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Function of CTLGA9 Amino Acid Residue Leucine-6 in Modulating Cry Toxicity

Intikhab Alam, Intikhab Alam, Intikhab Alam, Khadija Batool, Khadija Batool, Aisha Lawan Idris, Aisha Lawan Idris, Weilong Tan, Xiong Guan, Xiong Guan, Lingling Zhang, Lingling Zhang
2022 Frontiers in Immunology  
Aedes aegypti is a crucial vector for many arboviral diseases that cause millions of deaths worldwide and thus is of major public health concern. Crystal (Cry) proteins, which are toxins produced by Bacillus thuringiensis, are structurally organized into three-domains, of which domain II is the most variable in terms of binding towards various toxin receptors. The binding of Cry11Aa to putative receptor such as aminopeptidase-N (APN) is explicitly inhibited by midgut C-type lectins (CTLs). The
more » ... imilarity between the domain II fold of Cry11Aa toxin and the carbohydrate recognition domain in the CTLs is a possible structural basis for the involvement of Cry domain II in the recognition of carbohydrates on toxin receptors. In this study, a site-directed point mutation was introduced into the A. aegypti CTLGA9 gene on the basis of molecular docking findings, leading to substitution of the Leucine-6 (Leu-6) residue in the protein with alanine. Subsequently, functional monitoring of the mutated protein was carried out. Unlike the amino acid residues of wild-type CTLGA9, none of the residues of mutant (m) CTLGA9 were competed with Cry11Aa for binding to the APN receptor interface. Additionally, ligand blot analysis showed that both wild-type and mutant CTLGA9 had similar abilities to bind to APN and Cry11Aa. Furthermore, in the competitive ELISA in which labeled mutant CTLGA9 (10 nM) was mixed with increasing concentrations of unlabeled Cry11Aa (0–500 nM), the mutant showed no competition with Cry11Aa for binding to APN., By contrast, in the positive control sample of labeled wild type CTLGA9 mixed with same concentrations of Cry11Aa competition between the two ligands for binding to the APN was evident. These results suggest that Leucine-6 may be the key site involved in the competitive receptor binding between CTLGA9 and Cry11Aa. Moreover, according to the bioassay results, mutant CTLGA9 could in fact enhance the toxicity of Cry11Aa. Our novel findings provide further insights into the mechanism of Cry toxicity as wel [...]
doi:10.3389/fimmu.2022.906259 pmid:35865517 pmcid:PMC9294448 doaj:de9414be3154488cb029a9d01fed5452 fatcat:wly5udx7gjdwffmebk5woivqcm

Inti Research Paper.pdf [article]

Intikhab Alam Shamsi
2022 figshare.com  
MANSINGH MANRAL* AND INTIKHAB ALAM SHAMSI** The glossy multi-color supplements in newspaper appear for promotional purpose but the hopeless reader believes the report is independent.  ... 
doi:10.6084/m9.figshare.21257076.v1 fatcat:dusftm2singmnnqmo7acjsaqkq

No Evidence for Temperature-Dependence of the COVID-19 Epidemic [article]

Tahira Jamil, Intikhab Syed Alam, Takashi Gojobori, Carlos Duarte
2020 medRxiv   pre-print
The pandemic of the COVID-19 disease extended from China across the north-temperate zone, and more recently to the tropics and southern hemisphere. We find no evidence that spread rates decline with temperatures above 20 oC, suggesting that the COVID-19 disease is unlikely to behave as a seasonal respiratory virus.
doi:10.1101/2020.03.29.20046706 fatcat:z3m4r6p3ezd6boicjuelj4tcpy

BEACON: automated tool for Bacterial GEnome Annotation ComparisON

Manal Kalkatawi, Intikhab Alam, Vladimir B. Bajic
2015 BMC Genomics  
Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of
more » ... functional genome annotations generated by different annotation methods (AMs). Results: The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions: We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/. International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
doi:10.1186/s12864-015-1826-4 pmid:26283419 pmcid:PMC4539851 fatcat:oxz2am67kzba3aoisbcrj6vwwy

Importance of New Media Technology in Political Communication– A Case Study of Political Campaigning in India

Intikhab Alam Shamsi
2020 Zenodo  
Intikhab Alam Shamsi space?  ...  Vn. / 10 Intikhab Alam Shamsi www.bioglobia.in Volume 6 Issue 1, 2020 Int. Res.  ... 
doi:10.5281/zenodo.7132896 fatcat:xtjaaaexyncn5lkhmv763m7ln4

Rapid Evolution of SARS-CoV-2 Challenges Human Defenses [article]

Carlos M. Duarte, David Ketcheson, Victor M Eguiluz, Susana R Agusti, Juan F Gracia, Tahira Jamil, Elisa Laiolo, Takashi Gojobori, Intikhab Alam
2021 bioRxiv   pre-print
Laiolo, Takashi Gojobori, and Intikhab Alam Correspondence to: carlos.duarte@kaust.edu.sa. Figure legends This PDF file includes: Materials and Methods Fig.  ... 
doi:10.1101/2021.03.27.437300 fatcat:hxq3b7y23ffathy6iq4poqsjmu

No Evidence for Temperature-Dependence of the COVID-19 Epidemic

Tahira Jamil, Intikhab Alam, Takashi Gojobori, Carlos M. Duarte
2020 Frontiers in Public Health  
Copyright © 2020 Jamil, Alam, Gojobori and Duarte. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fpubh.2020.00436 pmid:32984240 pmcid:PMC7479095 fatcat:x4fyfwrry5eenhweu6cdu2u52y

The Role of Traditional Elders in the Establishment of the law and order in FATA, PAKISTAN

Shahid Iqbal, Intikhab Alam
2020 الإيضاح  
This study was carried out in Khyber Agency (FATA), with the main objective to determine the tribal thoughts towards the role of traditional elders in the establishment of law and order. The data was collected from randomly selected 380 sampled respondents, which includes people from commerce/trade community, students, Internally Displaced Persons (IDPs) and representatives from political administration was randomly drawn. To see the association between independent and dependent variables chi
more » ... uare statistics was used. The study reveals that the local people were not happy with the Malaks' role (traditional local leaders) for the reason of their personal interests which sustained their subjugation. It further indicates that the Malaks' role was weakened by the stronger influence of insurgents and even their tax collection act in view of the prevalent poor law and order situation. However, the Malaks' role was double-edged as they got benefits from the political administration on the one hand and looked for the insurgents' help in different issues on the other. Tribal elders remained silent over misdeed in the area. The local Malaks are enjoying like bourgeoisie class as political administration and masses are bound to go in accordance with their directions. They are not facing any kind of accountability for the financial benefits awarded by the political administration. The locals were found with oppressed feelings caused by the suppressive role of Malaks. Frontier crime Regulation (FCR) which is a tribal law has enshrined power to the local Malaks and political administration. The state law, which is not in vogue in the entire tribal belt, was observed as the only mechanism to bring normalcy by narrowing the spectrum of the Malaks' role and political administration. The local bourgeoisie (Malakān), operating around with all might's being enjoyed and exercised on their parts through a strong endorsement from the administration needs not to be overlooked. Their role must be defined under the provision of state law enshrined through constitutional cover. This would make them accountable and sense of accountability always brings honesty, dedication and loyalty. Moreover, oppressed feeling surfaced during the study from the local masses regarding the role of these Malak would also brought under the umbrella of check and balance and thus a democratic norms would prevail in aftermath.
doi:10.37556/al-idah.038.01.0348 fatcat:b66nr5h6abhc7inn2ynft267qy

Family Role in Settling Inheritance Feuds among Heirs

Aman Ullah, Intikhab Alam, Mussawar Shah, Saima Sarir
2016 Peshawar Journal of Psychology and Behavioral Sciences  
The current study deals with role of family with relation to feud settlement at family level. A sample size of 182 respondents was randomly selected of those respondents who had at least 10 acres of land. Frequency distribution of data was observed to have a comprehensive data layout. Moreover, Chi square (χ2) statistics was used to determine the level of association between dependent variable (Feud Settlement) with the independent variables (Role of Family)., The study depicted that family
more » ... an important role in division of property among the heirs with laid down propositions among the male and female and thus consider the transformation of inheritance and property obligatory to avoid feuds at family level but while the elder brother within the family had more rights in the division of property as compare to other members by virtue of occupying the place of leadership in terms of age while supposedly replacing the father. Moreover, incapability on part of the male gender regarding divisions of property in inheritance usually crops up in shape of tussles and feuds among the real heirs that in turn has brought instability to the family as an institution. In addition, such distributions of property is only practiced by the concerned family members with sole discretion on part of legal heirs only. As well as prohibiting all the discrimination, especially in respect of inherited property mainly on the basis of age, gender and custom could lead to the mitigation of inheritance related feuds at family level.
doaj:6db1c5d0fba740d39548c3b3e571fc3b fatcat:apapkufcfjh6voav4lflquu56u

A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

Intikhab Alam, Simon J Hubbard, Stephen G Oliver, Magnus Rattray
2007 BMC Genomics  
Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs), which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models. Results: Here we present a general approach to
more » ... ate domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam) using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustilago maydis, a fungal pathogen of maize, and the white rot fungus Phanerochaete chrysosporium. In addition, we include the Microsporidion Encephalitozoon cuniculi, an obligate intracellular parasite, and two non-fungal species, the oomycetes Phytophthora sojae and Phytophthora ramorum, both plant pathogens. We evaluate the performance in terms of coverage against the original 30 genomes used in training FPfam and against five more recently sequenced fungal genomes that can be considered as an independent test set. We show that kingdom-specific models such as FPfam can find instances of both novel and well characterized domains, increases overall coverage and detects more domains per sequence with typically higher bitscores than Pfam for the same domain families. An evaluation of the effect of changing E-values on the coverage shows that the performance of FPfam is consistent over the range of E-values applied. Conclusion: Kingdom-specific models are shown to provide improved coverage. However, as the models become more specific, some sequences found by Pfam may be missed by the models in FPfam and some of the families represented in the test set are not present in FPfam. Therefore, we recommend that both general and specific libraries are used together for annotation and we find that a significant improvement in coverage is achieved by using both Pfam and FPfam.
doi:10.1186/1471-2164-8-97 pmid:17425790 pmcid:PMC1854895 fatcat:uk5fixrnlfagtncaqnx4czcone

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

Nojood A. Aalismail, David K. Ngugi, Rubén Díaz-Rúa, Intikhab Alam, Michael Cusack, Carlos M. Duarte
2019 Scientific Reports  
Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene
more » ... logue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.
doi:10.1038/s41598-019-50194-0 pmid:31551441 pmcid:PMC6760216 fatcat:sfrn3yaytjacpaphskxhzlz5om

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
2021 Plants  
The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae
more » ... , of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.
doi:10.3390/plants10122700 pmid:34961171 pmcid:PMC8704796 fatcat:a2p2o6nuyjhj7fhwf7pkestqsm

A Methodology for Comparative Functional Genomics

Intikhab Alam, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, Norman W. Paton
2007 Journal of Integrative Bioinformatics  
AbstractThe continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value
more » ... hat can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.
doi:10.1515/jib-2007-69 fatcat:jdh6crvrkjf7fmjskpx6z4xcbm

Parents Attitude Towards Enrollments in Public and Private Schools

Alamgeer Khan, Hamad Ali, Mushtaq Ahmad Jadoon, Saima Sarir, Intikhab Alam, Muhammad Jawad
2016 Peshawar Journal of Psychology and Behavioral Sciences  
Education not only enables us to become acceptable members of social sphere but also enable us to take right decision at right time. Parents' decision play important role in the lives of their children. The major aim of the present study was to find out the major causes of enrolling students in public schools by parents. Data for the study were collected from 280 respondents belonging to three selected villages in Tehsil Oghi, District Mansehra. The study found significant association between
more » ... rception about enrollment in public schools and children's education was major priority of the educated parents, they understand their educational problems, teach them at home, give importance to sports, provides them latest technologies and facilities, provide tuition to children if needed, believed in hard work of parents and good grades of children in exams and ultimately educated parents' children obtain good grades. The study recommends that government should initiate mobilization campaign for illiterate parents, which will enhance the enrollment of children in public school.
doi:10.32879/pjpbs.2015.1.2.151-161 fatcat:kcpuj7lkkzap7hiwautgpbokna

Psychological Reasons for Committing Crimes: A Case Study of Central Jail Peshawar

Zarsanga ,, Intikhab Alam, Shahid Iqbal, Alamgeer Khan
2018 Peshawar Journal of Psychology and Behavioral Sciences  
The present study was conducted in District Central Jail, Peshawar, Khyber Pakhtunkhwa, Pakistan to assess the factors shaping the criminal attitude of adults. The study proceeded with the objectives to assess the relationship between psychological factors with criminal attitude among criminals. A sample size of N=196 was randomly drawn from the universe. Sampling covered all the adult criminal of the age group of 18-64 years from the total population of N=360 convicted criminals. Frequency
more » ... ribution and bi-vitiate analysis between dependent variable i.e. criminal attitude and independent variables namely psychological aspects were ascertain through cross tabulation while indexing the dependent variable. At bi-variate level, parents sentence several time was found significant, relatives' involvement in criminal activities, large family was responsible for crimes, parents using intoxicants, joint family generating criminal attitude. Moreover, feeling of low social status, unhappy family life, commitment to family cause, broken family, low moral values, internalization of criminal values and vicious tendencies of crimes were found significant with criminal attitude.. The study concluded that poor family with large size had high interaction with criminals were some of the attributing factors for committing crimes.
doi:10.32879/picp.2018.4.1.121 fatcat:uzdjmpyejveatpzupwxzcmy7cy
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