IÁ

Intikhab Álam

King Abdullah University of Science and Technology

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Vladimir B. Bajić

King Abdullah University of Science and Technology

Takashi Gojobori

King Abdullah University of Science and Technology

Carlos M. Duarte

King Abdullah University of Science and Technology

Allan Kamau

King Abdullah University of Science and Technology

Ulrich Stingl

University of Fort Lauderdale

Heribert Hirt

King Abdullah University of Science and Technology

Maged M. Saad

King Abdullah University of Science and Technology

David Kamanda Ngugi

King Abdullah University of Science and Technology

Salim Bougouffa

King Abdullah University of Science and Technology

Feras F. Lafi

Middle East University

Cooperative Institutions

King Abdullah University of Science and Technology

134

RIKEN Center for Integrative Medical Sciences

The University of Agriculture, Peshawar

RIKEN

Harvard University

Centre National de la Recherche Scientifique

The University of Tokyo

Consejo Superior de Investigaciones Científicas

Chinese Academy of Sciences

University of Queensland

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

First Insights into the Viral Communities of the Deep-Sea Anoxic Brines of the Red Sea

Genomics Proteomics & Bioinformatics (2015)

André Antunes Intikhab Álam Marta Filipa Simões Camille Daniels Ari J. S. Ferreira

Abstract The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.

Biotope

Brine

10.1016/j.gpb.2015.06.004

Cite

Citations (26)

avaBLAST: a fast way of doing all versus all BLAST

Cairo International Biomedical Engineering Conference (2008)

Intikhab Álam S. A. Nadeem John Brooke

All versus all BLAST sequence comparison is now a standard procedure in the comparative analysis of large numbers of genomes. Several approaches have been developed to speed up general BLAST searches but these are focused towards searching a limited number of sequences against a large database and thus do not address the computational issues faced when carrying out an all versus all BLAST. Furthermore, optimal speed ups in BLAST searches using existing approaches could not be obtained due to additional overheads such as re-calculation of original BLAST E-values and unnecessary copying of query or database fragments that causes messaging overload when using communication libraries. We have developed a program, called avaBLAST that significantly reduces running times for large-scale all versus all BLAST searches. In contrast to earlier approaches, avaBLAST provides a significant speed up by dividing up the large query set of sequences and searching small chunks of queries against the complete database. avaBLAST avoids additional overheads as it does not require re-calculation of BLAST E-values and it do not require any communication libraries. In an evaluation, comparing multiple datasets from 32 fungal genomes against each other using 32 processors at NW-GRID cluster, avaBLAST achieves speed ups of up to 150 times over mpiBLAST.

Copying

Speedup

Sequence (biology)

10.1109/cibec.2008.4786046

Cite

Citations (1)

A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool

FEBS Open Bio (2018)

Anastassja Akal Ram Karan Adrian Höhl Intikhab Álam Malvina Vogler

Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single-cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 m KCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl-methyl-ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo- and thermoadaptation.

Brine

Cinnamyl alcohol

10.1002/2211-5463.12557

Cite

Citations (21)

Recombinant Mosquito Densovirus with Bti Toxins Significantly Improves Pathogenicity against Aedes albopictus

Toxins (2022)

Khadija Batool Intikhab Álam Peiwen Liu Zeng Shu Siyu Zhao

Mosquito densoviruses (MDVs) are mosquito-specific viruses that are recommended as mosquito bio-control agents. The MDV Aedes aegypti densovirus (AeDNV) is a good candidate for controlling mosquitoes. However, the slow activity restricts their widespread use for vector control. In this study, we introduced the Bacillus thuringiensis (Bti) toxin Cry11Aa domain II loop α8 and Cyt1Aa loop β6-αE peptides into the AeDNV genome to improve its mosquitocidal efficiency; protein expression was confirmed using nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS). Recombinant plasmids were transfected into mosquito C6/36 cell lines, and the expression of specific peptides was detected through RT-PCR. A toxicity bioassay against the first instar Aedes albopictus larvae revealed that the pathogenic activity of recombinant AeDNV was significantly higher and faster than the wild-type (wt) viruses, and mortality increased in a dose-dependent manner. The recombinant viruses were genetically stable and displayed growth phenotype and virus proliferation ability, similar to wild-type AeDNV. Our novel results offer further insights by combining two mosquitocidal pathogens to improve viral toxicity for mosquito control.

Aedes albopictus

Bacillus thuringiensis

Mosquito control

10.3390/toxins14020147

Cite

Citations (7)

Picocyanobacteria Community and Cyanophage Infection Responses to Nutrient Enrichment in a Mesocosms Experiment in Oligotrophic Waters

Frontiers in Microbiology (2020)

A. Guyard Rubén Díaz‐Rúa Carlos M. Duarte Xabier Irigoien John K. Pearman

Prochlorococcus and Synechococcus are pico-sized cyanobacteria that play a fundamental role in oceanic primary production, being particularly important in warm, nutrient-poor waters. Their potential response to nutrient enrichment is expected to be contrasting and to differ from larger phytoplankton species. Here, we used a metagenomic approach to characterize the responses to nutrient enrichment in the community of picocyanobacteria and to analyze the cyanophage response during a mesocosms experiment in the oligotrophic Red Sea. Natural picoplankton community was dominated by Synechococcus clade II, with marginal presence of Prochlorococcus (0.3% bacterial reads). Increased nutrient input triggered a fast Synechococcus bloom, with clade II being the dominant, with no response of Prochlorococcus growth. The largest bloom developed in the mesocosms receiving a single initial input of nutrients, instead of daily additions. The relative abundances of cyanophage sequences in cellular metagenomes increased during the experiment from 12.6% of total virus reads up to 40% in the treatment with the largest Synechococcus bloom. The subsequent collapse of the bloom pointed to a cyanophage infection on Synechococcus that reduced its competitive capacity, and was then followed by a diatom bloom. The cyanophage attack appears to have preferentially affected the most abundant Synechococcus clade II, increasing the evenness within the host population. Our results highlight the relevance of host-phage interactions on determining population dynamics and diversity of Synechococcus populations.

Prochlorococcus

Mesocosm

Bloom

Picoplankton

10.3389/fmicb.2020.01153

Cite

Citations (17)

The genome sequence of the wild tomatoSolanum pimpinellifoliumprovides insights into salinity tolerance

bioRxiv (Cold Spring Harbor Laboratory) (2017)

Rozaimi Razali Salim Bougouffa Mitchell J. L. Morton Damien J. Lightfoot Intikhab Álam

SUMMARY Solanum pimpinellifolium , a wild relative of cultivated tomato, offers a wealth of breeding potential for several desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome and annotation of S. pimpinellifolium ‘LA0480’. The ‘LA0480’ genome size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the ‘LA0480’ protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit-and yield-related traits in S. pimpinellifolium compared with cultivated tomato. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum , we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in ‘LA0480’. Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium , and to discover the genomic basis underlying its environmental robustness.

Genome size

10.1101/215517

Cite

Citations (2)

e-Fungi: a data resource for comparative analysis of fungal genomes

BMC Genomics (2007)

Cornelia Hedeler Han Hsi Wong Michael Cornell Intikhab Álam Darren M. Soanes

The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species. To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows. The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the genomes stored in the database. The database is accessible at http://www.e-fungi.org.uk , as is the WSDL for the web services.

Comparative Genomics

Architecture domain

10.1186/1471-2164-8-426

Cite

Citations (38)

A promoter-level mammalian expression atlas

Nature (2014)

Alistair R. R. Forrest Hideya Kawaji Michael Rehli J. Kenneth Baillie Michiel de Hoon

Cell type

Transcription

10.1038/nature13182

Cite

Citations (1,930)

Deciphering the role of WRKY transcription factors in plant resilience to alkaline salt stress

Plant Stress (2024)

Sindho Wagan Maqsood Ali Muneer Ahmed Khoso Intikhab Álam Khuzin Dinislam

The WRKY gene family consists of unique transcription factors (TFs) found exclusively in plants. These TFs play a crucial role in regulating how plants respond to various abiotic stresses, such as saline-alkaline conditions, temperature fluctuations, drought, UV radiation and others. Scientists have been progressively studying the roles and mechanisms of WRKY in several plant species, including both model plants and essential agricultural crops. This study focus has emerged due to the understanding that alkaline and saline soil stressors considerably impede global agricultural productivity. Multiple research efforts have underscored the significant biological functions of WRKY TFs in assisting plants in coping with various abiotic challenges, particularly in enhancing their ability to withstand alkaline-salt stress. This review aims to investigate the structural capabilities of WRKY TFs and their impact on plant responses to alkaline and salt stresses. Additionally, it seeks to elucidate the role of these TFs in alleviating diverse abiotic and biotic stressors. The objective of this review study is to provide comprehensive insights into the current state of the field and the importance of WRKY TFs in regulating plant responses to salt and alkaline stress.

WRKY protein domain

Resilience

Transcription

10.1016/j.stress.2024.100526

Cite

Citations (3)

ANALYSIS OF THE MULTIDIMENSIONAL IMPACTS OF CORONA VIRUS DISEASE-2019 (COVID-19) PANDEMIC

Humanities & Social Sciences Reviews (2021)

Imran Imran Saima Sarir Mamoon Khan Khattak Intikhab Álam Seema Zubair

Purpose of the study: The twenty-first century has witnessed numerous impacts of the novel Corona Virus Disease-2019 (Covid-19) pandemic in different walks of life across the globe. The present study was designed to get a societal response regarding the multifaceted impacts of the Covid-19 pandemic on the lives of the populace of the study locale. Methodology: The researchers selected a qualitative research approach for gaining in-depth insights on the issue at hand, wherein the data was collected from the potential participants through purposive sampling. The In-depth Interviews were conducted in district Swat which is one of the most affected districts from Covid-19. The In-depth Interview was used as a research instrument. The data was analyzed through thematic analysis. Main Findings: The study findings revealed that human lives are severely affected by the Covid-19 pandemic. The routine life cycle was badly affected, and people were confined to their houses. Like other parts of the world, different sectors like education, health, rituals, social interaction, travel, and tourism are desperately affected. Resultantly, it drastically raised the socio-cultural and economic (especially unemployment) unrest situation in the region. Apart from these consequences, due to the Pandemic scenario, various socio-cultural rituals, events, and activities were at a halt due to the imposition of social distancing measures. Applications of this study: The findings can be utilized/generalized in the normal course of life keeping in view the multidimensional impacts of the Covid-19 in the region. This study could be utilized for future research studies on the same issue. Novelty/Originality of this study: Besides, the study has immense significance, such studies are novel in the region with such a distinct perspective that covers various aspects of the impacts of Covid-19 using a qualitative research approach.

Pandemic

Social distance

Thematic Analysis

Globe

10.18510/hssr.2021.919

Cite

Citations (1)