Anu Bashamboo

Publications (7)11.47 Total impact

• Source

  Available from: Sunita Bhatnagar

  Dataset: A 1.3 kb Satellite DNA from Bubalus bubalis not Conserved Evolutionarily is Transcribed

  Sunita Bhatnagar, Anu Bashamboo, Munmun Chattopadhyay, Supriya Gangadharan, Sher Ali
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  ABSTRACT: A 1.3 kb satellite DNA from a size defined genomic library of mammal Bubalus bubalis was cloned and sequenced. The clone pSB1 is AT rich with 447 A (33.6%), 262 C (19.7%), 240 G (19.0%) and 383 T (28.8%). There were about 1400 copies of contig in the bubaline genome but it did not uncover allele length variation when used as probe in conjunction with a number of restriction enzymes. The contig pSB1 is not conserved evolutionarily and cross hybridizes only with the Bovideae family. A set of primers from 5 (nt 422 to 441) and 3 (nt 962 to 947) deduced from the clone used for PCR amplification with four members of the Bovideae family gave the expected 530 bp band of equal intensity indicating a similar number of copies in all the four species namely Bos indicus, Capra hircus, Ovis aries and Bubalus bubalis. Expression studies with pSB1 following slot-blot hybridization with total RNA isolated from ovary, testes, kidney, lung and spleen revealed varying signal intensities in all the tissues with a most prominent signal in spleen but a faint one in ovary. Further sequence analysis revealed the presence of several eukaryotic transcriptional elements such as NF-E1, Poly-A signal, lariat consensus sequences, and CTF/NF1 binding sites. Blast search showed 90% sequence similarity with the reverse transcriptase gene of Bos taurus and se-quences from nt 283 to 636 within the contig showed highly conserved reverse transcriptase like signatures along with N-glycosylation and protein kinase C phosphorylation sites. From the data we conclude that the pSB1 representing satellite DNA is associated with transcribing sequences. The prospect of identifying functional genes linked with the satellite fraction in higher vertebrates is discussed.
• Article: Fate of SRY, PABY, DYS1, DYZ3 and DYZ1 loci in Indian patients harbouring sex chromosomal anomalies.

  Anu Bashamboo, Mohammed Mahidur Rahman, Aparna Prasad, Sebastian Padinjarel Chandy, Jamal Ahmad, Sher Ali
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  ABSTRACT: We analysed chromosomes, conducted hormonal assays and screened genomic DNA of 34 patients with or without detectable Y chromosome for the presence/absence of SRY, PABY, DYS1, DYZ3 and DYZ1 loci and for mutations in the SRY gene. The samples studied represented cases of oligozoospermia, cryptorchidism, Swyer syndrome, Turner syndrome, male pseudohermaphroditism, XXY female syndrome, Klinefelter's syndrome, repeated abortion and instances of male infertility. Chromosomal constitutions and the level of hormones (FSH, LH, PRL, E2 and TSH) were found to be abnormal in several cases. A phenotypic female (P20) positive for all the Y-linked loci screened, showed mutations upstream of the HMG box in the SRY gene. In addition, one or more of the Y-linked loci were detected in several phenotypic females. Fluorescence in-situ hybridization of metaphase chromosomes and interphase nuclei of an aborted fetus with DYZ1 probe detected signals from normal to low levels to its complete absence confirming a complex Y chromosome mosaicism. Upon DNA analysis, the fetus was found to be positive for all the above-mentioned Y-linked loci. Organizational variation within the DYZ1 arrays and its correlation with recurrent spontaneous abortion may be followed-up in subsequent studies to substantiate this observation. This would augment genetic counselling to the affected couples. Prospects of this approach in the overall management of clinical cases with sex chromosome-related anomalies are discussed.
  Molecular Human Reproduction 03/2005; 11(2):117-27. · 3.85 Impact Factor
• Article: Organizational variation of DYZ1 repeat sequences on the human Y chromosome and its diagnostic potentials.

  Mohammed Mahidur Rahman, Anu Bashamboo, Aparna Prasad, Deepali Pathak, Sher Ali
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  ABSTRACT: The long arm of the human Y chromosome is flecked with various fractions of repetitive DNA. DYZ1 is one such fraction, which is organized tandemly as an array of a 3.4-kb repeat ranging from 2000-4000 copies in normal males. We have studied the organizational variation of the DYZ1 fraction on the human Y chromosome using DNA samples from CEPH family members and the random population employing the RFLP approach, fluorescence in situ hybridization (FISH), and conducted a similarity search with GenBank sequences. Typing of genomic DNA using DYZ1 as a probe showed an allele length and copy number variations even between two male siblings. Hybridization of DNA from monochromosome hybrids with this probe showed its presence on chromosome 15 in addition to the Y chromosome. Fluorescence in situ hybridization of metaphase chromosomes from an apparently normal male showed DYZ1 sequences in the proximal region of chromosome 11 in addition to the long arm of the Y chromosome. Typing of sets of semen and blood DNA samples from the same human individuals showed discernible allelic variation between the two samples, indicating tissue-specific programmed sequence modulation. DYZ1 seems to be the first probe having the unique potential to discriminate unequivocally the difference between the DNA originating from semen and blood samples, and may be exploited in forensic cases. This probe may also be used as a diagnostic tool to ascertain Y chromosome mosaicism in patients (e.g., Turner), its aberrant status in somatic cells, and possible sequence modulation/rearrangement in the germline samples. Additionally, this can be used to uncover sequence polymorphism in the human population.
  DNA and Cell Biology 10/2004; 23(9):561-71. · 2.07 Impact Factor
• Article: Detection of Salmonella typhi by polymerase chain reaction: implications in diagnosis of typhoid fever.

  Ashwani Kumar, Vineet Arora, Anu Bashamboo, Sher Ali
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  ABSTRACT: The present study was conducted to detect Salmonella typhi by polymerase chain reaction (PCR) in a clinical setting. A group of 40 clinically suspected cases of typhoid fever, lasting for about 3-11 days, with or without chills and rigors and hepatosplenomegaly were selected. Of these, 20 were culture positive and the remaining 20 were found to be negative by conventional blood culture technique. Primary PCR was followed by nested PCR using two sets of primers corresponding to flagellar gene of S. typhi strain. Two bands of about 458 and 343 bp were detected in 20 blood culture positive cases and 12 of the 20 culture negative ones. In the simulated group of samples, no amplification was detected. Our results suggest that PCR-based diagnosis is particularly useful for all clinically suspected cases of typhoid fever. The sensitivity of PCR and its potential use in routine diagnosis and epidemiological studies of typhoid fever can be exploited to complement studies by including bone marrow culture, faeces and bile samples.
  Infection Genetics and Evolution 01/2003; 2(2):107-10. · 3.13 Impact Factor
• Source

  Available from: Kaur Anupam

  Article: Molecular characterization of aY-derived marker chromosome and identification of indels in the DYS1 region in a patient with stigmata oTurner syndromef

  Anu Bashamboo†, Sunita Bhatnagar, Anupam Kaur, Virinder Kaur Sarhadi, Jai Rup Singh, Sher Ali
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  ABSTRACT: Presence of the Y chromosome in human female and its absence in the male is an abnormal condition, implying a spectrum of genetic abnormalities. In this communication, we describe studies conducted on a 17-year-old patient (HK-459) with stigmata of Turner syndrome. We analysed the hormonal profile of the subject, chromosomal constitution and DNA for the five different loci encompassing both the arms of the Y chromosome. Chromosomal analysis showed mosaicism containing 45,X/46,X,+mar but no Y chromosome. The X chromosome and all the autosomes of the patient and her parents were normal. The Southern analysis of the patient’s genomic DNA with probes specific to DYZ1 locus did not detect the corresponding Y-specific signal. Similarly, primers RG4, RG7 and PABY, corresponding to SRY gene and pseudoautosomal boundary regions respectively, failed to generate Y-specific amplicons. However, primers DYZ3 and DYS1, representing centromeric heterochromatic and euchromatic regions respectively, on the long arm of the Y chromosome uncovered Y-specific signals in the patient and her mother. Sequence analysis of DYS1-specific (710 bp) amplicon from the patient, both of her parents and two normal males showed insertion/deletion mutation in the patient. It is inferred that the Y-derived marker chromosome in the patient is of maternal origin and had undergone post-zygotic mutational events. The possible prognostic implications of this combined approach in the patient(s) with stigmata of Turner syndrome are discussed here
  CURRENT SCIENCE, , 25 JANUARY 2003. 01/2003;
• Article: A bubaline-derived satellite DNA probe uncovers generic affinities of gaur with other bovids

  Pritha Ray, Supriya Gangadharan, Munmun Chattopadhyay, Anu Bashamboo, Sunita Bhatnagar, Pradeep Kumar Malik, Sher Ali
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  ABSTRACT: DNA typing using genome derived cloned probes may be conducted for ascertaining genetic affinities of closely related species. We analysed gaurBos gaurus, cattleBos indicus, buffaloBubalus bubalis, sheepOvis aries and goatCapra hircus DNA using buffalo derived cloned probe pDS5 carrying an array ofBamHI satellite fraction of 1378 base residues to uncover its genomic organization. Zoo-blot analysis showed that pDS5 does not cross hybridize with non-bovid animals and surprisingly with female gaur genomic DNA. The presence of pDS5 sequences in the gaur males suggests their possible location on the Y chromosome. Genotyping of pDS5 withBamHI enzyme detected mostly monomorphic bands in the bubaline samples and polymorphic ones in cattle and gaur giving rise to clad specific pattern. Similar typing withRsaI enzyme also revealed clad specific band pattern detecting more number of bands in buffalo and fewer in sheep, goat and gaur samples. Copy number variation was found to be prominent in cattle and gaur withRsaI typing. Our data based on matched band profiles (MBP) suggest that gaur is genetically closer to cattle than buffalo contradicting the age-old notion held by some that gaur is a wild buffalo. The pDS5 clone has a potential for estimating the generic and genetic relationship amongst closely related bovid species.
  Journal of Biosciences 04/1999; 24(3):295-299. · 1.65 Impact Factor
• Source

  Available from: Sunita Bhatnagar

  Article: A 1.3 kb satellite DNA from Bubalus bubalis not conserved evolutionarily is transcribed.

  Sunita Bhatnagar, Anu Bashamboo, Munmun Chattopadhyay, Supriya Gangadharan, Sher Ali
  [show abstract] [hide abstract]
  ABSTRACT: A 1.3 kb satellite DNA from a size defined genomic library of mammal Bubalus bubalis was cloned and sequenced. The clone pSB1 is AT rich with 447 A (33.6%), 262 C (19.7%), 240 G (19.0%) and 383 T (28.8%). There were about 1400 copies of contig in the bubaline genome but it did not uncover allele length variation when used as probe in conjunction with a number of restriction enzymes. The contig pSB1 is not conserved evolutionarily and cross hybridizes only with the Bovideae family. A set of primers from 5' (nt 422 to 441) and 3' (nt 962 to 947) deduced from the clone used for PCR amplification with four members of the Bovideae family gave the expected 530 bp band of equal intensity indicating a similar number of copies in all the four species namely Bos indicus, Capra hircus, Ovis aries and Bubalus bubalis. Expression studies with pSB1 following slot-blot hybridization with total RNA isolated from ovary, testes, kidney, lung and spleen revealed varying signal intensities in all the tissues with a most prominent signal in spleen but a faint one in ovary. Further sequence analysis revealed the presence of several eukaryotic transcriptional elements such as NF-E1, Poly-A signal, lariat consensus sequences, and CTF/NF1 binding sites. Blast search showed 90% sequence similarity with the reverse transcriptase gene of Bos taurus and sequences from nt 283 to 636 within the contig showed highly conserved reverse transcriptase like signatures along with N-glycosylation and protein kinase C phosphorylation sites. From the data we conclude that the pSB1 representing satellite DNA is associated with transcribing sequences. The prospect of identifying functional genes linked with the satellite fraction in higher vertebrates is discussed.
  Zeitschrift fur Naturforschung C 59(11-12):874-9. · 0.77 Impact Factor