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Muhammad Yasir

Bio: Muhammad Yasir is an academic researcher from University of New South Wales. The author has contributed to research in topics: Materials science & Medicine. The author has an hindex of 32, co-authored 293 publications receiving 4251 citations. Previous affiliations of Muhammad Yasir include Northwest University (China) & Petronas.


Papers
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Journal ArticleDOI
TL;DR: It is shown that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned, which doubles the number of species isolated at least once from the human gut.
Abstract: Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism1. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms2. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization–time of flight and 16S rRNA for identification2. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies3–5. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut. Optimization of culturing techniques has allowed the identification of 1,057 prokaryotic species within the human gut microbiome repertoire, doubling the previous number of isolated species from the human gut.

697 citations

Journal ArticleDOI
TL;DR: This paper proposes an indoor positioning system based on visible light communications (VLC) that achieves average position errors of less than 0.25 m and has low installation cost as it uses existing lighting sources as transmitters.
Abstract: Indoor positioning system is a critical part in location-based services. Highly precise positioning systems can support different mobile applications in future wireless systems. Positioning systems using existing wireless networks have low deployment costs, but the position error can be up to several meters. While there are positioning systems proposed in the literature that have low position error, they require extra hardware and are therefore costly to deploy. In this paper, we propose an indoor positioning system based on visible light communications (VLC). In contrast to existing works on VLC for positioning, our system estimates the location of the receiver in three dimensions even without: 1) the knowledge of the height of the receiver from ground; and 2) requiring the alignment of the receiver’s normal with the LED’s normal. Our system has low installation cost as it uses existing lighting sources as transmitters. Light sensor and accelerometer, which can be found in most smartphones, are used at the receiver’s side. They are used to measure the received light intensity and the orientation of the smartphone. A low-complexity algorithm is then used to find out the receiver’s position. Our system does not require the knowledge of the LED transmitters’ physical parameters. Experimental results show that our system achieves average position errors of less than 0.25 m.

224 citations

Journal ArticleDOI
TL;DR: The present study explored the eco-friendly approach of utilizing plant-growth-promoting rhizobacteria (PGPR) inoculation and foliar application of silicon (Si) to improve the physiology, growth, and yield of mung bean under saline conditions, and found that salt stress substantially reduced stomatal conductance, transpiration rate, relative water content, chlorophyll content, plant height, leaf area, dry biomass, seed yield, and salt tolerance index.
Abstract: The present study explored the eco-friendly approach of utilizing plant-growth-promoting rhizobacteria (PGPR) inoculation and foliar application of silicon (Si) to improve the physiology, growth, and yield of mung bean under saline conditions. We isolated 18 promising PGPR from natural saline soil in Saudi Arabia, and screened them for plant-growth-promoting activities. Two effective strains were selected from the screening trial, and were identified as Enterobacter cloacae and Bacillus drentensis using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rRNA gene sequencing techniques, respectively. Subsequently, in a 2-year mung bean field trial, using a randomized complete block design with a split-split plot arrangement, we evaluated the two PGPR strains and two Si levels (1 and 2 kg ha-1), in comparison with control treatments, under three different saline irrigation conditions (3.12, 5.46, and 7.81 dS m-1). The results indicated that salt stress substantially reduced stomatal conductance, transpiration rate, relative water content, total chlorophyll content, chlorophyll a, chlorophyll b, carotenoid content, plant height, leaf area, dry biomass, seed yield, and salt tolerance index. The PGPR strains and Si levels independently improved all the aforementioned parameters. Furthermore, the combined application of the B. drentensis strain with 2 kg Si ha-1 resulted in the greatest enhancement of mung bean physiology, growth, and yield. Overall, the results of this study provide important information for the benefit of the agricultural industry.

176 citations

Journal ArticleDOI
TL;DR: The major anti-biofilm mechanisms of antimicrobial peptides are: disruption or degradation of the membrane potential of biofilm embedded cells; interruption of bacterial cell signaling systems; and downregulation of genes responsible for biofilm formation and transportation of binding proteins.
Abstract: Microbes are known to colonize surfaces and form biofilms. These biofilms are communities of microbes encased in a self-produced matrix that often contains polysaccharides, DNA and proteins. Antimicrobial peptides (AMPs) have been used to control the formation and to eradicate mature biofilms. Naturally occurring or synthetic antimicrobial peptides have been shown to prevent microbial colonization of surfaces, to kill bacteria in biofilms and to disrupt the biofilm structure. This review systemically analyzed published data since 1970 to summarize the possible anti-biofilm mechanisms of AMPs. One hundred and sixty-two published reports were initially selected for this review following searches using the criteria ‘antimicrobial peptide’ OR ‘peptide’ AND ‘mechanism of action’ AND ‘biofilm’ OR ‘antibiofilm’ in the databases PubMed; Scopus; Web of Science; MEDLINE; and Cochrane Library. Studies that investigated anti-biofilm activities without describing the possible mechanisms were removed from the analysis. A total of 17 original reports were included which have articulated the mechanism of antimicrobial action of AMPs against biofilms. The major anti-biofilm mechanisms of antimicrobial peptides are: (1) disruption or degradation of the membrane potential of biofilm embedded cells; (2) interruption of bacterial cell signaling systems; (3) degradation of the polysaccharide and biofilm matrix; (4) inhibition of the alarmone system to avoid the bacterial stringent response; (5) downregulation of genes responsible for biofilm formation and transportation of binding proteins.

145 citations

Journal ArticleDOI
TL;DR: Populations of bacteria that inhibited plant fungal pathogens were higher in VC than in FS and particularly chitinolytic isolates were most active against the target fungi.

144 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

4,833 citations