Biomedical subjects

Ritu Khanna

Publications and source records attributed to Ritu Khanna.

8 recordsLinked to original sources

PubMed2006

CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration.

In developed countries, age-related macular degeneration is a common cause of blindness in the elderly. A common polymorphism, encoding the sequence variation Y402H in complement factor H (CFH), has been strongly associated with disease susceptibility. Here, we examined 84 polymorphisms in and around CFH in 726 affected individuals (including 544 unrelated individuals) and 268 unrelated controls. In this sample, 20 of these polymorphisms showed stronger association with disease susceptibility than the Y402H variant. Further, no single polymorphism could account for the contribution of the CFH locus to disease susceptibility. Instead, multiple polymorphisms defined a set of four common haplotypes (of which two were associated with disease susceptibility and two seemed to be protective) and multiple rare haplotypes (associated with increased susceptibility in aggregate). Our results suggest that there are multiple disease susceptibility alleles in the region and that noncoding CFH variants play a role in disease susceptibility.

Aged↗

PubMed2006

In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development.

Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors. NRL, CRX and NR2E3 are key transcriptional regulators that control photoreceptor differentiation. Mutations in NR2E3, a rod-specific orphan nuclear receptor, lead to loss of rods, increased density of S-cones and supernormal S-cone-mediated vision in humans. To better understand its in vivo function, NR2E3 was expressed ectopically in the Nrl-/- retina, where post-mitotic precursors fated to be rods develop into functional S-cones similar to the human NR2E3 disease. Expression of NR2E3 in the Nrl-/- retina completely suppressed cone differentiation and resulted in morphologically rod-like photoreceptors, which were however not functional. Gene profiling of FACS-purified photoreceptors confirmed the role of NR2E3 as a strong suppressor of cone genes but an activator of only a subset of rod genes (including rhodopsin) in vivo. Ectopic expression of NR2E3 in cone precursors and differentiating S-cones of wild-type retina also generated rod-like cells. The dual regulatory function of NR2E3 was not dependent upon the presence of NRL and/or CRX, but on the timing and level of its expression. Our studies reveal a critical role of NR2E3 in establishing functional specificity of NRL-expressing photoreceptor precursors during retinal neurogenesis.

Animals↗

PubMed2006

Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors.

The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that a 2.5-kb Nrl promoter segment directs the expression of enhanced GFP specifically to rod photoreceptors and the pineal gland of transgenic mice. GFP is detected shortly after terminal cell division, corresponding to the timing of rod genesis revealed by birthdating studies. In Nrl-/- retinas, the GFP+ photoreceptors express S-opsin, consistent with the transformation of rod precursors into cones. We report the gene profiles of freshly isolated flow-sorted GFP+ photoreceptors from wild-type and Nrl-/- retinas at five distinct developmental stages. Our results provide a framework for establishing gene regulatory networks that lead to mature functional photoreceptors from postmitotic precursors. Differentially expressed rod and cone genes are excellent candidates for retinopathies.

Animals↗

PubMed2006

Extraocular muscle morphogenesis and gene expression are regulated by Pitx2 gene dose.

PURPOSE: PITX2 gene dose plays a central role in Axenfeld-Rieger syndrome. The purpose of this study was to test the hypothesis that the effects of Pitx2 gene dose on eye development can be molecularly dissected in available Pitx2 mutant mice. METHODS: A panel of mice with Pitx2 gene dose ranging from wild-type (+/+) to none (-/-) was generated. Eye morphogenesis was assessed in animals with each Pitx2 gene dose. We also compared global gene expression in eye primordia taken from e12.5 Pitx2+/+, Pitx2+/-, Pitx2-/- embryos using gene microarrays. The validity of microarray results was confirmed by qRT-PCR. RESULTS: Morphogenesis of all extraocular muscle bundles correlated highly with Pitx2 gene dose, but there were some differences in sensitivity among muscle groups. Superior and inferior oblique muscles were most sensitive and disappeared before the four rectus muscles. Expression of muscle-specific genes was globally sensitive to Pitx2 gene dose, including the muscle-specific transcription factor genes Myf5, Myog, Myod1, Smyd1, Msc, and Csrp3. CONCLUSIONS: Pitx2 gene dose regulates both morphogenesis and gene expression in developing extraocular muscles. The expression of key muscle-specific transcription factor genes is regulated by Pitx2 gene dose, suggesting that sufficient levels of PITX2 protein are essential for early initiation of the myogenic regulatory cascade in extraocular muscles. These results document the first ocular tissue affected by Pitx2 gene dose in a model organism, where the underlying mechanisms can be analyzed, and provide a paradigm for future experiments designed to elucidate additional effects of Pitx2 gene dose during eye development.

Animals↗

PubMed2005

Network constrained clustering for gene microarray data.

UNLABELLED: Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering approach for inferring gene signaling pathways from gene microarray data. Based on the construction of co-expression networks that consists of both significantly linear and non-linear gene associations together with controlled biological and statistical significance, our approach tends to group functionally related genes into tight clusters despite their expression dissimilarities. We illustrate our approach and compare it to the traditional clustering approaches on a yeast galactose metabolism dataset and a retinal gene expression dataset. Our approach greatly outperforms the traditional approach in rediscovering the relatively well known galactose metabolism pathway in yeast and in clustering genes of the photoreceptor differentiation pathway. AVAILABILITY: The clustering method has been implemented in an R package "GeneNT" that is freely available from: http://www.cran.org.

Algorithms↗

PubMed2005

Psychophysical estimation of speed discrimination. I. Methodology.

Thresholds were assessed for a speed discrimination task with a pair of luminance-defined drifting gratings. The design and results of a series of experiments dealing in general with speed discrimination are described. Results show that for a speed discrimination task using drifting gratings, simultaneous presentation of the pair of gratings (spatially separated) was preferred over sequential presentation (temporally separated) in order to minimize the effects of eye movements and tracking. An interstimulus interval of at least 1000 ms was necessary to prevent motion aftereffects on subsequently viewed stimuli. For the two reference speeds tested of 2 and 8 deg/s using identical spatial frequency or randomizing spatial frequency for the pair of gratings did not affect speed discrimination thresholds. Implementing a staircase method of estimating thresholds was preferred over the method of constant stimuli or the method of limits. The results of these experiments were used to define the methodology for an investigation of aging and motion perception. These results will be of interest and use to psychophysicists designing and implementing speed discrimination paradigms.

Adaptation, Ocular↗

PubMed2005

Psychophysical estimation of speed discrimination. II. Aging effects.

We studied the effects of aging on a speed discrimination task using a pair of first-order drifting luminance gratings. Two reference speeds of 2 and 8 deg/s were presented at stimulus durations of 500 ms and 1000 ms. The choice of stimulus parameters, etc., was determined in preliminary experiments and described in Part I. Thresholds were estimated using a two-alternative-forced-choice staircase methodology. Data were collected from 16 younger subjects (mean age 24 years) and 17 older subjects (mean age 71 years). Results showed that thresholds for speed discrimination were higher for the older age group. This was especially true at stimulus duration of 500 ms for both slower and faster speeds. This could be attributed to differences in temporal integration of speed with age. Visual acuity and contrast sensitivity were not statistically observed to mediate age differences in the speed discrimination thresholds. Gender differences were observed in the older age group, with older women having higher thresholds.

Adaptation, Ocular↗

PubMed2003

A prospective 8 week trial of nasal interfaces vs. a novel oral interface (Oracle) for treatment of obstructive sleep apnea hypopnea syndrome.

OBJECTIVE: To compare efficacy, compliance rates, and side effects of a new strapless oral interface, the Oracle, with available nasal masks over 8 weeks of use for the treatment of obstructive sleep apnea hypopnea syndrome (OSAHS). METHODS: A total of 38 patients with OSAHS (respiratory disturbance index (RDI) >/=15/h) were enrolled after the diagnostic polysomnogram for subsequent continuous positive airway pressure (CPAP) therapy. After randomization, therapeutic pressures during a titration study were determined for 21 patients in the oral group and 17 patients in the nasal group. Comparisons for nasal and oral interfaces were made for baseline patient characteristics, average hours of CPAP use, side effects from therapy, and among questionnaires evaluating patients' subjective responses to therapy at months 1 and 2. RESULTS: No significant difference was observed in the average hours of CPAP use between the oral (4.5+/-2.1; 5.5+/-2.6) and nasal groups (4.0+/-2.6; 4.8+/-2.5) for either month 1 or 2 (P>0.05). The dropout rates were similar for both groups after 8 weeks of therapy. However, patients in the nasal group had higher occurrences of side effects such as nasal congestion, dryness, and air leaks, whereas patients in the oral group experienced more oral dryness and gum pain. CONCLUSION: Oral delivery of CPAP with the Oracle is an effective and suitable alternative for patients with OSAHS.

Adult↗