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1.  Functional Characterization of a Bidirectional Plant Promoter from Cotton Leaf Curl Burewala Virus Using an Agrobacterium-Mediated Transient Assay 
Viruses  2014;6(1):223-242.
The C1 promoter expressing the AC1 gene, and V1 promoter expressing the AV1 gene are located in opposite orientations in the large intergenic region of the Cotton leaf curl Burewala virus (CLCuBuV) genome. Agro-infiltration was used to transiently express putative promoter constructs in Nicotiana tabacum and Gossypium hirsutum leaves, which was monitored by a GUS reporter gene, and revealed that the bidirectional promoter of CLCuBuV transcriptionally regulates both the AC1 and AV1 genes. The CLCuBuV C1 gene promoter showed a strong, consistent transient expression of the reporter gene (GUS) in N. tabacum and G. hirsutum leaves and exhibited GUS activity two- to three-fold higher than the CaMV 35S promoter. The CLCuBuV bidirectional genepromoter is a nearly constitutive promoter that contains basic conserved elements. Many cis-regulatory elements (CREs) were also analyzed within the bidirectional plant promoters of CLCuBuV and closely related geminiviruses, which may be helpful in understanding the transcriptional regulation of both the virus and host plant.
doi:10.3390/v6010223
PMCID: PMC3917440  PMID: 24424501
cotton leaf curl Burewala virus; agro-infiltration; bidirectional promoter; cis-regulatory elements; geminivirus
2.  AIPL1 implicated in the pathogenesis of two cases of autosomal recessive retinal degeneration 
Molecular Vision  2014;20:1-14.
Purpose
To localize and identify the gene and mutations causing autosomal recessive retinal dystrophy in two consanguineous Pakistani families.
Methods
Consanguineous families from Pakistan were ascertained to be affected with autosomal recessive retinal degeneration. All affected individuals underwent thorough ophthalmologic examinations. Blood samples were collected, and genomic DNA was extracted using a salting out procedure. Genotyping was performed using microsatellite markers spaced at approximately 10 cM intervals. Two-point linkage analysis was performed with the lod score method. Direct DNA sequencing of amplified genomic DNA was performed for mutation screening of candidate genes.
Results
Genome-wide linkage scans yielded a lod score of 3.05 at θ=0 for D17S1832 and 3.82 at θ=0 for D17S938, localizing the disease gene to a 12.22 cM (6.64 Mb) region flanked by D17S1828 and D17S1852 for family 61032 and family 61227, which contains aryl hydrocarbon receptor interacting protein-like 1 (AIPL1), a gene previously implicated in recessive Leber congenital amaurosis and autosomal dominant cone-rod dystrophy. Sequencing of AIPL1 showed a homozygous c.773G>C (p.Arg258Pro) sequence change in all affected individuals of family 61032 and a homozygous c.465G>T (p.(H93_Q155del)) change in all affected members of family 61227.
Conclusions
The results strongly suggest that the c.773G>C (p.R258P) and c.465G>T (p.(H93_Q155del)) mutations in AIPL1 cause autosomal recessive retinal degeneration in these consanguineous Pakistani families.
PMCID: PMC3888496  PMID: 24426771
4.  Interaction and Inhibition of Dengue Envelope Glycoprotein with Mammalian Receptor DC-Sign, an In-Silico Approach 
PLoS ONE  2013;8(3):e59211.
Membrane fusion is the central molecular event during the entry of enveloped viruses into cells. The critical agents of this process are viral surface proteins, primed to facilitate cell bilayer fusion. The important role of Dendritic-cell-specific ICAM3-grabbing non-integrin (DC-SIGN) in Dengue virus transmission makes it an attractive target to interfere with Dengue virus Propagation. Receptor mediated endocytosis allows the entry of virions due to the presence of endosomal membranes and low pH-induced fusion of the virus. DC-SIGN is the best characterized molecule among the candidate protein receptors and is able to mediate infection with the four serotypes of dengue virus (DENV). Unrestrained pair wise docking was used for the interaction of dengue envelope protein with DC-SIGN and monoclonal antibody 2G12. Pre-processed the PDB coordinates of dengue envelope glycoprotein and other candidate proteins were prepared and energy minimized through AMBER99 force field distributed in MOE software. Protein-protein interaction server, ZDOCK was used to find molecular interaction among the candidate proteins. Based on these interactions it was found that antibody successfully blocks the glycosylation site ASN 67 and other conserved residues present at DC-SIGN-Den-E complex interface. In order to know for certain, the exact location of the antibody in the envelope protein, co-crystallize of the envelope protein with these compounds is needed so that their exact docking locations can be identified with respect to our results.
doi:10.1371/journal.pone.0059211
PMCID: PMC3601059  PMID: 23527139
5.  Novel mutations in RPE65 identified in consanguineous Pakistani families with retinal dystrophy 
Molecular Vision  2013;19:1554-1564.
Purpose
To identify pathogenic mutations responsible for retinal dystrophy in three consanguineous Pakistani families.
Methods
A thorough ophthalmic examination including fundus examination and electroretinography was performed, and blood samples were collected from all participating members. Genomic DNA was extracted, and genome-wide linkage and/or exclusion analyses were completed with fluorescently labeled short tandem repeat microsatellite markers. Two-point Lod scores were calculated, and coding exons along with exon-intron boundaries of RPE65 gene were sequenced, bidirectionally.
Results
Ophthalmic examinations of the patients affected in all three families suggested retinal dystrophy with an early, most probably congenital, onset. Genome-wide linkage and/or exclusion analyses localized the critical interval in all three families to chromosome 1p31 harboring RPE65. Bidirectional sequencing of RPE65 identified a splice acceptor site variation in intron 2: c.95–1G>A, a single base substitution in exon 3: c.179T>C, and a single base deletion in exon 5: c.361delT in the three families, respectively. All three variations segregated with the disease phenotype in their respective families and were absent from ethnically matched control chromosomes.
Conclusions
These results strongly suggest that causal mutations in RPE65 are responsible for retinal dystrophy in the affected individuals of these consanguineous Pakistani families.
PMCID: PMC3716412  PMID: 23878505
6.  Association of Pathogenic Mutations in TULP1 With Retinitis Pigmentosa in Consanguineous Pakistani Families 
Archives of ophthalmology  2011;129(10):1351-1357.
Objective
To identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa in 5 consanguineous Pakistani families.
Methods
Affected individuals in the families underwent a detailed ophthalmological examination that consisted of fundus photography and electroretinography. Blood samples were collected from all participating family members, and genomic DNA was extracted. A genome-wide linkage scan was performed, followed by exclusion analyses among our cohort of nuclear consanguineous families with microsatellite markers spanning the TULP1 locus on chromosome 6p. Two-point logarithm of odds scores were calculated, and all coding exons of TULP1 were sequenced bidirectionally.
Results
The results of ophthalmological examinations among affected individuals in these 5 families were suggestive of retinitis pigmentosa. The genome-wide linkage scan localized the disease interval to chromosome 6p, harboring TULP1 in 1 of 5 families, and sequential analyses identified a single base pair substitution in TULP1 that results in threonine to alanine substitution (p.T380A). Subsequently, we investigated our entire cohort of families with autosomal recessive retinitis pigmentosa and identified 4 additional families with linkage to chromosome 6p, all of them harboring a single base pair substitution in TULP1 that results in lysine to arginine substitution (p.K489R). Results of single-nucleotide polymorphism haplotype analyses were suggestive of a common founder in these 4 families.
Conclusion
Pathogenic mutations in TULP1 are responsible for the autosomal recessive retinitis pigmentosa phenotype in these consanguineous Pakistani families, with a single ancestral mutation in TULP1 causing the disease phenotype in 4 of 5 families.
Clinical Relevance
Clinical and molecular characterization of pathogenic mutations in TULP1 will increase our understanding of retinitis pigmentosa at a molecular level.
doi:10.1001/archophthalmol.2011.267
PMCID: PMC3463811  PMID: 21987678
7.  Mutations in RLBP1 associated with fundus albipunctatus in consanguineous Pakistani families 
The British journal of ophthalmology  2011;95(7):1019-1024.
Objective
To identify disease-causing mutations in two consanguineous Pakistani families with fundus albipunctatus.
Methods
Affected individuals in both families underwent a thorough clinical examination including funduscopy and electroretinography. Blood samples were collected from all participating members and genomic DNA was extracted. Exclusion analysis was completed with microsatellite short tandem repeat markers that span all reported loci for fundus albipunctatus. Two-point logarithm of odds (LOD) scores were calculated, and coding exons and exon–intron boundaries of RLBP1 were sequenced bi-directionally.
Results
The ophthalmic examination of affected patients in both families was consistent with fundus albipunctatus. The alleles of markers on chromosome 15q flanking RLBP1 segregated with the disease phenotype in both families and linkage was further confirmed by two-point LOD scores. Bi-directional sequencing of RLBP1 identified a nonsense mutation (R156X) and a missense mutation (G116R) that segregated with the disease phenotype in their respective families.
Conclusions
These results strongly suggest that mutations in RLBP1 are responsible for fundus albipunctatus in the affected individuals of these consanguineous Pakistani families.
doi:10.1136/bjo.2010.189076
PMCID: PMC3459316  PMID: 21447491
8.  GNAT1 Associated with Autosomal Recessive Congenital Stationary Night Blindness 
Congenital stationary night blindness is characterized by impaired night vision, decreased visual acuity, nystagmus, myopia, and strabismus. A genome-wide linkage scan was completed that localized the critical interval to the short arm of chromosome 3 and sequencing identified a novel missense mutation in GNAT1.
Purpose.
Congenital stationary night blindness is a nonprogressive retinal disorder manifesting as impaired night vision and is generally associated with other ocular symptoms, such as nystagmus, myopia, and strabismus. This study was conducted to further investigate the genetic basis of CSNB in a consanguineous Pakistani family.
Methods.
A consanguineous family with multiple individuals manifesting cardinal symptoms of congenital stationary night blindness was ascertained. All family members underwent detailed ophthalmic examination, including fundus photographic examination and electroretinography. Blood samples were collected and genomic DNA was extracted. Exclusion and genome-wide linkage analyses were completed and two-point LOD scores were calculated. Bidirectional sequencing of GNAT1 was completed, and quantitative expression of Gnat1 transcript levels were investigated in ocular tissues at different postnatal intervals.
Results.
The results of ophthalmic examinations were suggestive of early-onset stationary night blindness with no extraocular anomalies. The genome-wide scan localized the critical interval to chromosome 3, region p22.1-p14.3, with maximum two-point LOD scores of 3.09 at θ = 0, flanked by markers D3S3522 and D3S1289. Subsequently, a missense mutation in GNAT1, p.D129G, was identified, which segregated within the family, consistent with an autosomal recessive mode of inheritance, and was not present in 192 ethnically matched control chromosomes. Expression analysis suggested that Gnat1 is expressed at approximately postnatal day (P)7 and is predominantly expressed in the retina.
Conclusions.
These data suggest that a homozygous missense mutation in GNAT1 is associated with autosomal recessive stationary night blindness.
doi:10.1167/iovs.11-8026
PMCID: PMC3339909  PMID: 22190596
9.  Ectopia Lentis in a Consanguineous Pakistani Family and a Novel Locus on Chromosome 8q 
Archives of Ophthalmology  2010;128(8):1046-1049.
Objective
To investigate the genetic basis and molecular characteristics of the isolated form of ectopia lentis.
Methods
We ascertained a consanguineous Pakistani family with multiple individuals with ectopia lentis. All affected as well as unaffected members with isolated ectopia lentis underwent detailed ophthalmologic and medical examination. Blood samples were collected and DNA was extracted. A genome-wide scan was completed with 382 polymorphic microsatellite markers, and logarithm of odds (LOD) scores were calculated.
Results
Maximum 2-point LOD scores of 5.68 and 2.88 at θ=0 were obtained for markers D8S285 and D8S260, respectively, during the genome-wide scan. Additional microsatellite markers refined the disease locus to a 16.96-cM (14.07-Mb) interval flanked by D8S1737 proximally and D8S1117 distally.
Conclusions
We report on a new locus for nonsyndromic autosomal recessive ectopia lentis on chromosome 8q11.23-q13.2 in a consanguineous Pakistani family.
Clinical Relevance
Identification of genetic loci and genes involved in ectopia lentis will enhance our understanding of the disease at a molecular level, leading to better genetic counseling and family screening and possible future development of better treatment.
doi:10.1001/archophthalmol.2010.165
PMCID: PMC3398798  PMID: 20697006
10.  Nonsense mutation in MERTK causes autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family 
The British Journal of Ophthalmology  2010;94(8):1094-1099.
Background
Retinitis pigmentosa (RP) is one of the most common ophthalmic disorders affecting one in approximately 5000 people worldwide. A nuclear family was recruited from the Punjab province of Pakistan to study the genetic basis of autosomal recessive RP.
Methods
All affected individuals underwent a thorough ophthalmic examination and the disease was characterised based upon results for fundus photographs and electroretinogram recordings. Genomic DNA was extracted from peripheral leucocytes. Exclusion studies were performed with short tandem repeat (STR) markers flanking reported autosomal recessive RP loci. Haplotypes were constructed and results were statistically evaluated.
Results
The results of exclusion analyses suggested that family PKRP173 was linked to chromosome 2q harbouring mer tyrosine kinase protooncogene (MERTK), a gene previously associated with autosomal recessive RP. Additional STR markers refined the critical interval and placed it in a 13.4 cM (17 Mb) region flanked by D2S293 proximally and D2S347 distally. Significant logarithm of odds (LOD) scores of 3.2, 3.25 and 3.18 at θ=0 were obtained with markers D2S1896, D2S2269 and D2S160. Sequencing of the coding exons of MERTK identified a mutation, c.718G→T in exon 4, which results in a premature termination of p.E240X that segregates with the disease phenotype in the family.
Conclusion
Our results strongly suggest that the nonsense mutation in MERTK, leading to premature termination of the protein, is responsible for RP phenotype in the affected individuals of the Pakistani family.
doi:10.1136/bjo.2009.171892
PMCID: PMC3393880  PMID: 20538656
11.  RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis 
Bioinformation  2012;8(14):687-690.
RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available.
Availability
http://www.cemb.edu.pk/sw.html
Abbreviations
RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.
doi:10.6026/97320630008687
PMCID: PMC3449372  PMID: 23055611
Sequence analysis; DNA; nucleotides; Nussinov algorithm; C# language
12.  Selection of epitope-based vaccine targets of HCV genotype 1 of Asian origin: a systematic in silico approach 
Bioinformation  2012;8(20):957-962.
Hepatitis C is the major health problem over the globe affecting approximately 200 million people worldwide and about 10 million Pakistani populations. Developing countries are especially facing the problems of HCV infection. Hence the goal of the study was to find out the antigenic epitopes that could be effective vaccine targets of HCV genotype 1 of Asian origin against HLA alleles frequently distributed in Asian countries. A total of 85 complete genome sequences of HCV 1 of Asian origin were retrieved from the HCV sequence database. Using in silico tools, T cell epitopes were predicted from conserved regions of all the available HCV 1 subtypes against Asian HLA alleles. Using 10 MHC I supertypes 51 epitopes was predicted as promiscuous binders. MHC class I supertypes A2 and B7 were found to be good promiscuous binders for a large number of predicted epitopes. Other alleles of MHC I supertypes (B57, B27, BX, B44) either were not respondent as promiscuous binders or responded only to a limited number of epitopes. Against 8 predominantly found Asian alleles of DRB1 supertype, 42 epitopes was predicted as promiscuous binders. MHC class II alleles DRB1-0101, DRB1-0701 and DRB1-1501 were the highest binders to promiscuous predicted epitopes while DRB1-0301 was the least binder for the predicted promiscuous epitopes of HCV 1 genotype of Asian origin. Literature review survey of predicted epitopes via IEDB also confirmed that great numbers of predicted epitopes are true positive. Hence, sophisticated selection of viral proteins and MHCs provided conserved promiscuous epitopes that can be used as effective vaccine candidates for all Asian counties.
Abbreviations
HCV - hepatitis C virus, MHC - major histocompatability complex, HLA - human leukocyte antigen, CTL - cytotoxic T lymphocytes.
doi:10.6026/97320630008957
PMCID: PMC3524940  PMID: 23275687
Hepatitus C Virus; Immunoinformatics; MHC; Epitope; Conservancy; Asia
13.  Overexpression of the phytochrome B gene from Arabidopsis thaliana increases plant growth and yield of cotton (Gossypium hirsutum) 
The phytochrome B (PHYB) gene of Arabidopsis thaliana was introduced into cotton through Agrobacterium tumefaciens. Integration and expression of PHYB gene in cotton plants were confirmed by molecular evidence. Messenger RNA (mRNA) expression in one of the transgenic lines, QCC11, was much higher than those of control and other transgenic lines. Transgenic cotton plants showed more than a two-fold increase in photosynthetic rate and more than a four-fold increase in transpiration rate and stomatal conductance. The increase in photosynthetic rate led to a 46% increase in relative growth rate and an 18% increase in net assimilation rate. Data recorded up to two generations, both in the greenhouse and in the field, revealed that overexpression of Arabidopsis thaliana PHYB gene in transgenic cotton plants resulted in an increase in the production of cotton by improving the cotton plant growth, with 35% more yield. Moreover, the presence of the Arabidopsis thaliana PHYB gene caused pleiotropic effects like semi-dwarfism, decrease in apical dominance, and increase in boll size.
doi:10.1631/jzus.B1000168
PMCID: PMC3072596  PMID: 21462389
Transformation; Gossypium hirsutum; Phytochrome B; Overexpression; Plant growth; Yield
14.  Mutations in the β-subunit of rod phosphodiesterase identified in consanguineous Pakistani families with autosomal recessive retinitis pigmentosa 
Molecular Vision  2011;17:1373-1380.
Purpose
This study was designed to identify pathogenic mutations causing autosomal recessive retinitis pigmentosa (RP) in consanguineous Pakistani families.
Methods
Two consanguineous families affected with autosomal recessive RP were identified from the Punjab Province of Pakistan. All affected individuals underwent a thorough ophthalmologic examination. Blood samples were collected, and genomic DNAs were extracted. Exclusion analysis was completed, and two-point LOD scores were calculated. Bidirectional sequencing of the β subunit of phosphodiesterase 6 (PDE6β) was completed.
Results
During exclusion analyses both families localized to chromosome 4p, harboring PDE6β, a gene previously associated with autosomal recessive RP. Sequencing of PDE6β identified missense mutations: c.1655G>A (p.R552Q) and c.1160C>T (p.P387L) in families PKRP161 and PKRP183, respectively. Bioinformatic analyses suggested that both mutations are deleterious for the native three-dimensional structure of the PDE6β protein.
Conclusions
These results strongly suggest that mutations in PDE6β are responsible for the disease phenotype in the consanguineous Pakistani families.
PMCID: PMC3108895  PMID: 21655355
15.  A new locus for autosomal recessive congenital cataract identified in a Pakistani family 
Molecular Vision  2010;16:240-245.
Purpose
To identify the disease locus for autosomal recessive congenital cataract in a consanguineous Pakistani family.
Methods
All affected individuals underwent detailed ophthalmologic and medical examination. Blood samples were collected and DNA was extracted. A genome-wide scan was performed with polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and logarithm of odds (LOD) scores were calculated.
Results
The clinical records and ophthalmological examinations suggested that all affected individuals have nuclear cataracts. Maximum LOD scores of 5.01, 4.38, and 4.17 at θ=0 were obtained with markers D7630, D7S657, and D7S515, respectively. Fine mapping refined the critical interval and suggested that markers in a 27.78 cM (27.96 Mb) interval are flanked by markers D7S660 and D7S799, which co-segregate with the disease phenotype in family PKCC108.
Conclusions
We have identified a new locus for autosomal recessive congenital cataract, localized to chromosome 7q21.11-q31.1 in a consanguineous Pakistani family.
PMCID: PMC2822550  PMID: 20161816
16.  Autosomal recessive congenital cataract linked to EPHA2 in a consanguineous Pakistani family 
Molecular Vision  2010;16:511-517.
Purpose
To investigate the genetic basis of autosomal recessive congenital cataracts in a consanguineous Pakistani family.
Methods
All affected individuals underwent a detailed ophthalmological and clinical examination. Blood samples were collected and genomic DNAs were extracted. A genome-wide scan was performed with polymorphic microsatellite markers. Logarithm of odds (LOD) scores were calculated, and Eph-receptor type-A2 (EPHA2), residing in the critical interval, was sequenced bidirectionally.
Results
The clinical and ophthalmological examinations suggested that all affected individuals have nuclear cataracts. Genome-wide linkage analyses localized the critical interval to a 20.78 cM (15.08 Mb) interval on chromosome 1p, with a maximum two-point LOD score of 5.21 at θ=0. Sequencing of EPHA2 residing in the critical interval identified a missense mutation: c.2353G>A, which results in an alanine to threonine substitution (p.A785T).
Conclusions
Here, we report for the first time a missense mutation in EPHA2 associated with autosomal recessive congenital cataracts.
PMCID: PMC2846848  PMID: 20361013
17.  Autosomal recessive congenital cataract in consanguineous Pakistani families is associated with mutations in GALK1 
Molecular Vision  2010;16:682-688.
Purpose
To identify the pathogenic mutations responsible for autosomal recessive congenital cataracts in consanguineous Pakistani families.
Methods
All affected individuals underwent detailed ophthalmologic and medical examination. Blood samples were collected and genomic DNA was extracted. A genome-wide scan was performed with polymorphic microsatellite markers on genomic DNA from affected and unaffected family members and logarithm of odds (LOD) scores were calculated. All coding exons of galactokinase (GALK1) were sequenced to identify pathogenic lesions.
Results
Clinical records and ophthalmological examinations suggested that affected individuals have nuclear cataracts. Linkage analysis localized the critical interval to chromosome 17q with a maximum LOD score of 5.54 at θ=0, with D17S785 in family PKCC030. Sequencing of GALK1, a gene present in the critical interval, identified a single base pair deletion: c.410delG, which results in a frame shift leading to a premature termination of GALK1: p.G137fsX27. Additionally, we identified a missense mutation: c.416T>C, in family PKCC055 that results in substitution of a leucine residue at position 139 with a proline residue: p.L139P, and is predicted to be deleterious to the native GALK1 structure.
Conclusions
Here, we report pathogenic mutations in GALK1 that are responsible for autosomal recessive congenital cataracts in consanguineous Pakistani families.
PMCID: PMC2855732  PMID: 20405025
18.  Mapping of a new locus associated with autosomal recessive congenital cataract to chromosome 3q 
Molecular Vision  2010;16:2634-2638.
Purpose
To localize the disease interval for autosomal recessive congenital cataracts in a consanguineous Pakistani family.
Methods
All affected individuals underwent detailed ophthalmologic examination. Blood samples were collected and genomic DNA was extracted. A genome-wide scan was performed with fluorescently-labeled microsatellite markers on genomic DNA from affected and unaffected family members and logarithm of odds (LOD) scores were calculated.
Results
Clinical records and ophthalmological examinations suggested that affected individuals have bilateral congenital cataracts. Genome-wide linkage analysis localized the critical interval to chromosome 3q with a maximum LOD score of 3.87 at θ=0; with marker D3S3609. Haplotype analyses refined the critical interval to a 23.39 cM (18.01 Mb) interval on chromosome 3q, flanked by D3S1614 proximally and D3S1262, distally.
Conclusions
Here, we report a new locus for autosomal recessive congenital cataract localized to chromosome 3q in a consanguineous Pakistani family.
PMCID: PMC3002966  PMID: 21179239
19.  Mapping of a novel locus associated with autosomal recessive congenital cataract to chromosome 8p 
Molecular Vision  2010;16:2911-2915.
Purpose
To identify the disease locus for autosomal recessive congenital cataracts in a consanguineous Pakistani family.
Methods
All affected individuals underwent a detailed ophthalmologic examination. Blood samples were collected and genomic DNA was extracted. A genome-wide scan was completed with fluorescently-labeled microsatellite markers on genomic DNA from affected and unaffected family members. Logarithms of odds (LOD) scores were calculated under a fully penetrant autosomal recessive model of inheritance.
Results
Ophthalmic examination suggested that affected individuals have bilateral cataracts. Linkage analysis localized the critical interval to chromosome 8p with LOD scores of 3.19, and 3.08 at θ=0, obtained with markers D8S549 and D8S550, respectively. Haplotype analyses refined the critical interval to 37.92 cM (16.28 Mb) region, flanked by markers, D8S277 proximally and D8S1734 distally.
Conclusions
Here, we report a new locus for autosomal recessive congenital cataract mapped to chromosome 8p in a consanguineous Pakistani family.
PMCID: PMC3013063  PMID: 21203409
20.  Somatic embryogenesis in wild relatives of cotton (Gossypium Spp.) 
Wild cotton species can contribute a valuable gene pool for agronomically desirable cultivated tetraploid cultivars. In order to exploit diploid cotton a regeneration system is required to achieve transformation based goals. The present studies aimed at optimizing the conditions for regeneration of local varieties as well as wild species of cotton. Different callus induction media were tested with varying concentrations of hormones in which sucrose was used as nutritional source. Different explants (hypocotyls, cotyledon, root) were used to check the regeneration of both local cotton plants and wild relatives using T & G medium, BAP medium, CIM medium, EMMS medium, and cell suspension medium. Different stages of embryogenicity such as early torpedo stage, late torpedo stage, heart stage, globular stage and cotyledonary stage were observed in wild relatives of cotton. The results of this study pave the way for establishing future transformation methods.
doi:10.1631/jzus.2006.B0291
PMCID: PMC1447513  PMID: 16532531
Cotton; Callus; Somatic embryogenic; Wild species; Cell suspension culture

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