SHORT AND LONG TERM FOLLOW UP RESULTS OF (THE VERSATILE) GASTROCNEMIUS MUSCLE FLAP

Objective: To see the long and short term outcome of the Gastrocnemius muscle flap for coverage of soft tissue defects of knee and proximal Tibia. Study Design: Case series. Place and Duration of Study: Surgery Department of Combined Military Hospital Bahawalpur, from Dec 2014 to Oct 2017. Methodology: A total of 33 patients were enrolled for the study through consecutive sampling. Data was processed using SPSS-17. All patients were followed up at first and second week (early morbidity), and then at 06 months (late morbidity) from operation. During early follow up, they were examined for Hematoma at donor site, wound Infection, sural nerve injury, partial skin graft loss and Partial Flap Necrosis. In late follow up patients were examined for reduced Knee mobility and Gastrocnemius muscle contractions. Results: The studied 33 patients consisted of 30 (90.90%) men and 3 (9.09%) women. The mean age was 35 years (range: 16 to 64) years. Hematoma was commonest complication. It occurred in 6.06%. Wound infection, partial loss of flap, partial loss of skin graft and wound infection occurred in 3.03% patients. Late follow up revealed reduced knee mobility in 9.09% patients (n=3) and bothersome contraction of gastrocnemius muscle in same number of patients. Conclusion: The gastrocnemius flap is reliable, versatile, and very useful for provision of supple soft tissue coverage for defects around the knee and the upper leg.

Antibiotic susceptibility and drug prescription pattern in uropathogenic Escherichia coli in district Muzaffarabad, Azad Jammu and Kashmir, Pakistan

The present research study was done to determine the correlation between antibiotic susceptibility and drug prescription patterns in empirical treatment of uropathogenic Escherichia coli (E. coli) in two hospitals of district Muzaffarabad, Azad Kashmir, Pakistan. One hundred uropathogenic E. coli clinical isolates were collected from UTI patients who attended the Combined Military Hospital (CMH) and Abbas Institute of Medical Sciences (AIMS), district Muzaffarabad, AJK. All isolates were subjected to antibiotic susceptibility against seven commonly prescribed antibiotics by Kirby-Bauer disk diffusion method. However, all the E. coli isolates were susceptible to Imipenem. Eight percent and 10% of isolates from CMH and AIMS were found to be resistant against Nitrofurantoin drug respectively. Similarly, 94% and 74% isolates from CMH and 60% and 64% isolates from AIMS were found to be resistant against Co-trimoxazole and Coamoxiclave, respectively. Pipemedic acid resistance was also detected in 76% and 60% isolates from AIMS and CMH, respectively. Ciprofloxacin resistance was also observed in 54% and 36% isolates from AIMS and CMH, respectively. The finding of the study revealed that both hospitals have different drug susceptibility pattern against uropathogenic E. coli, which may be associated with patterns of drug prescription in empirical treatment of urinary tract infections. There is a vital need for appropriate development of hospital-specific antibiograms to determine appropriate empiric therapy of urinary tract infections.

Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration

The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.

Surgical Outcome of Peripheral Vascular Injuries in Adults

OBJECTIVE

To describe the management and outcome of adult patients after peripheral vascular injuries.

STUDY DESIGN

Observational study.

PLACE AND DURATION OF STUDY

Accident & Emergency Department, Mayo Hospital Lahore, Pakistan, from January 2014 to December 2018.

METHODOLOGY

All adult trauma patients (aged ≥13 years), who were admitted following injury to peripheral blood vessels regardless injuries, were included. Variables including patient data, mechanism of injury, vessel involved, injury severity score (ISS), surgical procedure etc. were retrospectively extracted from patient charts. Binary logistic and multinomial regression analyses were performed. The p-value <0.05 was considered significant for mortality and limb outcome.

RESULTS

There were 117 patients, with mean age of 28.9±11.6 years. The commonest cause was blunt trauma (55.6%). The popliteal artery was most commonly involved (44.4%). Complete transection of artery was the most common type of injury (58.1%). The mean ISS was 17.2 ± 10. Reverse saphenous vein graft (RSVG) was the most common surgical repair (49.6%) procedure. Wound infection (17.1%) was the main complication. Limb salvage rate was 73.5% and mortality rate was 5.1%. Variables significantly influencing the limb outcome (amputated vs. salvaged) were duration of injury (p <0.001), concomitant body injury (p=0.009), ISS (p <0.001), surgical procedure (p <0.001), hemoglobin on presentation (p<0.001), number of blood transfusion (p=0.05) complications after surgery (p <0.001) and referral or not (p=0.001). Factors significantly associated with mortality were duration of injury (p=0.008), ISS (p = 0.002) and complications after surgery (p=0.011).

CONCLUSION

Low hemoglobin on presentation, postoperative increased requirement of blood transfusions and having reverse saphenous graft as procedure were independent risk factors for amputation. ISS score and postoperative complications led to higher amputation and mortality rates after surgery. Key Words: Injury severity score (ISS), Glasgow coma scale (GCS), Reverse saphenous graft (RSVG), Fasciotomy, Popliteal artery, Mortality.

Identification of a recurrent nonsense mutation in HR gene responsible for atrichia with papular lesions in two Kashmiri families

BACKGROUND

Congenital atrichia (CA) is a rare form of irreversible alopecia with an autosomal recessive mode of inheritance. This form of hair loss is mainly associated with mutations in the human hairless (HR) gene located at chromosome 8p21.3. An additional unique feature atrichia with papular lesions (APL) comprises keratin-filled cysts known as papules. The present study aimed to uncover the underlying genetic causes of APL in two consanguineous Kashmiri families.

METHODS

In the present study, two consanguineous families of Kashmiri origin with APL displaying an autosomal recessive mode of inheritance were investigated. Whole exome and Sanger sequencing followed by bioinformatic studies, variant prioritization, Sanger validation and segregation analysis was performed to find the mutation.

RESULTS

A recurrent nonsense (NM_005144: c.2818C > T:p.Arg940*) mutation was detected in exon 13 of the human HR gene.

CONCLUSIONS

Whole exome sequencing analysis has widely been used in the screening of single gene disorders mutations, both in research and diagnostic laboratories. Sanger sequencing alone for genes such as HR becomes expensive and time consuming. Instead, it is recommended that a patient is to screen by whole exome sequencing and then special attention first focuses on known genes of the APL phenotype. This is helpful for intime diagnosis, being more efficient and economic. The results obtained in the present study may contribute to prenatal diagnosis, carrier secreening and the genetic counseling of families with the APL phenotype in Kashmiri poplution.

Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa

Purpose

Retinitis pigmentosa (RP) is a genetically heterogeneous trait with autosomal-recessive (ar) inheritance underlying 50% of genetic disease cases. Sixty-one arRP genes have been identified, and recently, DHX38 has been reported as a potential candidate gene for arRP with only a single family reported with a variant of unknown significance. We identified a missense variant in DHX38 that co-segregates with the arRP phenotype in two Pakistani families confirming the involvement of DHX38 in the etiology of early-onset RP.

Methods

Exome sequencing was performed using two DNA samples from affected members of Pakistani families (MA88 and MA157) with early onset arRP. Sanger sequencing of DNA samples from all family members confirmed the segregation of candidate variant within both families.

Results

A novel missense DHX38 variant c.971G>A; p.(Arg324Gln) was identified which segregates with the arRP phenotype and yielded a logarithm of the odds (LOD) score of 5.0 and 4.3 for families MA88 and MA157, respectively. This variant is predicted to be conserved and deleterious by several bioinformatics tools.

Conclusions

We identified a second deleterious DHX38 variant that segregates with arRP in two families, providing additional evidence that DHX38 is involved in RP etiology. DHX38 encodes for pre-mRNA splicing factor PRP16, which is important in catalyzing pre-mRNA splicing.

FAM92A Underlies Nonsyndromic Postaxial Polydactyly in Humans and an Abnormal Limb and Digit Skeletal Phenotype in Mice

Polydactyly is a common congenital anomaly of the hand and foot. Postaxial polydactyly (PAP) is characterized by one or more posterior or postaxial digits. In a Pakistani family with autosomal recessive nonsyndromic postaxial polydactyly type A (PAPA), we performed genomewide genotyping, linkage analysis, and exome and Sanger sequencing. Exome sequencing revealed a homozygous nonsense variant (c.478C>T, p.[Arg160*]) in the FAM92A gene within the mapped region on 8q21.13-q24.12 that segregated with the PAPA phenotype. We found that FAM92A is expressed in the developing mouse limb and E11.5 limb bud including the progress zone and the apical ectodermal ridge, where it strongly localizes at the cilia level, suggesting an important role in limb patterning. The identified variant leads to a loss of the FAM92A/Chibby1 complex that is crucial for ciliogenesis and impairs the recruitment and the colocalization of FAM92A with Chibby1 at the base of the cilia. In addition, we show that Fam92a^-/- homozygous mice also exhibit an abnormal digit morphology, including metatarsal osteomas and polysyndactyly, in addition to distinct abnormalities on the deltoid tuberosity of their humeri. In conclusion, we present a new nonsyndromic PAPA ciliopathy due to a loss-of-function variant in FAM92A. © 2018 American Society for Bone and Mineral Research.

Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability

Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including: EI24, FXR1 and TET3 for which knockout mouse models have brain defects; and CACNG7 and TRAPPC10 where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes CARNMT1 and GARNL3 lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes, GRAMD1B and TBRG1, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed in utero or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.

Sequence variants in four genes underlying Bardet-Biedl syndrome in consanguineous families

PURPOSE

To investigate the molecular basis of Bardet-Biedl syndrome (BBS) in five consanguineous families of Pakistani origin.

METHODS

Linkage in two families (A and B) was established to BBS7 on chromosome 4q27, in family C to BBS8 on chromosome 14q32.1, and in family D to BBS10 on chromosome 12q21.2. Family E was investigated directly with exome sequence analysis.

RESULTS

Sanger sequencing revealed two novel mutations and three previously reported mutations in the BBS genes. These mutations include two deletions (c.580_582delGCA, c.1592_1597delTTCCAG) in the BBS7 gene, a missense mutation (p.Gln449His) in the BBS8 gene, a frameshift mutation (c.271_272insT) in the BBS10 gene, and a nonsense mutation (p.Ser40*) in the MKKS (BBS6) gene.

CONCLUSIONS

Two novel mutations and three previously reported variants, identified in the present study, further extend the body of evidence implicating BBS6, BBS7, BBS8, and BBS10 in causing BBS.

DNA barcoding of Schizothorax species from the Neelum and Jhelum Rivers of Azad Jammu and Kashmir

The mitochondrial Cytochrome Oxidase 1 gene is used as a standardized, authenticated, and reliable genetic marker for a global species-level bio-identification system. The present study was conducted to determine whether barcoding can help accurate species identification in fishes. The overall base composition of Schizothorax species was 29.6% of T, 25.5% of C, 26.5% of A, and 18.4% of G, A + T content 56.1% and G + C content 43.9%. The Ts/Tv bias (R) was 2.51. Complete COI gene was amplified using PCR and sequenced from 17 samples collected from river Neelum and Jhelum, and identification of species were done by following Mirza (1991), Jhingran (1991) classification and also through BOLD (99.3 to 99.9%) and NCBI (99.6 to 99.9%) reference sequences of those species. Multiple alignments of CO1 mtDNA gene resulted in a range of 1535-1551 base pairs. Out of 1535 consensus sites, 1490 were constant, 61 characters were variable, in which 54 were parsimony informative, and 7 variables were parsimony uninformative. This is the very first study reported from a reservoir of cold water bodies of Azad Kashmir which have a great potential for conservation of cold water fish species. We emphasized that, DNA barcoding is an accurate, reliable and has the great potential for identification of freshwater fish species.