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Papers by salim islam

ABSTRACTSecretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiqu... more ABSTRACTSecretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes that implicate outer-membrane (OM) polysaccharide export (OPX) proteins in polymer translocation to the cell surface. In the social predatory bacterium Myxococcus xanthus, exopolysaccharide (EPS)-pathway WzaX, major spore coat (MASC)-pathway WzaS, and biosurfactant polysaccharide-pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning α-helices. Comparative genomics across all bacteria, complemented with cryo-electron tomography cell- envelope analyses, revealed WzaX/S/B architecture to be the most common amongst three defined OPX-protein structural classes independent of periplasmic thickness. Fold-recognition and deep- learning analyses revealed the conserved M. xanthus proteins MXAN_7418/32...

Biomolecules

The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a “glycocaly... more The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a “glycocalyx”, confers protection against toxic molecules. However, the effect of glycocalyx integrity on the tolerance to such agents is poorly understood. Using a modified disc-diffusion assay, we tested the susceptibility to a panel of antibiotics and oxidative stress-inducing compounds of various mutant strains of the social predatory Gram-negative soil bacterium Myxococcus xanthus; the selected mutants were those that manifest different physical states of their respective EPS glycocalyces. While the overall presence of an EPS layer was indeed beneficial for tolerance, the integrity of this layer was also found to affect the susceptibility of the bacterium to killing; however, this finding was not universal, and instead was dependent on the specific compound tested. Thus, the integrity of the cell-surface EPS glycocalyx plays an important role in the tolerance of M. xanthus to harmful compounds.

Jurnal Repositor, 2020

Perpustakaan UMM (Universitas Muhammadiyah Malang) merupakan salah satu sumber informasi yang dis... more Perpustakaan UMM (Universitas Muhammadiyah Malang) merupakan salah satu sumber informasi yang disediakan oleh universitas untuk menunjang pendidikan mahasiswa. Sistem informasi perpustakaan digital UMM telah diimplementasikan sejak tahun 2003 dengan pengguna yang mencakup seluruh civitas UMM. Penelitian ini bertujuan untuk mengukur kesuksesan sistem informasi perpustakaan digital UMM dengan menggunakan model kesuksesan sistem informasi Delone & McLean yang telah diperbarui. Variabel dari model DeLone & McLean yang digunakan adalah Kualitas Sistem, Kualitas Informasi, Kualitas Layanan, dan Kepuasan Pengguna. Data penelitian didapatkan dengan membagikan kuesioner kepada mahasiswa aktif pengguna sistem informasi perpustakaan digital UMM. Pengolahan data dilakukan menggunakan analisis regresi linear berganda dan analisis statistik deskriptif. Hasil penelitian menunjukkan bahwa secara simultan Kualitas Sistem, Kualitas Informasi dan Kualitas Layanan memiliki hubungan yang positif dan s...

Here in this paper we presented the modelling of Fiber Bragg Grating (FBG) as temperature sensor ... more Here in this paper we presented the modelling of Fiber Bragg Grating (FBG) as temperature sensor for structural health monitoring application is geometrically designed in the wavelength window of 1.568-1.580μm. Simulation has been done by using optical software R-Soft (GratingMOD).

This paper introduces the method of estimating functions (EF) in the estimation of the Asymmetric... more This paper introduces the method of estimating functions (EF) in the estimation of the Asymmetric GARCH family of models. This approach utilises the third and fourth moments which are common in financial time series data analysis and does not rely on distributional assumptions of the data. Optimal estimating functions have been constructed as a combination of linear and quadratic estimating functions. Estimates from the estimating functions approach are better than those of the traditional estimation methods such as the maximum likelihood estimation (MLE) especially in cases where distributional assumptions on the data are highly violated. We investigate the presence of asymmetric (leverage) effects in empirical time series and fit two of the most popular Asymmetric GARCH models (EGARCH and GJR-GARCH) under both the MLE and EF approaches. An empirical example demonstrates the implementation of the EF approach to Asymmetric GARCH models assuming a student’s – t distribution for the i...

International journal of statistics and applications, 2017

The concept of pool testing originated with Dorfman in the context of blood testing as an economi... more The concept of pool testing originated with Dorfman in the context of blood testing as an economical method of testing blood samples of army inductees in order to detect the characteristic of interest. Apart from classification problem, pool testing can also be used in estimating the prevalence rate of a trait in a population which was the focus of our study. In approximating the prevalence rate, one-at-a-time testing is time consuming, expensive and is bound to errors hence pool testing procedures have been proposed to address these problems. Despite these procedures, when pool testing strategies are used using imperfect kits, there tend to be loss of sensitivity. Lost sensitivity of a test is recovered by retesting pools classified positive in the initial test. This study has developed statistical model which is used to consecutively choosing some combination of the three experiments namely: one–at-a-time, pooled testing and pooled testing with retesting of the positive pools for ...

American Journal of Theoretical and Applied Statistics, 2020

Nonparametric methods are rich classes of statistical tools that have gained acceptance in most a... more Nonparametric methods are rich classes of statistical tools that have gained acceptance in most areas of statistics. They have been used in the past by researchers to fit missing values in the presence of auxiliary variables in a sampling survey. Nonparametric methods have been preferred to parametric methods because they make it possible to analyze data, estimate trends and conduct inference without having to fully specify a parametric model for the data. This study, therefore, presents some new attempts in the complex survey through the nonparametric imputation of missing values by the use of both penalized splines and neural networks. More precisely, the study adopted a neural network and penalized splines to estimate the functional relationship between the survey variable and the auxiliary variables. This complex survey data was sampled through a cluster-strata design where a population is divided into clusters which are in turn subdivided into strata. Once missing values have been imputed, this study performs a model calibration with auxiliary information assumed completely available at the cluster level. The reasoning behind model calibration is that if the calibration constraints are satisfied by the auxiliary variable, then it is expected that the fitted values of the variable of interest should satisfy such constraints too. The population total estimators are derived by treating the calibration problems at cluster level as optimization problems and solving it by the method of penalty functions. A Monte Carlo simulation was run to assess the finite sample performance of the estimators under complex survey data. The efficiency of the estimator's performance was then checked by MSE criterion. A comparison of the penalized spline model calibration and neural network model calibration estimators was done with Horvitz Thompson estimator. From the results, the two nonparametric estimator's performances seem closer to that of Horvitz Thompson estimator and are both unbiased and consistent.

ABSTRACTBacterial surface exopolysaccharide (EPS) layers are key determinants of biofilm establis... more ABSTRACTBacterial surface exopolysaccharide (EPS) layers are key determinants of biofilm establishment and maintenance, leading to the formation of higher-order 3D structures conferring numerous survival benefits to a cell community. In addition to a specific EPS glycocalyx, we recently revealed that the social δ-proteobacteriumMyxococcus xanthussecretes a novel biosurfactant polysaccharide (BPS), with both EPS and BPS polymers required for type IV pilus (T4P)-dependent swarm expansion via spatio-specific biofilm expression profiles. Thus the synergy between EPS and BPS secretion somehow modulates the multicellular lifecycle ofM. xanthus. Herein, we demonstrate that BPS secretion functionally-activates the EPS glycocalyx via its destabilization, fundamentally altering the characteristics of the cell surface. This impacts motility behaviours at the single-cell level as well as the aggregative capacity of cells in groups via EPS fibril formation and T4P assembly. These changes modulat...

OALib, 2020

The paper explores and establishes a unique Bayesian framework for estimating three shape paramet... more The paper explores and establishes a unique Bayesian framework for estimating three shape parameters of the McDonald generalized beta-binomial distribution. The mixture distribution is used in modelling overdispersed binomial data. Foundations of the framework have been enriched by knowledge of Bayesian statistics and Markov Chain Monte Carlo methods. A Metropolis within Gibbs Monte Carlo method to sample from the unknown posterior form of the distribution was used. The shape parameters (α, β and γ) were assigned flat gamma priors to ensure equal probabilities for all the values. McDonald generalized beta-binomial variables were simulated with fixed shape parameters set at () () , , 0.5, 0.5, 0.5 α β γ = respectively and samples generated were used to estimate the parameters, to evaluate if the method recovers estimates close to the true parameter values. Standard errors were also computed for the simulated data and real data. Further, credible regions and highest probability density intervals (HPD) were computed and their corresponding lengths. To evaluate the marginal posterior samples for every shape parameter generated trace plots presented, their respective correlation plots were also presented and the histograms to show the distributions assumed by every parameter. Bayesian framework provides a direct and flexible method of computation for a mixture distribution whose complexity may pose challenges of integration when using the classical methods of estimation.

The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacter... more The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacterial focal adhesion (bFA) sites to power gliding motility. Using TIRF and force microscopy, we herein identify the integrin αI-domain-like outer-membrane (OM) lipoprotein CglB as an essential substratum-coupling protein of the gliding motility complex. Similar to most known OM lipoproteins, CglB is anchored on the periplasmic side of the OM and thus a mechanism must exist to secrete it to the cell surface in order for it to interact with the underlying substratum. We reveal this process to be mediated by a predicted OM β-barrel structure of the gliding complex. This OM platform was found to regulate the conformational activation and secretion of CglB across the OM. These data suggest that the gliding complex promotes surface exposure of CglB at bFAs, thus explaining the manner by which forces exerted by inner-membrane motors are transduced across the cell envelope to the substratum; they ...

The development of multicellularity is a key evolutionary transition allowing for differentiation... more The development of multicellularity is a key evolutionary transition allowing for differentiation of physiological functions across a cell population that confers survival benefits; among unicellular bacteria, this can lead to complex developmental behaviours and the formation of higher-order community structures. Herein, we demonstrate that in the social δ-proteobacterium Myxococcus xanthus, the secretion of a novel secreted biosurfactant polysaccharide (BPS) is temporally and spatially modulated within communities, mediating swarm migration as well as the formation of multicellular swarm biofilms and fruiting bodies. BPS is a type IV pilus-inhibited acidic polymer built of randomly-acetylated β-linked tetrasaccharide repeats. Both BPS and the “shared good” EPS are produced by dedicated Wzx/Wzy-dependent polysaccharide assembly pathways distinct from that responsible for spore coat assembly. To our knowledge, such pathways have never-before been explicitly shown to synthesize a bio...

SSRN Electronic Journal, 2018

Directed surface motility of metazoan cells and protozoan parasites involves substratum engagemen... more Directed surface motility of metazoan cells and protozoan parasites involves substratum engagement by surface-exposed integrin(-like) adhesins, directionally transported by molecular motors via coupling to the internal cytoskeleton. The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacterial focal adhesions to power gliding motility. However, the mechanisms of gliding machinery-substratum coupling and force mechanotransduction between innermembrane motors and substratum are unknown. Herein, we use bead force spectroscopy and TIRF microscopy to characterize CglB as the essential substratum-coupling integrin αI-domain-like adhesin. Protease susceptibility reveals that CglB interacts with a globular-protein-accessorized β-barrel OM display platform, which regulates the cell-surface conformational state and accessibility of the adhesin. Surface retention of CglB is further regulated by a cell-surface metalloprotease, a phenomenon also modulated by the OM display platform. These data depict a complex mechanism for bacterial gliding adhesin secretion, cell-surface anchoring, and processing, with conserved themes between prokaryotic and eukaryotic cell motility.

Single cell microfluidics is powerful to study bacteria and determine their susceptibility to ant... more Single cell microfluidics is powerful to study bacteria and determine their susceptibility to antibiotics treatment. Glass treatment by adhesive molecules is a potential solution to immobilize bacterial cells and perform microscopy but traditional cationic polymers such as poly-lysine deeply affect bacterial physiology. In this work, we chemically characterized a class of chitosan polymers for their biocompatibility when adsorbed to glass. Chitosan chains of known length and composition allowed growth of Escherichia coli cells without any deleterious effects on cell physiology. Combined with a machine-learning approach, this method could measure the antibiotics susceptibility of a diversity of clinical strains in less than 1 hour and with higher accuracy than current methods. Last, chitosan polymers also supported growth of Klebsiella pneumoniae, another bacterial pathogen of clinical significance. The low cost of chitosan slides and their simple implementation makes them highly ver...

American Journal of Theoretical and Applied Statistics, 2017

The idea of pool testing originated with Dorfman during the World War II as an economical method ... more The idea of pool testing originated with Dorfman during the World War II as an economical method of testing blood samples of army inductees in order to detect the presence of infection. Dorfman proposed that rather than testing each blood sample individually, portions of each of the samples can be pooled and the pooled sample tested first. If the pooled sample is free of infection, all inductees in the pooled sample are passed with no further tests otherwise the remaining portions of each of the blood samples are tested individually. Apart from classification problem, pool testing can also be used in estimating the prevalence rate of a trait in a population which was the focus of our study. In approximating the prevalence rate, one-at-a-time testing is time consuming, non-cost effective and is bound to errors hence pool testing procedures have been proposed to address these problems. This study has developed statistical model which is used to sequentially switching between two experiments when the sensitivity and specificity of the test kits is less than 100%. The experiments are selected sequentially, so that at each stage, the information available at that stage is used to determine which experiment to carry out at the next stage. The method of maximum likelihood estimator (MLE) was used in obtaining the estimators. The fisher information of different experiments is compared and the cut off values where one experiment is better than the other are calculated. The variance of the estimators has also been compared. The joint model has been compared to one-at-a-time and pool testing models by computing ARE. The joint model is found to be more efficient.

International Journal of Neuroscience, 1980

Two recent studies reported that various poisons affecting the central nervous system do not elic... more Two recent studies reported that various poisons affecting the central nervous system do not elicit conditioned taste aversion (CTA). To test the validity of this statement, cobra and krait neurotoxins were used as the US in the CTA paradigm and compared with lithium chloride. The results indicate 10 and 7.5 μg of cobra venom and 20, and 15 μg of krait venom produce clear-cut CTA in mice.

Anesthesia and analgesia, Jul 1, 2017

Many methods used to improve hospital and perioperative services productivity and quality of care... more Many methods used to improve hospital and perioperative services productivity and quality of care have assumed that the hospital is essentially a factory, and therefore, that industrial engineering and manufacturing-derived redesign approaches such as Six Sigma and Lean can be applied to hospitals and perioperative services just as they have been applied in factories. However, a hospital is not merely a factory but also a complex adaptive system (CAS). The hospital CAS has many subsystems, with perioperative care being an important one for which concepts of factory redesign are frequently advocated. In this article, we argue that applying only factory approaches such as lean methodologies or process standardization to complex systems such as perioperative care could account for difficulties and/or failures in improving performance in care delivery. Within perioperative services, only noncomplex/low-variance surgical episodes are amenable to manufacturing-based redesign. On the other...

Nature, 2016

Various rod-shaped bacteria mysteriously glide on surfaces in the absence of appendages such as f... more Various rod-shaped bacteria mysteriously glide on surfaces in the absence of appendages such as flagella or pili. In the deltaproteobacterium Myxococcus xanthus, a putative gliding motility machinery (Agl-Glt) localizes to so-called Focal Adhesion sites (FA) that form stationary contact points with the underlying surface. We discovered that the Agl-Glt machinery contains an innermembrane motor complex that moves intracellularly along a right-handed helical path, and when it becomes stationary at FA sites, it powers a left-handed rotation of the cell around its long axis. At FA sites, force transmission requires cyclic interactions between the molecular motor and adhesion proteins of the outer membrane via a periplasmic interaction platform, which presumably involves Reprints and permissions information is

Seminars in Cell & Developmental Biology, 2015

Motility of bacterial cells promotes a range of important physiological phenomena such as nutrien... more Motility of bacterial cells promotes a range of important physiological phenomena such as nutrient detection, harm avoidance, biofilm formation, and pathogenesis. While much research has been devoted to the mechanism of bacterial swimming in liquid via rotation of flagellar filaments, the mechanisms of bacterial translocation across solid surfaces are poorly understood, particularly when cells lack external appendages such as rotary flagella and/or retractile type IV pili. Under such limitations, diverse bacteria at the single-cell level are still able to &amp;amp;amp;quot;glide&amp;amp;amp;quot; across solid surfaces, exhibiting smooth translocation of the cell along its long axis. Though multiple gliding mechanisms have evolved in different bacterial classes, most remain poorly characterized. One exception is the gliding motility mechanism used by the Gram-negative social predatory bacterium Myxococcus xanthus. The available body of research suggests that M. xanthus gliding motility is mediated by trafficked multi-protein (Glt) cell envelope complexes, powered by proton-driven flagellar stator homologues (Agl). Through coupling to the substratum via polysaccharide slime, Agl-Glt assemblies can become fixed relative to the substratum, forming a focal adhesion site. Continued directional transport of slime-associated substratum-fixed Agl-Glt complexes would result in smooth forward movement of the cell. In this review, we have provided a comprehensive synthesis of the latest mechanistic and structural data for the mechanism of focal adhesion-mediated gliding motility in M. xanthus, with emphasis on the role of each Agl and Glt protein. Finally, we have also highlighted the possible connection between the motility complex and a new type of spore coat assembly system, suggesting that gliding and cell envelope synthetic complexes are evolutionarily linked.