De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease.

Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.

Detection of genetic divergence among putative ethyl methane sulfonate mutants of super basmati using microsatellite markers.

BACKGROUND: Seeds of super basmati were mutagenized with different ethyl methane sulphonate (EMS) doses for creating genetic variability. METHODS AND RESULTS: A total of 48 randomly selected putative EMS mutants of super basmati were analyzed to dissect the genetic diversity by using 25 SSR primers located on twelve chromosomes of rice. SSRs analysis revealed that wide-range of genetic diversity is present among mutants of super basmati. A sum of 91 alleles were identified, out of these, 82 alleles were polymorphic and the rest of nine alleles were monomorphic in nature. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content was range between 0.039 (RM5) and 0.878 (RM44) with mean of 0.439 for each locus. A number of polymorphic markers showed unique bands of various sizes ranges from 75 to 1000 bp, during genetic dissection of mutant population. Dendrogram divided whole mutant population into four major groups. Phylogenic analyses revealed that 40-96%genetic similarity is present among individuals of mutant population. CONCLUSION: It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be handy for the selection of rice mutants as parents for functional genomic and molecular breeding program.

Human cancer risk due to chromium and its bioaccumulation in physids in Central Punjab, Pakistan.

The present study aims to assess the ecological risk of chromium [Cr(VI)] in the water and soil of Central Punjab and its natural bioremediation through physids. Members of the genus Physa are cosmopolitan as they are resistant to various pollutants. The snails of the genus Physa were sampled from October through March. Three species, i.e., P. acuta, P. fontinalis, and P. gyrina, were identified. The foot, shell, water, and soil samples were tested for the presence of the hexavalent chromium, using ICP-MS. The maximum mean concentration of chromium in soil was found in GB(R8), i.e., 2.66 ppb. The maximum mean concentration of chromium in water was found in RB(R4), 1.627 ppb. The highest maximum average daily dose (ADD) was found in RB:R6, with a hazard quotient (HQ) of 32.32 and a carcinogenic risk (CR) of approximately 20 in every 100 children as a result of water pollution which is quite similar to RB:R5 showing these are extremely polluted area due to chromium. The pollution level of chromium in soil of Faisalabad is less than zero and safe while water is unsuitable for drinking as the value of water quality index (WQI) is higher than 100. No significant difference among the three species was found regarding bioaccumulation of chromium, in the snail shell and body. Physids play an active role in the bioremediation of soil and water yet may become cancer-causing tablets in the food chains of the region.

A rare case of duodenal angiodysplasia-a case report.

Gastrointestinal bleeding can be manifested as a variety of symptoms and, often, it is difficult to classify as upper or lower gastrointestinal bleeding on mere symptomatology. This is a case report of a similar kind of patient who initially was diagnosed with fresh per rectum bleeding, subsequently diagnosed as bleeding angiodysplasia in duodenal diverticulum by a series of investigations and management including urgent oesophageal-gastroduodenoscopy (OGD), laparotomy, followed by computerized tomography-angiogram. As diagnosis was established after laparotomy, the patient was kept intubated and IR selective embolization was performed. Keeping this case report in view, it can be suggested that bleeding vascular malformation in any part duodenum should be considered as a cause of massive upper GI bleeding. Furthermore, if operative intervention is indicated, it should be preceded by OGD, not only for a therapeutic purpose but also as an adjunct for guidance for the operative plan.

An extremely rare complication of intestinal stoma formation: parastomal evisceration 1-year post-loop ileostomy.

Intestinal stoma formation is an important and frequently performed procedure in emergency and elective general surgery. Parastomal evisceration is an extremely rare complication of stoma formation. The literature to date consists of a small number of case reports only. We report the case of a 54-year-old patient who presented 1-year post-loop ileostomy formation with a large parastomal evisceration. This was managed with emergency laparotomy. Our case highlights the high morbidity of this rare complication and the importance of emergent management and patient's education.

Genetic variants of CSN1S1, CSN2, CSN3, and BLG genes and their association with dairy production traits in Sahiwal cattle and Nili-Ravi buffaloes.

Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes (CSN1S1, CSN2, CSN3, and BLG) genetic variants and their association with milk yield in Sahiwal cattle and Nili-Ravi buffaloes. One hundred animals from each species were selected to collect blood samples and milk production records. Primers were designed for these milk protein genes for PCR amplification. Sequencing of resultant PCR products revealed a higher number of SNPs (13 vs. 7, 5 vs. 1, and 6 vs. 2) in Sahiwal as compared to Nili-Ravi animals in CSN1S1, CSN2, and CSN3 genes, respectively. However, a single SNP was observed in BLG gene of both species. Association analysis revealed that one SNP in BLG gene of Nili-Ravi was associated (p < 0.05) with 305-day milk yield. Two SNPs at CSN1S1 gene in Sahiwal were associated with dry-period. Similarly, one SNP at CSN1S1 and two SNPs at CSN3 gene showed significant association (p < 0.05) with average calving-interval in Sahiwal while two SNPs in CSN1S1 gene were associated (p < 0.05) with this trait in Nili-Ravi. These SNPs could be helpful as candidate variants for marker-assisted selection in cattle and buffaloes for improvement of lactation performance.

Malignant peritoneal mesothelioma-a diagnostic challenge.

Malignant peritoneal mesothelioma is a rare cancer originating primarily from the peritoneum with a poor prognosis and non-specific clinical presentation. We present a case of a 60-year-old male, retired metallurgy engineer who initially presented with shortness of breath, lethargy, weight loss, vague abdominal pain and night sweats. Extensive workup for almost 2 months finally leads to the diagnosis of primary malignant peritoneal mesothelioma based on immunohistochemical analysis of loss of BAP1 gene. The patient was deemed non-suitable for surgical management and started on palliative carboplatin and pemetrexed. In conclusion, histological diagnosis is essential for peritoneal diseases before considering it as a metastasis from other primary tumours. Furthermore, immunohistochemical analysis and genetic profiling may also guide towards the diagnosis and possible treatment.

Genome-wide association studies of seedling quantitative trait loci against salt tolerance in wheat.

Salinity is one of the significant factors in decreasing wheat yield and quality. To counter this, it is necessary to develop salt-tolerant wheat varieties through conventional and advanced molecular techniques. The current study identified quantitative trait loci in response to salt stress among worldwide landraces and improved varieties of wheat at the seedling stage. A total of 125 landraces and wheat varieties were subjected to salt treatment (50, 100, and 150 mM) with control. Morphological seedling traits, i.e., shoot length, root length, and fresh and dry shoot and root weights for salinity tolerance were observed to assess salt tolerance and genetic analysis using SNP data through DArT-seq. The results showed that, at the seedling stage, 150 mM NaCl treatment decreased shoot length, root length, and fresh and dry weights of the shoot and root. The root length and dry root weight were the most affected traits at the seedling stage. Effective 4417 SNPs encompassing all the chromosomes of the wheat genome with marker density, i.e., 37%, fall in genome B, genome D (32%), and genome A (31%). Five loci were found on four chromosomes 6B, 6D, 7A, and 7D, showing strong associations with the root length, fresh shoot weight, fresh root weight, and dry root weight at the p < 0.03 significance level. The positive correlation was found among all morphological traits under study.

Mass-Producible 2D Nanocomposite-Based Temperature-Independent All-Printed Relative Humidity Sensor.

Relative humidity sensors are widely studied under the categories of both environmental and biosensors owing to their vast reaching applications. The research on humidity sensors is mainly divided into two concentration areas including novel material development and novel device structure. Another approach focuses on the development of printed sensors with performance comparable to the sensors fabricated via conventional techniques. The major challenges in the research on relative humidity sensors include the range of detection, sensitivity (especially at lower %RH), transient response time, and dependence on temperature. Temperature dependence is one of the least studied parameters in relative humidity sensor development. In this work, relative humidity sensors were fabricated using all-printed approaches that are also compatible with mass production, resulting in low cost and easy development. Laser-induced graphene (LIG)-based printed electrodes were used as the transducers, while the 2D MoS2 and graphene nanocomposite was used as the active layer material with the built-in property of temperature independence. The exfoliation process of 2D MoS2 was based on wet grinding, while graphene for the active layer was obtained by scratching the graphene grown on the polyimide (PI) surface via laser ablation. The resulting sensors showed an excellent output response for a full range of 0%RH to 100%RH, having no dependence on the surrounding temperature, and excellent response and recovery times of 4 and 2 s, respectively. The developed sensors can be confidently employed for a wide range of humidity sensing applications where the temperature of the surrounding environment is not constant.

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

Spring wheat (Triticum aestivum 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.

Coal fines migration: A holistic review of influencing factors.

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.

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

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-3, 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-3 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-3 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.

Effect of humic acid on CO2-wettability in sandstone formation.

HYPOTHESIS: Millions of tons of CO2 are stored in CO2 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 CO2-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 CO2-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 CO2-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.

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

Stripe rust caused by the pathogen Puccinia striiformis f. sp. tritici (Pst) 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.

Gender Identification in Date Palm Using Molecular Markers.

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.

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

Metallo-ß-lactamases (MBLs) are zinc ion dependent enzymes that are responsible for the emergence and spread of ß-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/ß/ß/α sandwich fold containing six α helices, twelve ß 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.

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

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.

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

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.

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

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.