Publications by authors named "Faisal Awan"

14 Publications

  • Page 1 of 1

Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat ( L.) Accessions.

Front Genet 2022 6;13:772517. Epub 2022 Apr 6.

Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.

Spring wheat ( L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
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http://dx.doi.org/10.3389/fgene.2022.772517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9019749PMC
April 2022

Coal fines migration: A holistic review of influencing factors.

Adv Colloid Interface Sci 2022 Mar 29;301:102595. Epub 2021 Dec 29.

Petroleum Engineering Discipline, School of Engineering, Edith Cowan University, 270 Joondalup Dr, Joondalup 6027, WA, Australia; Centre for Sustainable Energy and Resources, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Western Australia, Australia.

Coal fines can substantially influence coal seam gas reservoir permeability, thus impeding the flow of gas in coal microstructure. The coal fines generation and migration are influenced by several factors, wherein coal fines are generally hydrophobic and aggregate in natural coal seam gas (CSG) under prevailing conditions of pH, salinity, temperature and pressure. This aggregation behaviour can damage the coal matrix and cleat system permeabilities, leading to a considerable reduction of proppant pack conductivity (i.e. fracture conductivity). Several datasets have been reported within the literature on this subject in the last decade. However, a more up-to-date discussion of this area is key to understanding coal fines migration and associated knowledge. Thus, in this review, we conduct a systematic investigation of coal fines and their influencing factors. Here, coal fines are introduced, followed by an initial holistic investigation of their generation, plugging, movement, redistribution and production. Then, in order to enhance current understandings of the subject matter, a parametric evaluation of the factors noted earlier is conducted, based on recently published literature. Subsequently, the published mathematical and analytical models for fines generation are reviewed. Finally, the implications and challenges associated with coal fines mitigation are discussed.
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http://dx.doi.org/10.1016/j.cis.2021.102595DOI Listing
March 2022

Influence of mineralogy and surfactant concentration on zeta potential in intact sandstone at high pressure.

J Colloid Interface Sci 2022 Feb 11;607(Pt 1):401-411. Epub 2021 Aug 11.

School of Engineering, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Western Australia, Australia; Centre for Sustainable Energy and Resources, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Western Australia, Australia. Electronic address:

Hypothesis: Zeta-potential in the presence of brine has been studied for its application within hydrocarbon reservoirs. These studies have shown that sandstone's zeta-potential remains negatively charged, non-zero, and levels-off at salinities > 0.4 mol.dm, thus becoming independent of salinity when ionic strength is increased further. However, research conducted to date has not yet considered clay-rich (i.e. clay ≥ 5 wt%) sandstones.

Experiments: Firstly, streaming potential measurements were conducted on Bandera Gray sandstones (clay-rich and clay-poor) with 0.6 and 2 mol.dm NaCl brine-saturated in pressurised environments (6.895 MPa overburden and 3.447 MPa back-pressure). Secondly, the streaming potential was determined at identical conditions for the effect of two surfactants, SDBS and CTAB, at concentrations of 0.01 and 0.1 wt% on the clay-poor sample in 0.6 mol.dm NaCl. Thirdly, a comparison of zeta potentials determined via electrophoretic and streaming potential was conducted. Accordingly, this work analyses the effects of mineralogy and surfactants within this process.

Findings: Clay-rich sandstone possessed lower zeta-potentials than clay-poor sandstone at the two tested salinities. SDBS reduced zeta-potential and yielded higher repulsive forces rendering the rock more hydrophilic. Additionally, electrophoretic zeta-potentials were higher when compared to streaming zeta-potentials. Mechanisms for the observed phenomena are also provided.
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http://dx.doi.org/10.1016/j.jcis.2021.08.015DOI Listing
February 2022

Effect of humic acid on CO-wettability in sandstone formation.

J Colloid Interface Sci 2021 Apr 21;588:315-325. Epub 2020 Dec 21.

Petroleum Engineering Discipline, School of Engineering, Edith Cowan University, 270 Joondalup Dr, Joondalup 6027, WA, Australia.

Hypothesis: Millions of tons of CO are stored in CO geological storage (CGS) formations (depleted oil reservoirs and deep saline aquifers) every year. These CGS formations naturally contain small concentrations of water-soluble organic components in particular humic acid (HA), which may drastically affect the rock wettability - a significant factor determining storage capacities and containment security. Hence, it is essential to characterise the effect of humic acid concentration on CO-wettability and its associated impact on storage capacity.

Experimental: To achieve this, we measured advancing and receding contact angles at reservoir conditions using the pendant drop tilted plate method for various humic acid concentrations (1, 10, and 100 mg/L) as a function of pressure (0.1-25 MPa), temperature (303-333 K), and brine salinity (0-0.3 M NaCl). Further, the influence of humic acid adsorption on the mineral's surface was examined by several independent techniques.

Results: Our results demonstrate that humic acid significantly changes rock wettability from water-wet (0-50°) towards CO-wet (90-110°). An increase in pressure, temperature, and salinity had a similar effect. Humic acid adsorption also increased the surface roughness of the substrates. We conclude that even trace amounts of humic acid (i.e. 1 mg/L), which exist in storage aquifers, significantly increase CO-wettability and thus reduce structural and residual trapping capacities. Therefore, it is pertinent to account for these humic acid concentrations to de-risk CGS projects.
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http://dx.doi.org/10.1016/j.jcis.2020.12.058DOI Listing
April 2021

Genome-Wide Association Mapping for Stripe Rust Resistance in Pakistani Spring Wheat Genotypes.

Plants (Basel) 2020 Aug 19;9(9). Epub 2020 Aug 19.

Department of Biochemistry, University of Agriculture, Faisalabad 38000, Pakistan.

Stripe rust caused by the pathogen f. sp. () is a major threat for wheat, resulting in low yield and grain quality loss in many countries. Genetic resistance is a prevalent method to combat the disease. Mapping the resistant loci and their association with traits is highly exploited in this era. A panel of 465 Pakistani spring wheat genotypes were evaluated for their phenotypic response to stripe rust at the seedling and adult plant stages. A total of 765 single nucleotide polymorphism (SNP) markers were applied on 465 wheat genotypes to evaluate their stripe rust response against nine races during the seedling test and in three locations for the field test. Currently, twenty SNPs dispersed on twelve chromosomal regions (1A, 1B, 1D, 2A, 2B, 4A, 4B, 5B, 6A, 6B, 6D and 7B) have been identified that were associated with rust race-specific resistance at the seedling stage. Thirty SNPs dispersed on eighteen chromosomal regions (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6A, 6B, 6D, 7A, 7B and 7D) are associated with adult plant resistance. SNP loci IWB3662 was linked with all three Pakistani races, and likewise IWA2344 and IWA4096 were found to be linked with three different USA races. The present research findings can be applied by wheat breeders to increase their resistant capability and yield potential of their cultivars, through marker-assisted selection.
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http://dx.doi.org/10.3390/plants9091056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570266PMC
August 2020

Gender Identification in Date Palm Using Molecular Markers.

Methods Mol Biol 2017 ;1638:209-225

U.S.-Pakistan Center for Advanced Studies in Agriculture and Food Security (USPCAS-AFS), University of Agriculture, Faisalabad, Pakistan.

Breeding of date palm is complicated because of its long life cycle and heterozygous nature. Sexual propagation of date palm does not produce true-to-type plants. Sex of date palms cannot be identified until the first flowering stage. Molecular markers such as random amplified polymorphic DNA (RAPD), sequence-characterized amplified regions (SCAR), and simple sequence repeats (SSR) have successfully been used to identify the sex-linked loci in the plant genome and to isolate the corresponding genes. This chapter highlights the use of three molecular markers including RAPD, SCAR, and SSR to identify the gender of date palm seedlings.
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http://dx.doi.org/10.1007/978-1-4939-7159-6_18DOI Listing
April 2018

Identification and lead-in characterization of novel B3 metallo-β-lactamases.

Pak J Pharm Sci 2017 Jan;30(1 Suppl):335-340

Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan.

Metallo-β-lactamases (MBLs) are zinc ion dependent enzymes that are responsible for the emergence and spread of β-lactam resistance among bacterial pathogens. There are uncharacterized putative MBLs in the environment and their emergence is major interference in the generation of universal MBL inhibitors so it is important to identify and characterize novel MBLs. In this study two novel MBLs from Luteimonas sp. J29 and Pseudoxanthomonas mexicana were identified using B3 MBLs as query in BLAST database search. 3D models of putative MBLs generated by SWISS-MODEL server taking AIM-1 as a structural template were verified using web based structure assessment and validation programs. Multiple sequence alignment revealed that residues important for substrate binding were conserved and loop region residues (156-162 and 223-230) important for catalysis are variable in these novel MBLs. Homology models showed typical MBL α/β/β/α sandwich fold containing six α helices, twelve β strands and metal interacting residues are conserved in similar way as with other B3 MBLs. We report promising putative B3 MBLs with some variations and substrate docking studies revealed that novel MBLs have attributes close to acquired B3 MBLs.
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January 2017

A Radiologically Detected Intraperitoneal Foreign Body in a Patient Without Prior Surgery.

Am Surg 2017 Jan;83(1):e28-29

Department of Surgery, St. Luke's Hospital, Kilkenny, Ireland.

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January 2017

The RIPASA score is sensitive and specific for the diagnosis of acute appendicitis in a western population.

Int J Colorectal Dis 2017 Apr 15;32(4):491-497. Epub 2016 Dec 15.

Department of Surgery, St. Luke's Hospital, Kilkenny, Ireland.

Aim: The definitive diagnosis of acute appendicitis (AA) requires histopathological examination. Various clinical diagnostic scoring systems attempt to reduce negative appendectomy rates. The most commonly used in Western Europe and the USA is the Alvarado score. The Raja Isteri Pengiran Anak Saleha appendicitis (RIPASA) score achieves better sensitivity and specificity in Asian and Middle Eastern populations. We aimed to determine the diagnostic accuracy of the RIPASA score in Irish patients with AA.

Methods: All patients who presented to our institution with right iliac fossa pain and clinically suspected AA between January 1 and December 31, 2015, were indentified from our hospital inpatient enquiry database and retrospectively studied. Operating theatre records and histology reports confirmed those who underwent a non-elective operative procedure and the presence or absence of AA. SPSS version 22 was used for statistical analysis. Standard deviation is provided where appropriate.

Results: Two hundred eight patients were included in the study (106/51% male, mean age 22.7 ± 9.2 years). One hundred thirty-five (64.9%) had histologically confirmed AA (mean symptom duration = 36.19 ± 15.90 h). At a score ≥7.5, the previously determined score most likely associated with AA in Eastern populations, the RIPASA scoring system demonstrated a sensitivity of 85.39%, specificity of 69.86%, positive predictive value of 84.06%, negative predictive value of 72.86% and diagnostic accuracy of 80% in our cohort.

Conclusion: The RIPASA score is a useful tool to aid in the diagnosis of acute appendicitis in the Irish population. A score of ≥7.5 provides sensitivity and specificity exceeding that previously documented for the Alvarado score in Western populations. WHAT DOES THIS PAPER ADD TO THE LITERATURE?: This is the first study evaluating the utility of the RIPASA score in predicting acute appendicitis in a Western population. At a value of 7.5, a cut-off score suggestive of appendicitis in the Eastern population, RIPASA demonstrated a high-sensitivity, specificity, positive predictive value and diagnostic accuracy in our cohort and was more accurate than the commonly used Alvarado score.
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http://dx.doi.org/10.1007/s00384-016-2713-4DOI Listing
April 2017

Evidence based management of polyps of the gall bladder: A systematic review of the risk factors of malignancy.

Surgeon 2016 Oct 26;14(5):278-86. Epub 2016 Jan 26.

Department of Surgery, University of Dublin, Trinity College, at the Adelaide and Meath Hospital, Tallaght, Dublin, Ireland. Electronic address:

Background: There are no evidence-based guidelines to dictate when Gallbladder Polyps (GBPs) of varying sizes should be resected.

Aim: To identify factors that accurately predict malignant disease in GBP; to provide an evidence-based algorithm for management.

Methods: A systematic review following PRISMA guidelines was performed using terms "gallbladder polyps" AND "polypoid lesion of gallbladder", from January 1993 and September 2013. Inclusion criteria required histopathological report or follow-up of 2 years. RTI-IB tool was used for quality analysis. Correlation with GBP size and malignant potential was analysed using Euclidean distance; a logistics mixed effects model was used for assessing independent risk factors for malignancy.

Results: Fifty-three articles were included in review. Data from 21 studies was pooled for analysis. Optimum size cut-off for resection of GBPs was 10 mm. Probability of malignancy is approximately zero at size <4.15 mm. Patient age >50 years, sessile and single polyps were independent risk factors for malignancy. For polyps sized 4 mm-10 mm, a risk assessment model was formulated.

Conclusions: This review and analysis has provided an evidence-based algorithm for the management of GBPs. Longitudinal studies are needed to better understand the behaviour of polyps <10 mm, that are not at a high risk of malignancy, but may change over time.
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http://dx.doi.org/10.1016/j.surge.2015.12.001DOI Listing
October 2016

Study on colorectal cancer presentation, treatment and follow-up.

Int J Colorectal Dis 2016 Jul 7;31(7):1361-3. Epub 2016 Jan 7.

Saint Luke's Hospital Kilkenny, Kilkenny, Ireland.

Background: Colorectal carcinoma (CRC) is the second most common cancer in women and men affecting 9.7 % population worldwide. Although CRC mortality has been progressively declining since 1990 at a rate of about 3 % per year, it still remains the third most common cause of cancer deaths.

Objective: The objective of this study is to evaluate the patterns of clinical presentation, treatment options and follow-up of colorectal carcinoma.

Methodology: Medical records of patients with colorectal carcinoma admitted at St. Luke's Hospital Kilkenny from January 2009 to December 2014 were included in the study.

Results: Out of 113, 57 were males and 28 were 75 years or older. Sixty-seven percent presented in the outpatient clinic. The main presentation symptom was bleeding per rectum (40 %), followed by abdominal pain, altered bowel habit, bowel obstruction and weight loss. Mean time delay was 4.79, 6.20 and 4.83 weeks for surgical outpatient department (SOPD), colonoscopy and surgery, respectively. Ninety-eight percent of patients underwent preoperative staging with computed tomography of thorax, abdomen and pelvis (CTTAP) and 78 % had preoperative carcinoembryonic antigen (CEA) measurement. Thirty-four percent of cancers had already metastasized to distant organs. Twenty five percent underwent a right hemicolectomy. Seventy-eight percent received a primary anastomosis. Ninety-five percent achieved a R0 resection. Sixty-two percent were given adjuvant chemotherapy. Seventy-six percent had surgery follow-up and 57 % had excellent follow-up. Cancer recurred in two patients. Thirty day mortality was 2 %.

Conclusion: Our study shows that the mean age group at risk for colorectal cancer is 65 years (range 54-75). Still, 33 % of patients present to acute surgical assessment units with advanced disease. Though we did well in terms of operative resections, follow-up still remains a challenge.
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http://dx.doi.org/10.1007/s00384-015-2479-0DOI Listing
July 2016

Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers.

3 Biotech 2016 Jun 9;6(1):22. Epub 2016 Jan 9.

Institute of Horticultural Sciences, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan.

Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci. On average, there are 9.08 alleles per locus, with a range from 5 to 16 alleles, for primers mpdCIR15 and mpdCIR57, respectively. These primers produced 15 polymorphic loci specifically in male date palm samples and the seedlings harboring the unique fragments were further characterized as male plants. Increasingly, 38.46 % of these loci were scored as homozygous alleles while 61.53 % heterozygous allelic loci were determined. Primer mpdCIR48 produced a specific locus (250/250) in all male samples whereas the same locus was absent in female samples. Similarly, a locus of 300/310 bp reoccurred in 5 date palm male samples using marker DP-168 which indicated that these are the promising candidate marker to detect the sex in date palm seedlings at early stage. The data resulted from combination of 12 primers enabled the 16 seedling samples progeny (developed from parents breeding) of date palm cultivars to divide into two groups i.e., male and female regarding their sex expression comparative to the parents (male + female) using the principle coordinate analysis.
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http://dx.doi.org/10.1007/s13205-015-0321-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706835PMC
June 2016

Incarcerated thoracic gastric herniation after nephrectomy: a report of two cases.

Case Rep Surg 2013 16;2013:896452. Epub 2013 May 16.

Department of Surgery, St. James's Hospital, Dublin 8, Ireland.

Iatrogenic diaphragmatic hernias can occur after abdominal or thoracic surgery. Acute presentation of a diaphragmatic hernia varies depending on the extent and nature of the organ which has herniated. The initial diagnosis can be challenging due to the nonspecific nature of the presenting symptoms. Delay in diagnosis poses a significant risk to the patient, and a rapid deterioration can occur in the context of strangulation. We outline two cases of acute gastric herniation through a defect in the diaphragm after an open and a laparoscopic nephrectomy. Both had characteristic findings on imaging, required emergency, surgery and had a successful outcome. Both cases highlight the potential for late presentation with non-specific symptoms and the necessity for urgent surgical management where gastric perfusion is compromised.
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http://dx.doi.org/10.1155/2013/896452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670470PMC
June 2013

Partial herniation through the peritoneal defect of a pfannenstiel incision: a rare complication of non-closure.

J Obstet Gynaecol Can 2011 Jun;33(6):625-627

Department of Colorectal Surgery, St James's Hospital, Dublin, Ireland.

Background: The Pfannenstiel incision is used almost invariably in Caesarean section. With Caesarean section rates increasing, the Pfannenstiel is a commonly performed incision. The prevailing recommendation is not to close the peritoneum when closing a Pfannenstiel incision, and peritoneal non-closure does not appear to statistically influence postoperative complication rates.

Case: A 33-year-old woman presented with severe, intermittent lower abdominal pain one year after a Caesarean section. Laparoscopy showed a hernial defect at the Pfannenstiel incision, between the left rectus abdominis muscle and the anterior rectus sheath. Mesh repair was performed with uncomplicated postoperative outcome.

Conclusion: The current case illustrates that complications specific to non-closure of the peritoneum do arise. We advocate that laparoscopy should be considered for any patient with persistent, severe, or atypical pain following a Pfannenstiel incision.
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http://dx.doi.org/10.1016/S1701-2163(16)34912-XDOI Listing
June 2011
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