified before in Pakistan. Plants were found as a result of taxonomic studies performed in 2013 in Peshawar, Pakistan. Detail study was performed for the exact identification. Morphological results were compared with Flora of China and Flora of North America. Plant distribution along with its habitat and adjacent species was also recorded. Scanning electron and light microscopy was performed for the confirmation of epidermal appendages on leaf epidermis and palyno-morphological characters.
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http://dx.doi.org/10.1002/jemt.23000DOI Listing
May 2018

Palyno-morphological characteristics of gymnosperm flora of pakistan and its taxonomic implications with LM and SEM methods.

Microsc Res Tech 2018 Jan 17;81(1):74-87. Epub 2017 Oct 17.

Department of Plant Sciences, Quaidi -i- Azam University Islamabad, Pakistan.

The present study is intended to assess gymnosperms pollen flora of Pakistan using Light Microscope (LM) and Scanning Electron Microscopy (SEM) for its taxonomic significance in identification of gymnosperms. Pollens of 35 gymnosperm species (12 genera and five families) were collected from its various distributional sites of gymnosperms in Pakistan. LM and SEM were used to investigate different palyno-morphological characteristics. Five pollen types (i.e., Inaperturate, Monolete, Monoporate, Vesiculate-bisaccate and Polyplicate) were observed. Six In equatorial view seven types of pollens were observed, in which ten species were sub-angular, nine species were Traingular, six species were Perprolate, three species were Rhomboidal, three species were semi-angular, two species were rectangular and two species were prolate. While five types of pollen were observed in polar view, in which ten species were Spheroidal, nine species were Angular, eight were Interlobate, six species were Circular, two species were Elliptic. Eighteen species has rugulate and 17 species has faveolate ornamentation. Eighteen species has verrucate and 17 have gemmate type sculpturing. The data was analysed through cluster analysis. The study showed that these palyno-morphological features have significance value in classification and identification of gymnosperms. Based on these different palyno-morphological features, a taxonomic key was proposed for the accurate and fast identifications of gymnosperms from Pakistan.
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http://dx.doi.org/10.1002/jemt.22958DOI Listing
January 2018

Identification of a Gene Involved in the Negative Regulation of Pyomelanin Production in Ralstonia solanacearum.

J Microbiol Biotechnol 2017 Sep;27(9):1692-1700

Department of Applied Biology, Dong-A University, Busan 49315, Republic of Korea.

causes bacterial wilt in a wide variety of host plant species and produces a melanin-like blackish-brown pigment in stationary phase when grown in minimal medium supplemented with tyrosine. To study melanin production regulation in , five mutants exhibiting overproduction of melanin-like pigments were selected from a transposon (Tn) insertion mutant library of SL341. Most of the mutants, except one (SL341T), were not complemented by the original gene or overproduced melanins. SL341T showed Tn insertion in a gene containing a conserved domain of eukaryotic transcription factor. The gene was annotated as a hypothetical protein, given its weak similarity to any known proteins. Upon complementation with its original gene, the mutant strains reverted to their wild-type phenotype. SL341T produced 3-folds more melanin at 72 h post-incubation compared with wild-type SL341 when grown in minimal medium supplemented with tyrosine. The chemical analysis of SL341T cultural filtrate revealed the accumulation of a higher amount of homogentisate, a major precursor of pyomelanin, and a lower amount of dihydroxyphenylalanine, an intermediate of eumelanin, compared with SL341. The expression study showed a relatively higher expression of (encoding hydroxyphenylpyruvate dioxygenase) and lower expression of (encoding homogentisate dioxygenase) and (encoding maleylacetoacetate isomerase) in SL341T than in SL341. SL341 showed a significantly higher expression of tyrosinase gene compared with SL341T at 48 h post-incubation. These results indicated that produced both pyomelanin and eumelanin, and the novel hypothetical protein is involved in the negative regulation of melanin production.
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http://dx.doi.org/10.4014/jmb.1705.05049DOI Listing
September 2017

Scanning electron and light microscopy of foliar epidermal characters: A tool for plant taxonomists in the identification of grasses.

Microsc Res Tech 2017 Oct 12;80(10):1123-1140. Epub 2017 Jul 12.

Centre of Plant Biodiversity, University of Peshawar, Khyber Pakhtun khwa, Pakistan.

SEM and light microscopy are of special interest for biologist to observe various features of the living bodies. In the current study we observed the foliar epidermal micro-morphological characters of 44 grass species using SEM and Light microscopy to assess their taxonomic utility for taxonomists in the identification process. The aim of this study is to use the foliar epidermal structural variations in both upper and lower surfaces for identification of grasses. Significant diversity was observed in both qualitative and quantitative characters using SEM and Light microscopy. Variations were observed in stomatal number, size, guard cells shape, silica bodies, macro-hairs, micro-hairs, epidermal cell number, subsidiary cells, prickles, hooks, papillae, and short and long cells. A taxonomic key is prepared using these variations for the identification of grass species. Based on these findings, SEM and Light microscopy of foliar epidermal features can be of special interest for taxonomists in the identification of complex grass taxa.
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http://dx.doi.org/10.1002/jemt.22909DOI Listing
October 2017

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes.

Sci Rep 2016 08 31;6:32322. Epub 2016 Aug 31.

Department of Applied Biology, Dong-A University, Busan 604-714, Republic of Korea.

Triclosan (TCS) is a widely used antimicrobial agent and TCS resistance is considered to have evolved in diverse organisms with extensive use of TCS, but distribution of TCS resistance has not been well characterized. Functional screening of the soil metagenome in this study has revealed that a variety of target enoyl acyl carrier protein reductases (ENR) homologues are responsible for the majority of TCS resistance. Diverse ENRs similar to 7-α-hydroxysteroid dehydrogenase (7-α-HSDH), FabG, or the unusual YX7K-type ENR conferred extreme tolerance to TCS. The TCS-refractory 7-α HSDH-like ENR and the TCS-resistant YX7K-type ENR seem to be prevalent in human pathogenic bacteria, suggesting that a selective enrichment occurred in pathogenic bacteria in soil. Additionally, resistance to multiple antibiotics was found to be mediated by antibiotic resistance genes that co-localize with TCS resistance determinants. Further comparative analysis of ENRs from 13 different environments has revealed a huge diversity of both prototypic and metagenomic TCS-resistant ENRs, in addition to a selective enrichment of TCS-resistant specific ENRs in presumably TCS-contaminated environments with reduced ENR diversity. Our results suggest that long-term extensive use of TCS can lead to the selective emergence of TCS-resistant bacterial pathogens, possibly with additional resistance to multiple antibiotics, in natural environments.
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http://dx.doi.org/10.1038/srep32322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006077PMC
August 2016
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