Publications by authors named "Shivani Dixit"

30 Publications

  • Page 1 of 1

Forensic characterization and genomic diversity of Assam population viewed from 23 autosomal STRs.

Int J Legal Med 2021 Jun 8. Epub 2021 Jun 8.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

In order to find out the genetic structure and characterize the forensic features of 23 autosomal STRs in the population of Assam, PowerPlex® Fusion 6C amplification kit was employed to genotype 292 unrelated individuals from Assam, India. A total of 79 different alleles were observed across 23 autosomal STRs with the corresponding frequency of alleles, which ranges from 0.002 to 0.406. Selected 23 loci were observed useful together with the highest value of combined discrimination power (CPD = 1), combined exclusion power (CPE = 0.999999999914), combined paternity index (CPI = 3.04 × 10), and all studied loci combined showing the lowest matching probability which is (CPM = 1.29 × 10). Additionally, in comparison with neighboring population, Assam population showed genetic closeness with Indian population. The genetic data of the present study will enrich the existing Indian autosomal DNA database and be useful for forensic and genealogical applications.
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http://dx.doi.org/10.1007/s00414-021-02625-9DOI Listing
June 2021

Molecular characterization of 23 Y chromosomal STR markers in the Gurjar population of National Capital Region (NCR), India.

Int J Legal Med 2021 May 31. Epub 2021 May 31.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

In the present study, DNA samples of 202 unrelated male individuals of Gurjar population were evaluated for the molecular diversity at 23 Y chromosomal Y-STR markers. Out of selected individuals, results showed 143 unique haplotypes. Highest degree of gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was observed as 0.7941, 0.7590, and 0.7902, respectively, for the locus DYS385a/b. Haplotype diversity (HD), gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was found to be 0.7079, 0.999999999989, 0.9999999996, and 0.999999999986, respectively, for the studied 23 Y-STR markers. Allele 11 of locus DYS392 was found to be the most frequent allele with the frequency of 0.762. In inter-population relationship, studied population showed genetic relatedness with the population of Jammu and Kashmir, India, and Ladakh, India. The haplotype data of the present study will not only enrich the existing Indian Y-STR data but will also be useful for forensic DNA application.
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http://dx.doi.org/10.1007/s00414-021-02623-xDOI Listing
May 2021

Genetic diversity and forensic characterization of 15 autosomal microsatellite markers in the North-east Indian Tripuri population.

Int J Legal Med 2021 May 8. Epub 2021 May 8.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

This study was conducted to explore the genomic diversity and forensic characterization of 15 autosomal microsatellite markers in the East Indian Tripuri population. In the studied population, we observed 158 different alleles with the average 10.53 alleles per locus. The locus D2S1338 (PIC= 0.862) was found to be the most polymorphic wheres locus TPOX (PIC= 0.647) as the least polymorphic, among all the studied loci. The locus FGA was found with the highest number of effective alleles (Nall=19) whereas locus TH01 showed least number of effective alleles (Nall=6). The cumulative values for matching probability (CPm), power of discrimination (CPD), power of exclusion CPE), and paternity index (CPI) were found as 1.94×10, 1, 0.999998, and 4.8×10 respectively. The studied population showed genetic closeness with the Gorkha population. In neighbor-joining tree, Tripura population pooled with the population of Nepal and Tibet. The genetic data obtained from the present study will not only enrich the existing autosomal STR database but will also be useful for forensic DNA application and genealogical studies.
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http://dx.doi.org/10.1007/s00414-021-02614-yDOI Listing
May 2021

Correction to: Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C™ Multiplex System.

Int J Legal Med 2021 May;135(3):1103

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.

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http://dx.doi.org/10.1007/s00414-021-02573-4DOI Listing
May 2021

Genomic insight into Y-STR diversity in the population of Odisha, India.

Int J Legal Med 2021 Mar 9. Epub 2021 Mar 9.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

This study evaluated the haplotype diversity of 17 Y chromosomal genetic markers among 202 unrelated males who were randomly selected in the population of Odisha, India. Out of total 196 haplotypes observed in this study, 190 were unique haplotypes. Forensic relevant parameters, viz., gene diversity (GD) and discrimination capacity (DC), were calculated as 0.999999998 and 0.970 respectively, for the studied population. The highest genetic diversity was observed at the locus DYS385a/b (0.9541) and lowest at the locus DYS437 (0.3326) among all the studied Y chromosomal loci. The polymorphic information content (PIC), power of discrimination (PD), and matching probability (PM) was found to be 0.999999965, 0.999999998, and 1.6×10 for the tested Y STR loci. The genetic data observed in this study would enrich the existing Y STR data of the Indian population and would also be useful for forensic application.
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http://dx.doi.org/10.1007/s00414-021-02545-8DOI Listing
March 2021

A study of genomic diversity in populations of Maharashtra, India, inferred from 20 autosomal STR markers.

BMC Res Notes 2021 Feb 23;14(1):69. Epub 2021 Feb 23.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India.

Objective: This study was planned to evaluate the genetic diversity in the admixed and Teli (a Hindu caste) populations of Maharashtra, India using 20 autosomal Short Tandem Repeat (STR) genetic markers. We further investigated the genetic relatedness of the studied populations with other Indian populations.

Results: The studied populations showed a wide range of observed heterozygosity viz. 0.690 to 0.918 for the admixed population and 0.696 to 0.942 for the Teli population. This might be due to the multi-directional gene flow. The admixed and Teli populations also showed a high degree polymorphism which ranged from 0.652 to 0.903 and 0.644 to 0.902, respectively. Their combined value of matching probability for all the studied loci was 4.29 × 10 and 5.01 × 10, respectively. The results of Neighbor-Joining tree and Principal Component Analysis showed that the studied populations clustered with the general populations of Jharkhand, UttarPradesh, Rajasthan and Central Indian States, as well as with the specific populations of Maharashtra (Konkanastha Brahmins) and Tamil Nadu (Kurmans). Overall, the obtained data showed a high degree of forensic efficacy and would be useful for forensic applications as well as genealogical studies.
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http://dx.doi.org/10.1186/s13104-021-05485-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7903603PMC
February 2021

Forensic characterization and genetic evaluation in the Central Indian population using 27 Y-STRs.

Int J Legal Med 2021 May 6;135(3):791-792. Epub 2021 Jan 6.

Cytogenetics Laboratory, Dept. of Zoology, Banaras Hindu University, Varanasi, 221005, India.

Introduction: Forensic characterization and genetic evaluation study in the 539 randomly selected unrelated adult healthy individuals belonging to the Central Indian population was undertaken.

Methods: The study was performed using a multiplex of 27 Y-STRs incoporated in Yfiler™ Plus multiplex kit.

Results: Out of 539 samples, 6 samples were observed for large deletion and tri-allelic patterns, which were removed from the analysis, and out of 533 samples, a total of 507 haplotypes were found, and out of these haplotypes, 482 unique haplotypes were found in this piece of work. The forensically important parameters, i.e., gene diversity (GD) and discrimination capacity (DC), were found to be 0.669 and 0.951, respectively, for the tested Y STR loci. The genetic data of this study will enrich the Y STR data bank and being used as a potential tool for forensic DNA and various genetic studies.
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http://dx.doi.org/10.1007/s00414-020-02486-8DOI Listing
May 2021

Paclitaxel-Loaded Colloidal Silica and TPGS-Based Solid Self-Emulsifying System Interferes Akt/mTOR Pathway in MDA-MB-231 and Demonstrates Anti-tumor Effect in Syngeneic Mammary Tumors.

AAPS PharmSciTech 2020 Nov 9;21(8):313. Epub 2020 Nov 9.

Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India.

A solid self-emulsifying drug delivery system (SEDDS) of paclitaxel (PTX) was developed that could enhance its oral bioavailability and neutralize other niggles associated with conventional delivery systems of PTX. TPGS-centered SEDDS containing PTX was optimized by Box-Behnken experimental design and then formulated as fumed colloidal silica-based solid SEDDS microparticles (Si-PTX-S-SEDDS). AFM analysis exhibited round-shaped microparticles of approximately 2-3 μM diameter, whereas after reconstitution, particle size measurement showed nanoemulsion droplets of 30.00 ± 2.00 nm with a zeta potential of 17.38 ± 2.88 mV. Si-PTX-S-SEDDS displayed improved efficacy proven by reduced IC of 0.19 ± 0.03 μM against MDA-MB-231 cells and a 45.83-fold higher cellular uptake in comparison to free PTX. Molecular mechanistic studies showed mitochondria-mediated intrinsic pathway of apoptosis following Akt/mTOR pathway, which is accompanied by survivin downregulation. Rhodamine 123 assay and chylomicron flow blocking studies revealed P-gp inhibition potential and lymphatic uptake of Si-PTX-S-SEDDS, responsible for over 4-fold increment in oral bioavailability compared to PTX administered as Taxol. In vivo anti-tumor studies in syngeneic mammary tumor model in SD rats revealed higher efficacy of Si-PTX-S-SEDDS as evident from significant reduction in tumor burden. In total, the developed Si-PTX-S-SEDDS formulation was found as an appropriate option for oral delivery of PTX.
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http://dx.doi.org/10.1208/s12249-020-01855-1DOI Listing
November 2020

A comparison of the corneal biomechanics in pseudoexfoliation glaucoma, primary open-angle glaucoma and healthy controls using Corvis ST.

PLoS One 2020 26;15(10):e0241296. Epub 2020 Oct 26.

Department of glaucoma, Narayana Nethralaya Eye Hospital, Bangalore, Karnataka, India.

Purpose: To compare the corneal biomechanical parameters between pseudoexfoliation glaucoma (PXG), primary open-angle glaucoma (POAG) and healthy controls using Corvis ST.

Methods: A prospective, cross-sectional study was conducted which included 132 treatment-naïve eyes which underwent Corvis ST. The study cohort comprised of 44 eyes with PXG, 42 eyes with POAG and 46 healthy controls. Corneal biomechanical parameters, which included corneal velocities, length of corneal applanated surface, deformation amplitude (DA), peak distance and radius of curvature, were compared between the groups using analysis of variance models.

Results: The 3 groups were demographically similar. The mean IOP was 15.7 ±3 mmHg in the control group, 21.3 ±5 mmHg in the POAG group and 25.8 ±7 mmHg in the PXG group (p<0.0001). Corneal pachymetry was similar across the 3 groups. Mean DA was significantly lower (p<0.0001) in the PXG group (0.86 ±0.18 mm) compared to the POAG group (0.97 ±0.14mm) and the control group (1.10 ±0.15mm). Corneal velocities were also found to be statistically significantly different between the groups. However, after adjusting for IOP, there was no difference in any of the biomechanical parameters between the 3 groups.

Conclusion: Corneal biomechanical parameters measured on Corvis ST are not different between eyes with PXG, POAG and healthy controls after adjusting for IOP.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241296PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588080PMC
December 2020

Genetic variation of 20 autosomal STRs in Jats belonging to Delhi, India.

Int J Legal Med 2021 May 12;135(3):771-773. Epub 2020 Sep 12.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

The present study based on 20 autosomal STR polymorphism reveals the genetic diversity of the Jat population of Delhi, India (n = 120). A total of 240 alleles were observed for this study. The allele frequency ranged from 0.004 to 0.508. The studied loci followed the Hardy-Weinberg equilibrium (HWE), and the heterozygosity ranged from 0.658 to 0.908. The locus Penta-E was found the most polymorphic and discriminating in the studied population with the value 0.910 and 0.981, respectively, whereas the locus TPOX was found least polymorphic and discriminating with the value 0.612 and 0.833, respectively. The combined paternity index (CPI) was 1.46 × 109, and the probability of match (CPm) was 2.68 × 10 for all 20 autosomal STR loci. The generated data adds to the Indian population database. It will be used for forensic purposes and in other population-based genetic studies.
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http://dx.doi.org/10.1007/s00414-020-02423-9DOI Listing
May 2021

Prevalence of New Onset Anosmia in COVID-19 Patients: Is The Trend Different Between European and Indian Population?

Indian J Otolaryngol Head Neck Surg 2020 Jul 21:1-4. Epub 2020 Jul 21.

Department of ENT, Bharati Vidyapeeth Medical College, Pune, 411046 India.

COVID-19 outbreak is major pandemic affecting lakhs of people all across the globe. Along with other nonspecific clinical features, reports mention anosmia to be an important symptom in COVID-19 positive patients. To study the prevalence of anosmia in confirmed COVID-19 patients, in Indian population and to ascertain its significance as a symptom of COVID 19. Study was done at a tertiary care COVID treating hospital. While eliciting detailed history from Covid-19 positive patients, all patients were asked about symptom of anosmia. Same was asked from control group of subjects who were COVID-19 negative. The history of anosmia was also elicited on discharge after the patients tested negative for COVID-19. 74 patients formed part of the study. 11 of 74 (14.8%) patients had anosmia. On using the chi square test for significance the difference was significant ( < .01), suggesting anosmia to be a significant clinical feature in COVID-19 patients. On comparing with world literature it was observed that the prevalence of anosmia is higher in European population as compared to Indian Also the symptom of anosmia improved when the patient recovered from the disease. Prevalence of new onset anosmia in Indian population with COVID-19 is 14.8%. Symptom of anosmia in present times should be considered as a important clinical feature and should raise a suspicion of COVID-19. The prevalence of anosmia in Indian population is much lesser than that reported in European population.
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http://dx.doi.org/10.1007/s12070-020-01986-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373335PMC
July 2020

Estimating genetic polymorphism in Bhuiyan population of eastern India using 20 autosomal STR loci.

Int J Legal Med 2020 Nov 6;134(6):2067-2069. Epub 2020 Aug 6.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, 470001, Sagar, India.

We conducted a study of 182 unrelated adult individuals belonging to Bhuiyan population resident of Eastern India in order to estimate genetic polymorphism by using 20 autosomal STR loci. The results obtained from this study were compared with the published data of Indian and neighbouring countries' populations. This research study is expected to contribute significantly to forensic investigations for human identification and parentage testing.
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http://dx.doi.org/10.1007/s00414-020-02391-0DOI Listing
November 2020

PEDF deficiency increases the susceptibility of rd10 mice to retinal degeneration.

Exp Eye Res 2020 09 25;198:108121. Epub 2020 Jul 25.

Section of Protein Structure and Function, LRCMB-NEI-NIH, Bethesda, MD, USA. Electronic address:

The SERPINF1 gene encodes pigment epithelium-derived factor (PEDF), a member of the serpin superfamily with neurotrophic and antiangiogenic properties in the retina. We hypothesized that absence of PEDF would lead to increased stress-associated retinal degeneration in Serpinf1 null mice. Accordingly, using a Serpinf1 null mouse model, we investigated the impact of PEDF absence on retinal morphology, and susceptibility to induced and inherited retinal degeneration. We studied the pattern of Serpinf1 expression in the mouse retina layers. PEDF protein was detected by western blotting. Transmission electron microscopy was performed on mouse retina. Serpinf1 null mice and wild type littermates were injected with NaIO (30 mg/kg body weight) intraperitonially. At post-injection day 1, 3, 4, 6 and 8 mice were euthanized, and eyes were enucleated. Serpinf1 null and rd10 double mutant mice were generated and their eyes enucleated at different time points from post-natal day 15 to post-natal day 28. Enucleated eyes were processed for hematoxylin and eosin staining and histopathological evaluations. We found that Serpinf1 was expressed in the retinal pigment epithelium, in the inner nuclear layer and in the ganglion cell layer, but undetectable in the outer nuclear layer of wild type mice. Plasma PEDF protein levels were undetectable in Serpinf1 null animals. RPE atrophy and retinal thinning were observed in NaIO-treated wild type mice that progressed with time post-injection. NaIO-treated Serpinf1 null mice showed comparatively better retinal morphology than wild type mice at day 4 post-injection. However, the absence of PEDF in Serpinf1 null x rd10 mice increased the susceptibility to retinal degeneration relative to that of rd10 mice. We concluded that histopathological evaluation of retinas lacking PEDF showed that removal of the Serpinf1 gene may activate PEDF-independent compensatory mechanisms to protect the retina against oxidative stress, while it increases the susceptibility to degenerate the retina in inherited retinal degeneration models.
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http://dx.doi.org/10.1016/j.exer.2020.108121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508969PMC
September 2020

A genomic exploration of 15 autosomal STR loci for establishment of a DNA profile database of the population of Himachal Pradesh.

Leg Med (Tokyo) 2020 Sep 30;46:101719. Epub 2020 May 30.

Cytogenetics Laboratory, Dept of Zoology, Banaras Hindu University, Varanasi 221005, UP, India.

In order to create an autosomal STR loci population database for Himachal Pradesh, 259 blood samples were taken from people residing in various regions of the state and AmpFlSTR® Identifiler® Plus PCR amplification kit was used for evaluation of 15 autosomal STR markers. A total of 149 alleles were investigated in this study with a mean allele number of 9.933 per locus. The locus D2S1338 was most informative in our data, as it had the highest discrimination power (PD-0.967) and the highest polymorphic information content (PIC-0.86). The matching probability and typical paternity index for all the studied loci were observed as 2.9x10 and 4.7x10, respectively. Discrimination power (CPD) and exclusion power (CPE) for all the studied loci were observed as 1 and 0.999998.
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http://dx.doi.org/10.1016/j.legalmed.2020.101719DOI Listing
September 2020

A comparison of the corneal biomechanics in pseudoexfoliation syndrome, pseudoexfoliation glaucoma, and healthy controls using Corvis® Scheimpflug Technology.

Indian J Ophthalmol 2020 05;68(5):787-792

Department of Glaucoma, Narayana Nethralaya Foundation, Bengaluru, Karnataka, India.

Purpose: To compare the corneal biomechanical parameters among pseudoexfoliation syndrome (PXF), pseudoexfoliation glaucoma (PXG), and healthy controls using Corvis Scheimpflug Technology (ST).

Methods: A prospective, cross-sectional study of 141 treatment-naïve eyes that underwent Corvis ST was conducted. These included 42 eyes with PXF, 17 eyes of PXF with ocular hypertension (PXF + OHT) defined as intraocular pressure (IOP)> 21 mmHg without disc/field changes, 37 eyes with PXG, and 45 healthy controls. Corneal biomechanical parameters, which included corneal velocities, length of corneal applanated surface, deformation amplitude (DA), peak distance, and radius of curvature, were compared among the groups using analysis of variance models.

Results: The four groups were demographically similar. The mean IOP was lower in the controls (15.6 ± 3 mmHg) and PXF group (16.0 ± 3 mmHg) compared to the other two groups (>24 mmHg). Corneal pachymetry was similar across the four groups. Mean DA was significantly lower (P < 0.0001) in the PXG group (0.91 ± 0.18 mm) and the PXF + OHT group (0.94 ± 0.13 mm) when compared to the PXF (1.10 ± 0.11 mm) and control groups (1.12 ± 0.14 mm). Corneal velocities were also found to be statistically significantly lower in PXG and PXF + OHT compared to the PXF and control groups. However, after adjusting for age and IOP, there was no difference in any of the biomechanical parameters among the four groups.

Conclusion: Corneal biomechanical parameters measured on Corvis ST are not different between healthy controls and eyes with PXF and PXG. Since PXG is a high-pressure glaucoma, corneal biomechanics may not play an important role in its diagnosis and pathogenesis.
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http://dx.doi.org/10.4103/ijo.IJO_1550_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350500PMC
May 2020

Allelic frequency database of 15 polymorphic autosomal STRs in the Malayalam-speaking population of Kerala, India.

Int J Legal Med 2020 Sep 1;134(5):1679-1681. Epub 2020 Apr 1.

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, UP, India.

In this study, we assessed and established an allelic frequency database of Malayalam-speaking population of south western Indian state Kerala, using 15 polymorphic short tandem repeats (STRs) genetic markers. For this study, 464 unrelated healthy individuals were randomly selected following the ethical standards. The most polymorphic and most discriminating locus was D2S1338, with a value of 0.860 and 0.968, respectively. The range of heterozygosity extended from a minimum of 0.668 (TH01) to a maximum of 0.847 (D2S1338). The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999997861, respectively, for all 15 autosomal STR loci under study. The combined probability of match (CPM) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 9.85 × 10 and 4.18 × 10, respectively.
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http://dx.doi.org/10.1007/s00414-020-02286-0DOI Listing
September 2020

Genomic blueprint of population of Rajasthan based on autosomal STR markers.

Ann Hum Biol 2020 Feb 27;47(1):70-75. Epub 2020 Jan 27.

DNA fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Government of MP, Sagar, India.

Genetic diversity and forensic efficacy of 20 autosomal STR genetic markers were investigated in a highly diverse population of Rajasthan, a state in north-western India. In this study, 317 blood samples from unrelated healthy individuals were directly amplified using the PowerPlex 21 multiplex system (Promega). Amplified products were separated by capillary electrophoresis using a Genetic Analyser -3500 XL (Thermo Fisher Scientific). The data thus obtained was statistically analysed using population genetic software. The studied population showed genetic affinity with the geographically close populations. The locus Penta-E was found to be the most polymorphic with a value of 0.90 in the studied population. The combined discrimination power (CPD) and combined power of exclusion (CPE) were observed as >0.999999999 and 0.999999997, respectively, for all the studied 20 autosomal STR loci. The combined probability of match (CPm) was 1.39 × 10 and combined paternity index (CPI) was 3.66 × 10 for all the studied loci. The results conclusively support the hypothesis that the studied autosomal STR loci are polymorphic in nature and, besides being useful in forensic applications they can also be applied in anthropological and other population genetic studies. This study supports the 'isolation-by-distance' model. Genetic data obtained from this study will enrich the population data bank.
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http://dx.doi.org/10.1080/03014460.2019.1705390DOI Listing
February 2020

Forensic effectiveness and genetic distribution of 23 autosomal STRs included in Verifiler Plus multiplex in a population sample from Madhya Pradesh, India.

Int J Legal Med 2020 Jul 11;134(4):1327-1328. Epub 2019 Nov 11.

Cytogenetics Laboratory, Dept. of Zoology, Banaras Hindu University, Varanasi, UP, 221005, India.

We report here the first ever global study on genetic polymorphism using a Verifiler Plus autosomal STR multiplex system. The study evaluated genetic characteristics of 23 autosomal STRs in 200 unrelated residents of Guna district of Madhya Pradesh, India. Allele frequencies and forensic parameters are reported. Population comparison analysis was also performed using NJ tree and PCA plot. Penta E marker showed highest power of discrimination (0.938) among all 23 studied markers. The study also presents the first ever global forensic assessment in Indian population on D6S1043 marker (PD 0.937). The results demonstrated that all the 23 markers were highly polymorphic and the Verifiler Plus kit is suitable for forensic purposes in Indian population.
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http://dx.doi.org/10.1007/s00414-019-02172-4DOI Listing
July 2020

Choroidal Microvascular Dropout in Pseudoexfoliation Glaucoma.

Invest Ophthalmol Vis Sci 2019 05;60(6):2146-2151

University Eye Clinic Maastricht, University Medical Center, Maastricht, the Netherlands.

Purpose: To compare the prevalence of choroidal microvasculature dropout (CMvD) in pseudoexfoliation glaucoma (PXG) and disease severity-matched primary open-angle glaucoma (POAG) eyes.

Methods: In a cross-sectional study, 39 eyes with PXG (33 patients) and 39 glaucoma severity-matched POAG eyes (34 patients) underwent visual fields, optical coherence tomography and optical coherence tomography angiography examination. Peripapillary vessel density (VD) was evaluated from the radial peripapillary capillary slab, parafoveal VD was measured on the superficial vascular plexus slab of the macula, and CMvD was evaluated on the choroidal slabs of the optic disc scan.

Results: The PXG and POAG groups were similar with respect to average mean deviation on visual fields (-12.1 vs. -12.0 decibel, P = 0.96) and average peripapillary retinal nerve fiber layer thickness on optical coherence tomography (71 vs. 74 μ, P = 0.29). Average peripapillary superficial VD (49.7% vs. 51.3%, P = 0.35) and parafoveal VD (44.8% vs. 45.8%, P = 0.33) were similar between the PXG and POAG groups. CMvD was seen in 18 PXG and 31 POAG eyes (46.2% vs. 79.5%, P = 0.002). On multivariate analysis that accounted for the severity of glaucoma, the odds of CMvD was significantly lower in the PXG group when compared with the POAG group (odds ratio: 0.18-0.21, P < 0.01).

Conclusions: The prevalence of CMvD was significantly lower in the PXG eyes when compared with the POAG eyes.
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http://dx.doi.org/10.1167/iovs.19-26844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528839PMC
May 2019

Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C Multiplex System.

Int J Legal Med 2019 May 14;133(3):803-805. Epub 2019 Feb 14.

Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.

Performance of PowerPlex Fusion 6C kit (PP F6C) was assessed in 374 unrelated individuals belonging to Madhya Pradesh, an Indian state. The study evaluated the forensic parameters for the loci included in PP F6C Multiplex System. The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999999995, respectively, for all 23 autosomal STR loci. SE33 showed the greatest power of discrimination (0.990) in the studied population, whereas TPOX showed the lowest (0.843). The availability of three Y-STR loci in the Multiplex System is suitable for assessing male contribution and amelogenin deletion in a single Multiplex PCR simultaneously. The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. The results revealed that the studied STR Multiplex System is highly polymorphic and suitable for forensic purposes.
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http://dx.doi.org/10.1007/s00414-019-02017-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469663PMC
May 2019

Genetic data for PowerPlex 21™ autosomal and PowerPlex 23 Y-STR™ loci from population of the state of Uttar Pradesh, India.

Int J Legal Med 2019 Sep 4;133(5):1381-1383. Epub 2019 Jan 4.

DNA fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

In the present study, the statistical forensic parameters were evaluated for the loci present in PowerPlex 21 autosomal and PowerPlex 23 Y-STR multiplex systems in 168 unrelated individuals living in the state of Uttar Pradesh, India. The combined discrimination power (CPD) and combined exclusion power (CPE) was 1 and 0.999999 respectively for all 20 autosomal STR loci. Penta E showed the greatest (0.980) and CSF1PO showed the lowest (0.855) power of discrimination in the studied population. The haplotype diversity for 23 Y-STR loci was observed to be 0.999. The study also presents the first global report on polymorphism on D1S1656, D6S1043 and D12S391 autosomal STR loci in the Indian population. The resulting data revealed that these STR multiplex systems are highly polymorphic and can be used for forensic purposes.
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http://dx.doi.org/10.1007/s00414-018-01993-zDOI Listing
September 2019

Choroidal Microvascular Dropout in Primary Open-angle Glaucoma Eyes With Disc Hemorrhage.

J Glaucoma 2019 03;28(3):181-187

Shiley Eye Institute, Hamilton Glaucoma Center and Department of Ophthalmology, University of California, San Diego, La Jolla, CA.

Purpose: The main purpose of this study was to compare the prevalence of choroidal microvascular dropout (CMvD) in primary open-angle glaucoma (POAG) eyes with and without disc hemorrhage (DH).

Methods: In a cross-sectional study, 44 eyes of 44 control subjects, 32 eyes of 32 POAG patients with DH, and 41 eyes of 41 POAG patients without DH underwent visual fields (VFs), optical coherence tomography (OCT) and OCT angiography (OCTA). Presence of CMvD was evaluated on the choroidal OCTA slab. VF defect in the glaucoma eyes were classified into initial nasal defect, initial parafoveal scotoma, and combined nasal and parafoveal defect.

Results: CMvD was detected in 17 POAG eyes with DH (53.1%) and 13 POAG eyes without DH (31.7%; P=0.06). On univariate analysis, CMvD in POAG eyes was associated with DH [odds ratio (OR): 2.44, P=0.06] and measures of glaucoma severity: VF mean deviation (OR: 0.85, P=0.02), retinal nerve fiber layer thickness (OR: 0.95, P=0.03), and peripapillary vessel density (OR: 0.94, P=0.09). On multivariate models that accounted for the measures of glaucoma severity, CMvD in POAG eyes was statistically significantly associated with DH (OR≥3, P<0.05). CMvD was more frequently seen in eyes with initial parafoveal scotoma than initial nasal defect both in POAG eyes with DH (P=0.06) and POAG eyes without DH (P<0.001).

Conclusions: Prevalence of CMvD was significantly greater in POAG eyes with DH compared with POAG eyes without DH. CMvD in POAG eyes was also significantly associated with central VF defects and greater severity of glaucomatous damage.
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http://dx.doi.org/10.1097/IJG.0000000000001173DOI Listing
March 2019

Choroidal Microvascular Dropout in Primary Angle Closure Glaucoma.

Am J Ophthalmol 2019 03 12;199:184-192. Epub 2018 Dec 12.

University Eye Clinic Maastricht, University Medical Center, Maastricht, Netherlands.

Purpose: To determine the prevalence and factors associated with the presence of choroidal microvascular dropout (CMvD) in primary angle-closure glaucoma (PACG) eyes compared to primary open-angle glaucoma (POAG) eyes.

Design: Cross-sectional study.

Methods: Thirty-six POAG eyes (36 patients) and 28 PACG eyes (28 patients) underwent optical coherence tomography angiography (OCTA). Presence of CMvD was evaluated on choroidal OCTA slabs. Visual field (VF) defects in the glaucoma eyes were classified into initial nasal defect (IND), initial parafoveal scotoma (IPFS), and combined nasal and parafoveal defect, and the association between type of VF defect and CMvD was evaluated.

Results: CMvD was detected in 21 POAG (58.3%) and 10 PACG (35.7%) eyes (P = .07). CMvD in POAG eyes was associated with pretreatment intraocular pressure (odds ratio [OR] = 0.91/mm Hg higher intraocular pressure, P = .06), VF mean deviation (MD, OR = 0.75/dB higher MD, P = .007), retinal nerve fiber layer thickness (OR = 0.92/μm increase in thickness, P = .02), and peripapillary vessel density (OR = 0.80/unit increase in density, P = .01). CMvD in PACG eyes was associated only with VF MD (OR = 0.90/dB higher MD, P = .05). When analyzed in the entire cohort of glaucoma patients (64 eyes), CMvD was significantly associated with POAG (OR > 3.5, P < .05) after accounting for glaucoma severity. CMvD was seen in 6 of 7 eyes with IPFS and 1 of 13 with IND in the POAG group (P < .05) and 1 of 2 eyes with IPFS and 0 of 10 with IND in the PACG group (P < .05).

Conclusions: Prevalence of CMvD was significantly lower in PACG compared to POAG. As in POAG, CMvD in PACG was associated with advanced VF damage and with IPFS on VF.
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http://dx.doi.org/10.1016/j.ajo.2018.11.021DOI Listing
March 2019

Paclitaxel-loaded TPGS enriched self-emulsifying carrier causes apoptosis by modulating survivin expression and inhibits tumour growth in syngeneic mammary tumours.

Artif Cells Nanomed Biotechnol 2018 4;46(sup3):S344-S358. Epub 2018 Oct 4.

a Pharmaceutics and Pharmacokinetics Division , CSIR-Central Drug Research Institute , Lucknow , UP , India.

Paclitaxel (PTX) in its commercial products exhibits adverse effects owing to excipients and also has poor oral bioavailability. Present work is directed towards development of tocopheryl polyethylene glycol succinate-assisted self-nanoemulsifying system (SEDDS) for oral delivery of PTX. Box-Behnken design of experiment was employed to optimize PTX-SEDDS and was characterized for droplet size (29.76 ± 2.64 nm), zeta potential (-21.46 ± 2.52 mV), PDI (0.177 ± 0.012), drug content (4.97 ± 0.98 mg), entrapment efficiency (98.33 ± 0.54%) and in vitro drug release (51.03 ± 2.23% PTX at 72 h). PTX-SEDDS exhibited IC; 1.58 ± 0.12 µM and a 52.46-folds higher cell uptake in MDA-MB-231 cells along with cellular and nuclear morphology changes. Significantly higher GM cell cycle arrest, apoptosis, mitochondrial membrane potential disruption and ROS production was exhibited by PTX-SEDDS in comparison to Taxol. Up-regulation of Bax, p21, cleaved-caspase 3, -caspase 9 and down-regulation of Bcl2 and survivin suggested apoptosis via intrinsic pathways. Pharmacokinetic study showed approximately 4-folds higher oral bioavailability of PTX-SEDDS than Taxol. Significant reduction in tumour volume and weight was observed in syngeneic mammary tumour in SD rats. Tumour histopathology and TUNEL assay showed apoptosis in tumour tissue. PTX-SEDDS caused low lung metastasis, and was safe and stable. Conclusively, PTX-SEDDS could be suitable option for oral delivery of PTX.
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http://dx.doi.org/10.1080/21691401.2018.1492933DOI Listing
June 2019

Differential genomics and transcriptomics between tyrosine kinase inhibitor-sensitive and -resistant BCR-ABL-dependent chronic myeloid leukemia.

Oncotarget 2018 Jul 13;9(54):30385-30418. Epub 2018 Jul 13.

All India Institute of Medical Sciences, Rishikesh, India.

Previously, it has been stated that the BCR-ABL fusion-protein is sufficient to induce Chronic Myeloid Leukemia (CML), but additional genomic-changes are required for disease progression. Hence, we profiled control and tyrosine kinase inhibitors (TKI) alone or in combination with other drug-treated CML-samples in different phases, categorized as drug-sensitive and drug-resistant on the basis of BCR-ABL transcripts, the marker of major molecular-response. Molecular-profiling was done using the molecular-inversion probe-based-array, Human Transcriptomics-Array2.0, and Axiom-Biobank genotyping-arrays. At the transcript-level, clusters of control, TKI-resistant and TKI-sensitive cases were correlated with BCR-ABL transcript-levels. Both at the gene- and exon-levels, up-regulation of MPO, TPX2, and TYMS and down-regulation of STAT6, FOS, TGFBR2, and ITK lead up-regulation of the cell-cycle, DNA-replication, DNA-repair pathways and down-regulation of the immune-system, chemokine- and interleukin-signaling, TCR, TGF beta and MAPK signaling pathways. A comparison between TKI-sensitive and TKI-resistant cases revealed up-regulation of LAPTM4B, HLTF, PIEZO2, CFH, CD109, ANGPT1 in CML-resistant cases, leading to up-regulation of autophagy-, protein-ubiquitination-, stem-cell-, complement-, TGFβ- and homeostasis-pathways with specific involvement of the Tie2 and Basigin signaling-pathway. Dysregulated pathways were accompanied with low CNVs in CP-new and CP-UT-TKI-sensitive-cases with undetectable BCR-ABL-copies. High CNVs (previously reported gain of 9q34) were observed in BCR-ABL-independent and -dependent TKI, non-sensitive-CP-UT/AP-UT/B-UT and B-new samples. Further, genotyping CML-CP-UT cases with BCR-ABL 0-to-77.02%-copies, the identified, rsID239798 and rsID9475077, were associated with FAM83B, a candidate for therapeutic resistance. The presence of BCR-ABL, additional genetic-events, dysregulated-signaling-pathways and rsIDs associated with FAM83B in TKI-resistant-cases can be used to develop a signature-profile that may help in monitoring therapy.
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http://dx.doi.org/10.18632/oncotarget.25752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084383PMC
July 2018

A Sectoral Analysis of Vessel Density Measurements in Perimetrically Intact Regions of Glaucomatous Eyes: An Optical Coherence Tomography Angiography Study.

J Glaucoma 2018 06;27(6):525-531

University Eye Clinic Maastricht, University Medical Center, Maastricht, the Netherlands.

Purpose: To study sectoral vessel density (VD) and structural alterations in the peripapillary and parafoveal hemiretina corresponding to perimetrically intact regions of glaucomatous eyes with hemifield defects and to compare these with healthy eyes using optical coherence tomography.

Methods: This cross-sectional study included 37 eyes with open-angle glaucoma having visual fields defects restricted to 1 hemifield and 45 age-matched controls. Peripapillary VD and retinal nerve fiber layer (RNFL) thickness were measured in 8 sectors. Parafoveal VD and ganglion cell complex thickness were measured in the superior and inferior hemispheres of the macula. These parameters were compared between the intact hemiretinae of glaucomatous eyes and corresponding sectors of healthy eyes using the t test.

Results: Within the perimetrically intact regions of glaucomatous eyes, the mean VD and RNFL thickness were significantly reduced in inferotemporal, superonasal, and nasal upper peripapillary sectors as compared with healthy eyes (P<0.008). The temporal upper sector had reduced mean VD (60.3% vs. 62.9%, P=0.04) despite similar mean RNFL thickness (P=0.18). The superotemporal sector had decreased mean RNFL thickness (121 vs. 138 µm, P=0.0001) despite similar VD (P=0.06). At the macula, ganglion cell complex thickness was reduced in the superior and inferior hemispheres, but mean VD was reduced in the superior parafoveal region only.

Conclusions: Peripapillary and parafoveal vascular changes precede functional decline. The extent of VD reduction and RNFL thinning varies in different peripapillary sectors and longitudinal studies are required to better understand the temporal relationship of vascular and RNFL loss.
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http://dx.doi.org/10.1097/IJG.0000000000000950DOI Listing
June 2018

Does the Presence of a Disc Hemorrhage Affect OCT-Measured Vessel Density and Retinal Nerve Fiber Layer Thickness?

Ophthalmol Glaucoma 2018 Nov - Dec;1(3):152-157. Epub 2018 Oct 4.

University Eye Clinic Maastricht, University Medical Center, Maastricht, The Netherlands.

Purpose: To determine if the presence of disc hemorrhage (DH) causes any artifactual change in peripapillary vessel density (VD) and retinal nerve fiber layer (RNFL) thickness as measured by OCT.

Design: Cohort study.

Participants: Glaucoma patients having a single peripapillary DH.

Methods: Fifteen glaucoma patients having a single peripapillary DH underwent OCT and OCT angiography. Patients were reviewed every 2 months and scans were repeated on disappearance of the DH. Peripapillary VD and RNFL thickness were evaluated at these 2 time points in the DH sector to determine whether the presence of a DH affects these measurements. The mirror-image sector (e.g., superotemporal sector if DH is inferotemporal) was used as a control. Statistical analysis was carried out using the paired t test. Additionally, the analysis of covariance test was used to determine if there was any difference in the measurements between the visits after controlling for signal strength index (SSI).

Main Outcome Measures: Peripapillary VD and RNFL thickness were measured in the presence of a DH, and then after DH resolution.

Results: The mean ± standard deviation (SD) interval between scans was 4.0±0.4 months. The inferotemporal sector was the most common site of DH (66.6%). The mean ± SD intraocular pressure was reduced medically from 16.1±4.7 mmHg at the time of DH to 13.4±4.2 mmHg at the time of DH resolution (P = 0.001). The mean ± SD VD in the DH sector was 52.5±9.7% at the time of DH and 51.1±8.7% on DH resolution (P = 0.30). The mean ± SD RNFL thickness in the DH quadrant was 91±20 μm in the presence of DH and 92±21 μm after DH resolution (P = 0.26). There was no significant difference between the mean VD or the mean RNFL thickness in the DH and control quadrants at these 2 time points after controlling for change in SSI (P > 0.05).

Conclusions: The presence of a DH does not artifactually alter the VD or RNFL thickness measurements. Therefore, OCT scans obtained in the presence of a DH may be included in series used for studying progression.
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http://dx.doi.org/10.1016/j.ogla.2018.09.002DOI Listing
October 2018

Syntheses of conformationally restricted benzopyran based triarylethylenes as growth inhibitors of carcinoma cells.

Bioorg Med Chem Lett 2017 11 30;27(22):5040-5045. Epub 2017 Sep 30.

Medicinal Chemistry Department, CSIR-Central Institute of Medicinal and Aromatic Plants, PO CIMAP, Kukrail Road, Lucknow 226015, India. Electronic address:

A series of conformationally restricted benzopyran based triarylethylenes has been synthesized and characterized as potential growth inhibitors of breast carcinoma cells. The synthesized compounds (14a-b, 15a and 16a-e) presented significant growth inhibition of ER+ and ER- breast cancer cells within the range of IC 0.55-9.96µM. Amongst other, 16c showed potent anticancer activity at IC 0.95µM in MCF-7 cells with good selectivity (Selectivity Index 4.47) towards healthy cells. The mechanistic studies for 16c were performed to elucidate possible mode of action which showed 16c elicited anticancer activity through necroptosis process.
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http://dx.doi.org/10.1016/j.bmcl.2017.09.060DOI Listing
November 2017

Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize.

Proteins 2018 Jan 24;86(1):21-34. Epub 2017 Oct 24.

Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India.

Histone lysine methylation by histone lysine methyltransferases (HKMTs) has been implicated in regulation of gene expression. While significant progress has been made to understand the roles and mechanisms of animal HKMT functions, only a few plant HKMTs are functionally characterized. To unravel histone substrate specificity, degree of methylation and catalytic activity, we analyzed Arabidopsis Trithorax-like protein (ATX), Su(var)3-9 homologs protein (SUVH), Su(var)3-9 related protein (SUVR), ATXR5, ATXR6, and E(Z) HKMTs of Arabidopsis, maize and rice through sequence and structure comparison. We show that ATXs may exhibit methyltransferase specificity toward histone 3 lysine 4 (H3K4) and might catalyse the trimethylation. Our analyses also indicate that most SUVH proteins of Arabidopsis may bind histone H3 lysine 9 (H3K9). We also predict that SUVH7, SUVH8, SUVR1, SUVR3, ZmSET20 and ZmSET22 catalyse monomethylation or dimethylation of H3K9. Except for SDG728, which may trimethylate H3K9, all SUVH paralogs in rice may catalyse monomethylation or dimethylation. ZmSET11, ZmSET31, SDG713, SDG715, and SDG726 proteins are predicted to be catalytically inactive because of an incomplete S-adenosylmethionine (SAM) binding pocket and a post-SET domain. E(Z) homologs can trimethylate H3K27 substrate, which is similar to the Enhancer of Zeste homolog 2 of humans. Our comparative sequence analyses reveal that ATXR5 and ATXR6 lack motifs/domains required for protein-protein interaction and polycomb repressive complex 2 complex formation. We propose that subtle variations of key residues at substrate or SAM binding pocket, around the catalytic pocket, or presence of pre-SET and post-SET domains in HKMTs of the aforementioned plant species lead to variations in class-specific HKMT functions and further determine their substrate specificity, the degree of methylation and catalytic activity.
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http://dx.doi.org/10.1002/prot.25399DOI Listing
January 2018

Syntheses of lipophilic chalcones and their conformationally restricted analogues as antitubercular agents.

Bioorg Med Chem Lett 2013 Mar 9;23(5):1322-5. Epub 2013 Jan 9.

Chemical Sciences Division, Central Institute of Medicinal and Aromatic Plants, PO CIMAP, Kukrail Picnic Spot Road, Lucknow 226 015, India.

Lipophilic chalcones and their conformationally restricted analogues were synthesized and evaluated for their antitubercular efficacy against Mycobacterium tuberculosis H37Rv strain. Compounds 16, 24, 25a and 25c were found to be active MIC at 60, 30, 3.5 and 7.5 μg-mL(-1). In vitro cytotoxicity of compounds 16, 24, 25a, 25c and 26 in non-cancerous human epithelial kidney cell line (HEK-293) showed that most active compound 25a was approximately 2.85 times selective towards tubercular versus healthy cells whereas compound 24 was found to be 16 times selective.
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http://dx.doi.org/10.1016/j.bmcl.2012.12.096DOI Listing
March 2013