A K M Firoj Mahmud

A K M Firoj Mahmud

Umeå universitet

H-index: 8

Europe-Sweden

About A K M Firoj Mahmud

A K M Firoj Mahmud, With an exceptional h-index of 8 and a recent h-index of 8 (since 2020), a distinguished researcher at Umeå universitet,

His recent articles reflect a diverse array of research interests and contributions to the field:

A core transcriptional response for biofilm formation by Y. pseudotuberculosis

RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration‐resistant prostate cancer

Molecular mechanisms of Yersinia pseudotuberculosis for adaptation and establishment of infection in host tissue

ProkSeq for complete analysis of RNA-Seq data from prokaryotes

Antimicrobial resistance profiling and molecular epidemiological analysis of extended spectrum β-lactamases produced by extraintestinal invasive Escherichia coli isolates from …

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules

A K M Firoj Mahmud Information

University

Umeå universitet

Position

___

Citations(all)

226

Citations(since 2020)

170

Cited By

99

hIndex(all)

8

hIndex(since 2020)

8

i10Index(all)

7

i10Index(since 2020)

6

Email

University Profile Page

Umeå universitet

Top articles of A K M Firoj Mahmud

A core transcriptional response for biofilm formation by Y. pseudotuberculosis

Authors

AKMF Mahmud,Kristina Nilsson,Dharmendra Kumar Soni,Rajdeep Choudhury,Roberto Navais,Simon Tuck,K Avican,M Fällman

Journal

bioRxiv

Published Date

2022/3/11

Previous transcriptional profiling of the enteropathogen Yersinia pseudotuberculosis during persistent stages of colonisation of mouse cecal lymphoid follicles indicated the possible involvement of biofilm in infection maintenance. Not much is known about the mechanisms responsible for biofilm formation by this pathogen, and most current knowledge is based on results of experiments conducted using the related Y. pestis pathogen that forms biofilm in the flea gut. In this study, we performed transcriptional profiling of Y. pseudotuberculosis in biofilms from different biofilm-inducing conditions, bile exposure, amino acid deprivation and in vivo mimicking conditions with and without oxygen. The comparison of differential expression of genes in biofilm versus planktonic bacteria showed a set of 54 core genes that were similarly regulated, independent of inducing condition. This set included many genes that were previously shown to be associated with biofilms, such as hutG, hsmF, hmsT and cpxP that were upreg-ulated and other genes such as hmsP and rfaH that were downregulated. There were also novel biofilm-associated genes, including genes encoding hypothetical proteins. To identify the genes involved in inducing biofilm formation, the gene expression of bacteria during an early initial phase when biofilm starts to form after induction by bile or amino acid depletion was determined. Comparisons of the resulting gene expression profiles with the profiles of non-induced bacteria incubated for the same period of time showed a set of core genes associated with early biofilm formation. This set included genes involved in quorum sensing, pili …

RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis

Authors

AKMF Mahmud,Roberto Navais,Kristina Nilsson,R Choudhury,K Avican,M Fallman

Journal

bioRxiv

Published Date

2022/2/11

Pathogenic bacteria use a broad range of virulence factors to thrive within their host. Yersinia pseudotuberculosis, a gram-negative enteropathogen in humans, utilises a Type III secretion system to overcome the host’s innate immune response. A global regulator previously shown to be essential for virulence in Y. pseudotuberculosis is RpoN. We show here that a strain lacking RpoN has a severely reduced capacity to secrete Yop effectors. This strain has a substantially reduced expression of genes encoding structural components of the secretion apparatus, the ysc operons, while expression of genes encoding effectors and translocators is less affected. We show that RpoN regulates a complex network, where one part is suggested to contribute to inducing Type III secretion via the enhancer-binding protein GlrR/RpoN regulon. By analogy, during inducement of Type III secretion, RpoN has a positive effect on expression of the sigma factor RpoE, which also is known to act downstream of GlrR. Interestingly, we found putative RpoE binding sites upstream of the ysc operons, and also a partial rescue of Yop secretion in the rpoN mutant strain by overexpression of RpoE. Our findings suggest that the RpoN-mediated effect on expression of type III genes involves a sigma factor hierarchy, where RpoN via RpoE contributes to inducing Type III secretion.

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Authors

Kemal Avican,Jehad Aldahdooh,Matteo Togninalli,AKM Firoj Mahmud,Jing Tang,Karsten M Borgwardt,Mikael Rhen,Maria Fällman

Journal

Nature Communications

Published Date

2021/6/2

Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific ‘universal stress responders’, that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses …

Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration‐resistant prostate cancer

Authors

Julius Semenas,Tianyan Wang,Azharuddin Sajid Syed Khaja,AKM Firoj Mahmud,Athanasios Simoulis,Thomas Grundström,Maria Fällman,Jenny L Persson

Journal

Molecular Oncology

Published Date

2021/4

Selective ERα modulator, tamoxifen, is well tolerated in a heavily pretreated castration‐resistant prostate cancer (PCa) patient cohort. However, its targeted gene network and whether expression of intratumor ERα due to androgen deprivation therapy (ADT) may play a role in PCa progression is unknown. In this study, we examined the inhibitory effect of tamoxifen on castration‐resistant PCa in vitro and in vivo. We found that tamoxifen is a potent compound that induced a high degree of apoptosis and significantly suppressed growth of xenograft tumors in mice, at a degree comparable to ISA‐2011B, an inhibitor of PIP5K1α that acts upstream of PI3K/AKT survival signaling pathway. Moreover, depletion of tumor‐associated macrophages using clodronate in combination with tamoxifen increased inhibitory effect of tamoxifen on aggressive prostate tumors. We showed that both tamoxifen and ISA‐2011B exert their on …

Molecular mechanisms of Yersinia pseudotuberculosis for adaptation and establishment of infection in host tissue

Authors

AKM Mahmud

Published Date

2021

Bacterial pathogens can evade the host’s immune defence to adapt and establish an infection within the host. Some even slip into a quiescent state to establish themselves without acutely harming the host. Phylogenetically unrelated bacteria can share similar strategies for the establishment of infection and for persistence. Our lab previously showed that Yersinia pseudotuberculosis underwent a dramatic reprogramming from a virulent phenotype expressing virulence genes, including T3SS and Yop effectors during early infection, to an adapted phenotype capable of persisting in tissue. The overall aim of my PhD study was to dissect the mechanisms behind bacterial adaptation and maintenance of infection within host tissue using Y. pseudotuberculosis as a model pathogen. The ultimate goal is to identify key players of critical importance for the ability of the bacterium to maintain and establish infection in host tissue. In my studies, I mainly focused on bacterial biofilm and the role of the alternative sigma factor RpoN. Much of my studies involve RNA-Seq analyses, encouraging me to develop a convenient, time-efficient, and all-purpose RNA-Seq data analysis package especially designed for prokaryotic organisms. The package is available online as a free tool and can be used by any biologist with minimal computational knowledge. We systematically examined biofilm formation of Y. pseudotuberculosis under different stress conditions and found that biofilm development involved a series of adaptive responses against various stressors, including bile, pH, amino acid deprivation, and temperature and oxygen-level changes. Analyses of …

ProkSeq for complete analysis of RNA-Seq data from prokaryotes

Authors

AKM Firoj Mahmud,Nicolas Delhomme,Soumyadeep Nandi,Maria Fällman

Journal

Bioinformatics

Published Date

2021/1/1

Summary Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results. Availability and implementation ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container …

Antimicrobial resistance profiling and molecular epidemiological analysis of extended spectrum β-lactamases produced by extraintestinal invasive Escherichia coli isolates from …

Authors

Abebe Aseffa Negeri,Hassen Mamo,Jyoti M Gurung,AKM Firoj Mahmud,Maria Fällman,Eyasu Tigabu Seyoum,Adey Feleke Desta,Matthew S Francis

Journal

Frontiers in Microbiology

Published Date

2021/8/2

The treatment of invasive Escherichia coli infections is a challenge because of the emergence and rapid spread of multidrug resistant strains. Particular problems are those strains that produce extended spectrum β-lactamases (ESBL’s). Although the global characterization of these enzymes is advanced, knowledge of their molecular basis among clinical E. coli isolates in Ethiopia is extremely limited. This study intends to address this knowledge gap. The study combines antimicrobial resistance profiling and molecular epidemiology of ESBL genes among 204 E. coli clinical isolates collected from patient urine, blood, and pus at four geographically distinct health facilities in Ethiopia. All isolates exhibited multidrug resistance, with extensive resistance to ampicillin and first to fourth line generation cephalosporins and sulfamethoxazole-trimethoprim and ciprofloxacin. Extended spectrum β-lactamase genes were detected in 189 strains, and all but one were positive for CTX-Ms β-lactamases. Genes encoding for the group-1 CTX-Ms enzymes were most prolific, and CTX-M-15 was the most common ESBL identified. Group-9 CTX-Ms including CTX-M-14 and CTX-27 were detected only in 12 isolates and SHV ESBL types were identified in just 8 isolates. Bacterial typing revealed a high amount of strains associated with the B2 phylogenetic group. Crucially, the international high risk clones ST131 and ST410 were among the sequence types identified. This first time study revealed a high prevalence of CTX-M type ESBL’s circulating among E. coli clinical isolates in Ethiopia. Critically, they are associated with multidrug resistance phenotypes and high …

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules

Authors

AKM Firoj Mahmud,Doo Yang,Per Stenberg,Ilya Ioshikhes,Soumyadeep Nandi

Journal

Journal of Computational Biology

Published Date

2020/8/1

Multiple transcription factors (TFs) bind to specific sites in the genome and interact among themselves to form the cis-regulatory modules (CRMs). They are essential in modulating the expression of genes, and it is important to study this interplay to understand gene regulation. In the present study, we integrated experimentally identified TF binding sites collected from published studies with computationally predicted TF binding sites to identify Drosophila CRMs. Along with the detection of the previously known CRMs, this approach identified novel protein combinations. We determined high-occupancy target sites, where a large number of TFs bind. Investigating these sites revealed that Giant, Dichaete, and Knirp are highly enriched in these locations. A common TAG team motif was observed at these sites, which might play a role in recruiting other TFs. While comparing the binding sites at distal and proximal …

Genome-scale mapping reveals complex regulatory activities of RpoN in Yersinia pseudotuberculosis

Authors

AKM Firoj Mahmud,Kristina Nilsson,Anna Fahlgren,Roberto Navais,Rajdeep Choudhury,Kemal Avican,Maria Fällman

Journal

Msystems

Published Date

2020/12/22

RpoN, an alternative sigma factor commonly known as σ54, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN binding motif located at 103 inter- and intragenic sites on both sense and antisense strands. Deletion of rpoN had a large impact on gene expression, including downregulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also …

See List of Professors in A K M Firoj Mahmud University(Umeå universitet)

A K M Firoj Mahmud FAQs

What is A K M Firoj Mahmud's h-index at Umeå universitet?

The h-index of A K M Firoj Mahmud has been 8 since 2020 and 8 in total.

What are A K M Firoj Mahmud's top articles?

The articles with the titles of

A core transcriptional response for biofilm formation by Y. pseudotuberculosis

RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration‐resistant prostate cancer

Molecular mechanisms of Yersinia pseudotuberculosis for adaptation and establishment of infection in host tissue

ProkSeq for complete analysis of RNA-Seq data from prokaryotes

Antimicrobial resistance profiling and molecular epidemiological analysis of extended spectrum β-lactamases produced by extraintestinal invasive Escherichia coli isolates from …

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules

...

are the top articles of A K M Firoj Mahmud at Umeå universitet.

What is A K M Firoj Mahmud's total number of citations?

A K M Firoj Mahmud has 226 citations in total.

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