Abdul Nasir

Optimizing the physical parameters for bio-hydrogen production from food waste co-digested with mixed consortia of clostridium

Food waste along with its two individual components, noodle waste and rice waste, were tested for bio-hydrogen production by using sludge as a source of mix consortia of Clostridium under different physical conditions (pH 5, 6, and 7; temperature 37 °C and 55 °C). The increase in pH increased the bio-hydrogen yield for all tested wastes, whereas an increase in temperature increased the bio-hydrogen yield just for food waste. The highest experimental yield of 115.76 ml/VSremoved was produced in the mesophilic noodle waste reactor at pH 7. The drop in pH from 7 to 4.8 ± 0.2 was found optimum for bio-hydrogen production for all tested wastes under mesophilic as well as thermophilic conditions. Most of the hydrogen production was observed within 72 h of incubation, which can be used as the optimum bio-hydrogen production period for food waste. The bio-hydrogen yield, final volatile fatty acids (VFA), and glucose consumption at 72 h were analyzed with the help of the response surface methodology. The resultant...

A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family

BackgroundPure hair and nail ectodermal dysplasia (PHNED) is a congenital disorder of hair abnormalities and nail dysplasia. Both autosomal recessive and dominant inheritance fashion of PHNED occurs. In literature, to date, five different forms of PHNED have been reported at molecular level, having three genes known and two loci with no gene yet.MethodsIn this study, a four generations consanguineous family of Pakistani origin with autosomal recessive PHNED was investigated. Affected members exhibited PHNED phenotypes with involvement of complete hair loss and nail dysplasia. To screen for mutation in the genes (HOXC13, KRT74, KRT85), its coding exons and exons-intron boundaries were sequenced. The 3D models of normal and mutated HOXC13 were predicted by using homology modeling.ResultsThrough investigating the family to known loci, the family was mapped to ectodermal dysplasia 9 (ECTD9) loci with genetic address of 12q13.13. Mutation screening revealed a novel missense mutation (c.929A > C; p.Asn310Thr) in homeobox DNA binding domain of HOXC13 gene in affected members of the family. Due to mutation, loss of hydrogen bonding and difference in potential energy occurs, which may resulting in alteration of protein function.ConclusionThis is the first mutation reported in homeodomain, while 5th mutation reported in HOXC13 gene causing PHNED.

Hypomorphic MKS1 mutation in a Pakistani family with mild Joubert syndrome and atypical features: Expanding the phenotypic spectrum of MKS1‐related ciliopathies

Postaxial polydactyly (PAP) is one of the most common congenital malformations observed in the general population. However, it can also occur as part of a syndrome. Unbiased genetic screening techniques such as exome sequencing are highly appropriate methods to provide a molecular diagnosis in patients with polydactyly due to the large number of mutated genes associated with it. The present study describes a consanguineous family of Pakistani origin with PAP, speech impairment, hearing impairment of variable degree, and proportionate short stature with no prominent intellectual disability or ophthalmological abnormalities. One affected individual of the family was subjected to exome sequencing which resulted in the identification of four homozygous variants including an in‐frame deletion (c.1115_1117delCCT; p.(Ser372del) in MKS1, which was later shown to be the only variant segregating with the phenotype. In silico predictions supported the potential pathogenicity of the identified mutation. Additional clinical tests and MRI features of a patient in the family showed a molar tooth sign, which is a hallmark of Joubert syndrome. In conclusion, we have described a pathogenic variant in the MKS1 resulting in a mild Joubert syndrome phenotype, which broadens the spectrum of mutations in the MKS1.

Impact of pH Management Interval on Biohydrogen Production from Organic Fraction of Municipal Solid Wastes by Mesophilic Thermophilic Anaerobic Codigestion.

The biohydrogen productions from the organic fraction of municipal solid wastes (OFMSW) were studied under pH management intervals of 12 h (PM12) and 24 h (PM24) for temperature of 37 ± 0.1°C and 55 ± 0.1°C. The OFMSW or food waste (FW) along with its two components, noodle waste (NW) and rice waste (RW), was codigested with sludge to estimate the potential of biohydrogen production. The biohydrogen production was higher in all reactors under PM12 as compared to PM24. The drop in pH from 7 to 5.3 was observed to be appropriate for biohydrogen production via mesophilic codigestion of noodle waste with the highest biohydrogen yield of 145.93 mL/g CODremoved under PM12. When the temperature was increased from 37°C to 55°C and pH management interval was reduced from 24 h to 12 h, the biohydrogen yields were also changed from 39.21 mL/g CODremoved to 89.67 mL/g CODremoved, 91.77 mL/g CODremoved to 145.93 mL/g CODremoved, and 15.36 mL/g CODremoved to 117.62 mL/g CODremoved for FW, NW, and RW, respectively. The drop in pH and VFA production was better controlled under PM12 as compared to PM24. Overall, PM12 was found to be an effective mean for biohydrogen production through anaerobic digestion of food waste.

Novel homozygous sequence variants in the CDH3 gene encoding P-cadherin underlying hypotrichosis with juvenile macular dystrophy in consanguineous families

Human juvenile macular dystrophy (HJMD) results from a rare autosomal recessive genetic anomaly, manifesting with hypotrichosis and gradual loss of vision due to progressive macular degeneration. Variants in the CDH3 gene, encoding a trans-membrane glycoprotein P-cadherin, have been reported to result in HJMD [1] and its closely associated form, ectodermal dysplasia, ectrodactyly, macular dystrophy (EEM) [2].In the present study, two consanguineous families, A and B (figures 1A, B), in which HJMD [...]

A disease-causing novel missense mutation in the ST14 gene underlies autosomal recessive ichthyosis with hypotrichosis syndrome in a consanguineous family

BackgroundAutosomal recessive ichthyosis with hypotrichosis (ARIH; MIM 602400) syndrome is characterized by diffused congenital ichthyosis and generalized non-scarring hypotrichosis. The underlying genetic cause ofARIHsyndrome has been associated with sequence variants of the gene ST14, encoding type II transmembrane serine protease matriptase, which maps to chromosome 11q24.3.ObjectivesThe current report aimed to investigate the clinical features and genetic cause of ARIH syndrome in a large consanguineous family of Pakistani origin.Materials & MethodsThe technique of homozygosity mapping with highly polymorphic microsatellite markers was employed to establish linkage within the family. Sanger sequencing of exons and intron-exon boundaries of ST14 was performed to identify the potential pathogenic sequence variants, followed by structural analysis of the mutated protein.ResultsLinkage was established to chromosome 11q24.3, comprising the gene ST14. Sequence analysis led to the identification of a novel homozygous missense variant (c.1315G>A, p.Gly439Ser) in the ST14 gene that co-segregated with the disease phenotype in all affected members. Homology modelling and molecular docking analysis of ST14 with wild-type TMEFF1 protein was performed which revealed that glycine at position 439 is crucial for maintaining normal structural confirmation and interaction with the EGF domain of TMEFF1 protein.ConclusionsTaken together, the data strongly advocate this ST14 variant as the underlying genetic cause of ARIH syndrome in this first reported affected family from Pakistan. Moreover, the present study adds to the spectrum of mutations in the ST14 gene, implicating them in the pathogenesis of ARIH syndrome.

Novel homozygous sequence variants in the GDF5 gene underlie acromesomelic dysplasia type-grebe in consanguineous families

Acromesomelic dysplasia Grebe type (AMDG) is characterized by severe knob like non‐functional fingers and short acromesomelic limbs, and is inherited in an autosomal recessive manner. Disease causing sequence variants in the GDF5 (Growth Differentiation Factor 5) gene located on chromosome 20q11.22 are responsible for causing AMDG. In the study, presented here, two consanguineous families with AMDG were clinically and genetically characterized. After establishing linkage in the two families (A and B) to GDF5 gene on chromosome 20q11.22, Sanger DNA sequencing was performed in all available affected and unaffected members. Sequence analysis of the GDF5 gene revealed two novel variants including a duplication (c.157_158dupC, p.Leu53Profs*41) in family A, and a nonsense (p.Trp291*) in family B. Our findings extend the body of evidence that supports the importance of GDF5 in the development of limbs.

COMPARING THE EFFECT OF TOTAL SOLIDS CONCENTRATION ON BIO- HYDROGEN PRODUCTION POTENTIAL OF FOOD WASTE AND ITS DERIVATIVES UNDER MESOPHILIC THERMOPHILIC CONDITIONS

The effect of three total solid (TS) concentrations of 7.5, 10 and 12.5% on bio-hydrogen production potential of food waste (FW) in comparison with noodle waste (NW) and rice waste (RW) derived from FW were studied after co-digesting the wastes with heat shocked sludge under mesophilic (37°C) and thermophilic (55°C) conditions. The increase in TS concentration from 7.5% to 10% found an effective way to improve cumulative bio-hydrogen production from all tested wastes. As a whole, 7.5% TS concentration represented higher conversion efficiency of volatile solids into bio-hydrogen and the highest experimental yield of 95.8mL/VSfed was observed in 7.5%NW digester under thermophilic conditions. The increase in temperature within experimental range found an effective way to increase bio-hydrogen production potential of FW and NW only, whereas the same increase in temperature caused negative impact on bio-hydrogen production potential of RW. The optimum time period for active bio-hydrogen production found to be 24-72h of incubation. After 72h of incubation, the bio-hydrogen production reduced considerably in all reactors due to an abrupt increase in volatile fatty acid, and due to inhibition of bio-hydrogen production the drop in pH was also decreased.

A novel mutation in the HPGD gene causing primary hypertrophic osteoarthropathy with digital clubbing in a Pakistani family

Primary hypertrophic osteoarthropathy (PHO) is a congenital multisystemic entity characterized by three major clinical symptoms: pachydermia, periostosis, and digital clubbing. Recently it has been reported that pathogenic mutations in two genes are known to be associated with PHO: HPGD and SLCO2A1. In the present study, a five‐generation consanguineous Pakistani family harboring primary hypertrophic osteoarthropathy in autosomal‐recessive pattern was ascertained. Whole genome single nucleotide polymorphisms (SNPs) genotyping and sequence analysis revealed a novel homozygous missense mutation (c.577T˃C) of the human HPGD gene in all affected members of the family. The study presented here demonstrate the first case of primary hypertrophic osteoarthropathy reported in Pashtun population.

EXPERIMENTAL AND MODELING APPROACH FOR SOIL PHYSICAL DEGRADATION DUE TO DIFFERENT IRRIGATION TECHNIQUES

The total land of Pakistan is 79.6 million hectares (Mha) and about 70% lies in arid to semiarid zone. About 63.9% (50.88 Mha) is lying on rangeland and 26.1% (22Mha) is culture able land, area of KPK and northern areas lie in humid to semiarid region. The Sindh province is lying completely in arid zone, Punjab and Baluchistan has arid to semi-arid ratio 58:29 and 43:57, respectively (PCRWR, 1999; Iqbal, et al. 2000). The two-third portion of Pakistan lies in semi-arid to arid zones according to report of Pakistan’s agro climatic classification (Chaudhry et al., 2004). Due to shortage of fresh water the availability of water for irrigation purpose in arid zone is a major problem (Asma et al., 2012). However, significant uncertainties exist in determining irrigated areas which globally consume nearly 80% of all human water use. Total 6,685 to 7,500 km/yr water is used by the agriculture land from which 4,586 km/yr is by rain fed croplands and the rest by irrigated croplands (Thenkabail et al., 2009). Irrigated areas use about 2,099 km/yr (1,180 km/yr of canal irrigation water and the rest is obtained from rain). However, 1.6 to 2.5 times of the irrigated water required by irrigated croplands is actually withdrawn from pumping of ground water, with an irrigation efficiency of 40–62% (Thenkabail et al., 2009). It also reflects the increasing water shortage and soil degradation. In combination, these factors keep farmers for realizing the benefits of new technologies and thus undercut their incentive to adopt them (Nasir et al., 2016). By 2025, agriculture share of water from current situation will decrease from 70%-80% to 60%-70% due to increase of urbanization and diminishing water share (Eriyagama et al., 2009). Fresh water availability has direct link for fulfilling the crop water requirement along with crop production. Wheat demand in the developing countries will increase up to 60% in 2050 (Rosegrant and Agcoaili, 2010). On the other hand, climate change will decrease the wheat production by 20-30%, it means overall production will be 66% (Easterling et al., 2007; Lobel et al., 2008; Rosegrant and Agcoaili, 2010). This decrease of wheat production is due to decreasing of water supply, soil fertility and threats from pests. Wheat production in Pakistan in rabi season decreased to 4.2% per hectare due to decrease in cropping area of wheat by 2.6% (PBS, 2010). It is essential to introduce proper measurement techniques to ensure food security of the planet (Thenkabail et al., 2009). Wisely estimation of indicators must be identified which are harnessing the food security (Hussain et al., 2003). In the Pak. J. Agri. Sci., Vol. 53(2), 511-516; 2016 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/16.2287 http://www.pakjas.com.pk