Publications by authors named "Nitin Udpa"

Article Synopsis
  • Genetic factors are believed to contribute to how humans adapt to high altitudes, but this has not been thoroughly verified until now.
  • The study focuses on native Ethiopians living at 3,500 meters and identifies a significant gene-rich region on chromosome 19 linked to hypoxia tolerance, demonstrating a potential selective sweep for adaptation.
  • The findings underscore the importance of whole genome sequencing, revealing key genes that improve survival in low oxygen, which may have been missed in earlier studies that used less comprehensive methods.
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The hypoxic conditions at high altitudes present a challenge for survival, causing pressure for adaptation. Interestingly, many high-altitude denizens (particularly in the Andes) are maladapted, with a condition known as chronic mountain sickness (CMS) or Monge disease. To decode the genetic basis of this disease, we sequenced and compared the whole genomes of 20 Andean subjects (10 with CMS and 10 without).

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Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality.

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The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery.

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For smaller organisms with faster breeding cycles, artificial selection can be used to create sub-populations with different phenotypic traits. Genetic tests can be employed to identify the causal markers for the phenotypes, as a precursor to engineering strains with a combination of traits. Traditional approaches involve analyzing crosses of inbred strains to test for co-segregation with genetic markers.

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Article Synopsis
  • * By comparing the genomes of these specially selected flies with controls, we identified key DNA regions, especially on the X chromosome, linked to the Notch signaling pathway, which was also found to be activated in the hypoxia-tolerant flies.
  • * Further experiments using inhibitors and mutations showed that proper activation of the Notch pathway is critical for survival in low-oxygen environments, indicating its central role in helping these flies tolerate hypoxia.
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The quality of life of breast cancer survivors is maintained by minimizing adverse effects on their physical appearance. In this study, we present an automated method for computing a common measure of breast symmetry, the normalized Breast Retraction Assessment (pBRA), from routine clinical photographs taken to document breast reconstruction procedures.

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