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  1. Article ; Online: Genomic Analysis Reveals Subdivision of Black Rats (

    Baig, Mumtaz / Farah, Sameera / Atkulwar, Ashwin / Searle, Jeremy B

    Genes

    2022  Volume 13, Issue 2

    Abstract: In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, ...

    Abstract In contrast to the detailed and globally extensive studies on the spread of the commensal black rat,
    MeSH term(s) Animals ; DNA, Mitochondrial/genetics ; Genomics ; India ; Phylogeny ; Phylogeography ; Rats
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2022-01-29
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13020267
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  2. Article: Genomic Analysis Reveals Subdivision of Black Rats (Rattus rattus) in India, Origin of the Worldwide Species Spread

    Baig, Mumtaz / Farah, Sameera / Atkulwar, Ashwin / Searle, Jeremy B.

    Genes. 2022 Jan. 29, v. 13, no. 2

    2022  

    Abstract: In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a ... ...

    Abstract In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a genomic approach, we typed 27 R. rattus samples from Peninsular India using the genotyping-by-sequencing (GBS) method. Filtering and alignment of the FASTQ files yielded 1499 genome-wide SNPs. Phylogenomic tree reconstruction revealed a distinct subdivision in the R. rattus population, manifested as two clusters corresponding to the east and west coasts of India. We also identified signals of admixture between these two subpopulations, separated by an Fst of 0.20. This striking genomic difference between the east and west coast populations mirrors what has previously been described with mitochondrial DNA sequencing. It is notable that the west coast population of R. rattus has been spread globally, reflecting the origins of commensalism of the species in Western India and the subsequent transport by humans worldwide.
    Keywords Rattus rattus ; coasts ; commensalism ; genetic variation ; genomics ; genotyping by sequencing ; mitochondrial DNA ; phylogeny ; phylogeography ; India
    Language English
    Dates of publication 2022-0129
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13020267
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Low genetic diversity of the endangered Indian wild ass Equus hemionus khur, as revealed by microsatellite analyses.

    Khaire, Devendra / Atkulwar, Ashwin / Farah, Sameera / Baig, Mumtaz

    Journal of genetics

    2017  Volume 96, Issue 2, Page(s) e31–e34

    MeSH term(s) Animals ; Endangered Species ; Equidae/genetics ; Genetic Variation ; India ; Microsatellite Repeats/genetics
    Language English
    Publishing date 2017-06-27
    Publishing country India
    Document type Journal Article
    ZDB-ID 3039-9
    ISSN 0973-7731 ; 0958-8361 ; 0022-1333
    ISSN (online) 0973-7731
    ISSN 0958-8361 ; 0022-1333
    DOI 10.1007/s12041-017-0784-9
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    Ub I Zs.72: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)
    Zs.MA 8: Show issues

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  4. Article ; Online: A new allele of the kappa-casein gene in local zebu cattle breeds.

    Ahmad, Tauseef / Atkulwar, Ashwin / Farah, Sameera / Singh, Vijendra / Baig, Mumtaz

    The Journal of dairy research

    2017  Volume 85, Issue 1, Page(s) 3–6

    MeSH term(s) Animals ; Base Sequence ; Caseins/genetics ; Cattle/genetics ; Genetic Variation ; Genotype ; India ; Phylogeny
    Chemical Substances Caseins
    Language English
    Publishing date 2017-11-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 242089-2
    ISSN 1469-7629 ; 0022-0299
    ISSN (online) 1469-7629
    ISSN 0022-0299
    DOI 10.1017/S0022029917000656
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A single point mutation converts a proton-pumping rhodopsin into a red-shifted, turn-on fluorescent sensor for chloride.

    Tutol, Jasmine N / Lee, Jessica / Chi, Hsichuan / Faizuddin, Farah N / Abeyrathna, Sameera S / Zhou, Qin / Morcos, Faruck / Meloni, Gabriele / Dodani, Sheel C

    Chemical science

    2021  Volume 12, Issue 15, Page(s) 5655–5663

    Abstract: The visualization of chloride in living cells with fluorescent sensors is linked to our ability to design hosts that can overcome the energetic penalty of desolvation to bind chloride in water. Fluorescent proteins can be used as biological ... ...

    Abstract The visualization of chloride in living cells with fluorescent sensors is linked to our ability to design hosts that can overcome the energetic penalty of desolvation to bind chloride in water. Fluorescent proteins can be used as biological supramolecular hosts to address this fundamental challenge. Here, we showcase the power of protein engineering to convert the fluorescent proton-pumping rhodopsin GR from
    Language English
    Publishing date 2021-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d0sc06061e
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  6. Article ; Online: Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

    Khaire, Devendra / Atkulwar, Ashwin / Farah, Sameera / Baig, Mumtaz

    Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

    2017  Volume 28, Issue 5, Page(s) 681–686

    Abstract: The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ...

    Abstract The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.
    MeSH term(s) Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Endangered Species ; Equidae/classification ; Equidae/genetics ; Genetic Variation ; India ; Phylogeny ; Sequence Analysis, DNA/methods
    Chemical Substances DNA, Mitochondrial ; Cytochromes b (9035-37-4)
    Language English
    Publishing date 2017-09
    Publishing country England
    Document type Journal Article
    ISSN 2470-1408
    ISSN (online) 2470-1408
    DOI 10.3109/24701394.2016.1174221
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Phylogenomics and phylodynamics of SARS-CoV-2 retrieved genomes from India

    Farah, Sameera / Atkulwar, Ashwin / Praharaj, Manas Ranjan / Khan, Raja / Gandham, Ravikumar / Baig, Mumtaz

    medRxiv

    Abstract: The ongoing SARS-CoV-2 pandemic is one of the biggest outbreaks after the Spanish flu of 1918. Understanding the epidemiology of viral outbreaks is the first step towards vaccine development programs. This is the first phylodynamics study attempted on of ...

    Abstract The ongoing SARS-CoV-2 pandemic is one of the biggest outbreaks after the Spanish flu of 1918. Understanding the epidemiology of viral outbreaks is the first step towards vaccine development programs. This is the first phylodynamics study attempted on of SARS-CoV-2 genomes from India to infer its current evolution in the context of an ongoing pandemic. Out of 286 retrieved SARS-CoV-2 whole genomes from India, 138 haplotypes were generated and analyzed. Median-joining network was built to investigate the relatedness of SARS-CoV-2 haplotypes in India. The BDSIR package of BEAST2 was used to calculate the reproduction number (R0) and the infectious rate of the virus. Past and current population trend was investigated using the stamp date method in coalescent Bayesian skyline plot, implemented in BEAST2 and by exponential growth prior in BEAST 1.10.4. Median-joining network reveals two distinct ancestral clusters A and B showing genetic affinities with Wuhan outbreak sample. The network also illustrates the autochthonous development of isolates in a few instances. High basic reproduction number of SARS-nCoV-2 in India points towards the phase of active community transmission. The Bayesian skyline plot revel exponential rise in the effective population size (Ne) of Indian isolates from the first week of January to the first week of April 2020. More genome sequencing and analyses of the virus will be required in coming days to monitor COVID19 after the upliftment of lock down in India.
    Keywords covid19
    Language English
    Publishing date 2020-06-26
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.06.23.20138222
    Database COVID19

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  8. Article ; Online: Identification and Characterization of the Caspase-Mediated Apoptotic Activity of

    Panicker, Neena Gopinathan / Balhamar, Sameera Omar Mohammed Saeed / Akhlaq, Shaima / Qureshi, Mohammed Mansour / Rizvi, Tania Shamim / Al-Harrasi, Ahmed / Hussain, Javid / Mustafa, Farah

    Molecules (Basel, Switzerland)

    2019  Volume 24, Issue 5

    Abstract: Plants of the ... ...

    Abstract Plants of the genus
    MeSH term(s) Antineoplastic Agents, Phytogenic/chemistry ; Antineoplastic Agents, Phytogenic/pharmacology ; Apoptosis/drug effects ; Apoptosis Regulatory Proteins/genetics ; Apoptosis Regulatory Proteins/metabolism ; Caspases/metabolism ; Cell Line, Tumor ; Enzyme Activation/drug effects ; Humans ; Plant Extracts/chemistry ; Plant Extracts/pharmacology ; Teucrium/chemistry
    Chemical Substances Antineoplastic Agents, Phytogenic ; Apoptosis Regulatory Proteins ; Plant Extracts ; Caspases (EC 3.4.22.-)
    Language English
    Publishing date 2019-03-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules24050977
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  9. Article ; Online: Organic extracts from Cleome droserifolia exhibit effective caspase-dependent anticancer activity.

    Panicker, Neena Gopinathan / Balhamar, Sameera Omar Mohammed Saeed / Akhlaq, Shaima / Qureshi, Mohammed Mansoor / Rehman, Najeeb Ur / Al-Harrasi, Ahmed / Hussain, Javid / Mustafa, Farah

    BMC complementary medicine and therapies

    2020  Volume 20, Issue 1, Page(s) 74

    Abstract: Background: This study investigated the anticancer potential of the medicinal herb, Cleome droserifolia (CD), a local plant of the Arabian Peninsula. C. droserifolia is traditionally known for its rubefacient, anti-diabetic, anti-oxidant, and anti- ... ...

    Abstract Background: This study investigated the anticancer potential of the medicinal herb, Cleome droserifolia (CD), a local plant of the Arabian Peninsula. C. droserifolia is traditionally known for its rubefacient, anti-diabetic, anti-oxidant, and anti-inflammatory properties.
    Methods: Organic fractions of the aerial parts of Cleome droserifolia harvested from the Arabian Peninsula were tested in human breast and cervical cancer cell lines for their anticancer potential. This was accomplished by using biochemical and cellular assays, including MTT, caspase Glo, western blot, and annexin V/propidium iodide-based flow cytometry analyses.
    Results: Test of the dichloromethane fraction of the methanolic extract of C. droserifolia, (CDD) revealed potent cytotoxic activity (from 70 to 90%) against several human cancer cell lines, including MCF-7, MDA-MB-231, and HeLa. Further characterization of the CDD fraction in MCF-7 cells revealed that it could activate the enzymatic activity of various caspases in a statistically significant manner, and induce cleavage of both caspase 7 and poly ADB ribose polymerase (PARP) proteins, but not the ethyl acetate fraction. Test of the ability of CDD to induce early signs of apoptosis was validated by annexin V/propidium iodide assay using FACS analysis. Induction of apoptosis was completely reversed by the classic pan inhibitor of apoptosis, Z-VAD-FMK, reducing early apoptosis from 29.7 to 0.6%, confirming that CDD could induce caspase-dependent apoptosis.
    Conclusions: Altogether, our results reveal that C. droserifolia is a valuable medicinal plant with bioactive molecules that can induce apoptosis in human cancer cells. Thus, this plant should be explored further for its potential as an anticancer natural therapy as well as the isolation of novel molecules with anticancer properties.
    MeSH term(s) Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Caspases/metabolism ; Cell Line, Tumor ; Cleome/chemistry ; HeLa Cells ; Humans ; MCF-7 Cells ; Oman ; Plant Extracts/pharmacology
    Chemical Substances Antineoplastic Agents ; Plant Extracts ; Caspases (EC 3.4.22.-)
    Language English
    Publishing date 2020-03-06
    Publishing country England
    Document type Journal Article
    ISSN 2662-7671
    ISSN (online) 2662-7671
    DOI 10.1186/s12906-020-2858-0
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  10. Article: A new allele of the kappa-casein gene in local zebu cattle breeds

    Ahmad, Tauseef / Atkulwar, Ashwin / Farah, Sameera / Singh, Vijendra / Baig, Mumtaz

    Journal of dairy research. 2018 Feb., v. 85, no. 1

    2018  

    Abstract: Local zebu cattle breeds in Indian villages are crossbred with exotic breeds at an unprecedented rate without utilising the full potential of genomic technologies. In addition to agriculture produce, livestock, particularly cattle, constitute a vital ... ...

    Abstract Local zebu cattle breeds in Indian villages are crossbred with exotic breeds at an unprecedented rate without utilising the full potential of genomic technologies. In addition to agriculture produce, livestock, particularly cattle, constitute a vital source of livelihood for farmers in India. Age-old agricultural practices, errant monsoon, and frequent crop failures have resulted in Maharashtra having the highest number of farmer suicides in the country. Local cattle breeds are considered low-yield breeds and thus are primarily used as beasts of burden. Information on functional gene variants in Indian cattle breeds is scant and limited to PCR-RFLP study in few breeds. In this study, 32 samples from 8 cattle breeds were obtained from remote villages of Maharashtra state. By using the re-sequencing technology, we sequenced 403 bp of the exon IV CSN3 allele and inferred its haplotypes. From 32 samples, 14 genotypes (G1–G14) defined by 7 single-nucleotide polymorphisms (SNP's) were identified. From these 14 genotypes, we reconstructed 3 haplotypes (H01, H02, and H03) and estimated their frequencies. Of the 3 haplotypes, two (H01 and H03) corresponded to CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles, respectively. The third haplotype H02 was identified as a new allele and differed from CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles by one nonsynonymous mutation at the position C5306T-Ile100Thr. The neighbour-joining tree reconstruction revealed haplotype sharing or hybridisation between B. t. indicus and B. t. taurus because the 3 haplotypes originated in this study clustered with A1, B2, B4, B, G, and H alleles, which were reported previously in both the subspecies of B. taurus. The occurrence of one new allele in a small sample size highlights the urgency to screen local zebu cattle breeds by using genomic tools for circumventing genetic erosion that is widespread in Indian villages in India.
    Keywords alleles ; cattle ; crossbreds ; exons ; farmers ; genetic erosion ; genomics ; haplotypes ; hybridization ; kappa-casein ; livelihood ; monsoon season ; polymerase chain reaction ; restriction fragment length polymorphism ; single nucleotide polymorphism ; suicide ; villages ; zebu breeds ; India
    Language English
    Dates of publication 2018-02
    Size p. 3-6.
    Publishing place Cambridge University Press
    Document type Article
    ZDB-ID 242089-2
    ISSN 1469-7629 ; 0022-0299
    ISSN (online) 1469-7629
    ISSN 0022-0299
    DOI 10.1017/S0022029917000656
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    Z 1073: Show issues

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