Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny.

Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.

In silico analysis and expression profiling of Expansin A4, BURP domain protein RD22-like and E6-like genes associated with fiber quality in cotton.

BACKGROUND: To supply high-quality cotton fibre for the textile industry, the development of long, strong and fine fibre cotton varieties is imperative. An interlinked approach was used to comprehend the role of fibre genes by analyzing interspecific progenies of cotton species. Wild Gossypium species and races are rich source of genetic polymorphism due to environmental dispersal and continuous natural selection. These genetic resources hold mass of outclass genes that can be used in cotton improvement breeding programs to exploit possible traits such as fibre quality, abiotic stress tolerance, and disease and insect resistance. Therefore, use of new molecular techniques such as genomics, transcriptomics and bioinformatics is very important to utilize the genetic potential of wild species in cotton improvement programs. METHODS: Interspecific lines and Gossypium species used in the study were grown at Central Cotton Research Institute (CCRI), Multan. After retrieving DNA sequence of the genes from NCBI, the primers for gene expression and full-length gene sequence were designed. Expression profiling of Expansin A4, BURP Domain protein RD22-like and E6-like fibre genes was performed through Real Time PCR. BLAST and DNA sequence alignment was conducted for sequence comparison of interspecific lines and Gossypium species. Different in silico analysis were used for characterization of fibre genes and identification of cis acting promoter elements in promoter region. RESULTS: Variable expression of genes related to fibre development was observed at different stages. BLAST and DNA sequence alignment demonstrated resemblance of interspecific lines with G. hirsutum. In silico analysis on the sequence data also confirmed the role of Expansin A4, BURP Domain protein RD22-like and E6-like fibre genes in fibre development. Genetic engineering is also recommended by transferring E6-like, Expansin A4 and BURP Domain RD22-like genes in local cotton cultivars. Similarly, several stress tolerant and light responsive cis acting elements were identified through promotor analysis, which may contribute for fibre development in the breeding programs. CONCLUSION: Expansin A4, BURP Domain RD22-like and E6-like have positive role in fibre development with variable expression at fiber length and strength associated stages.

Using Multiplexed CRISPR/Cas9 for Suppression of Cotton Leaf Curl Virus.

In recent decades, Pakistan has suffered a decline in cotton production due to several factors, including insect pests, cotton leaf curl disease (CLCuD), and multiple abiotic stresses. CLCuD is a highly damaging plant disease that seriously limits cotton production in Pakistan. Recently, genome editing through CRISPR/Cas9 has revolutionized plant biology, especially to develop immunity in plants against viral diseases. Here we demonstrate multiplex CRISPR/Cas-mediated genome editing against CLCuD using transient transformation in N. benthamiana plants and cotton seedlings. The genomic sequences of cotton leaf curl viruses (CLCuVs) were obtained from NCBI and the guide RNA (gRNA) were designed to target three regions in the viral genome using CRISPR MultiTargeter. The gRNAs were cloned in pHSE401/pKSE401 containing Cas9 and confirmed through colony PCR, restriction analysis, and sequencing. Confirmed constructs were moved into Agrobacterium and subsequently used for transformation. Agroinfilteration in N. benthamiana revealed delayed symptoms (3-5 days) with improved resistance against CLCuD. In addition, viral titer was also low (20-40%) in infected plants co-infiltrated with Cas9-gRNA, compared to control plants (infected with virus only). Similar results were obtained in cotton seedlings. The results of transient expression in N. benthamiana and cotton seedlings demonstrate the potential of multiplex CRISPR/Cas to develop resistance against CLCuD. Five transgenic plants developed from three experiments showed resistance (60-70%) to CLCuV, out of which two were selected best during evaluation and screening. The technology will help breeding CLCuD-resistant cotton varieties for sustainable cotton production.

Resistance status of Helicoverpa armigera against Bt cotton in Pakistan.

Transgenic cotton expressing the toxin Cry1Ac from Bacillus thuringiensis L. (Bt) is widely cultivated in Pakistan after its formal approval in 2010. The exposure of the local target pests to the Cry1Ac endotoxin for this duration might have changed the baseline susceptibility. To probe the status of resistance in one of the main target pests, Helicoverpa armigera, field-collected larvae were reared in the lab for conducting leaf fed bioassays. Twenty-six cotton accessions collected from farmers, including 25 Bt-cotton and one non-Bt, were tested to quantify the level of Cry1Ac, an insecticidal crystalline protein (ICP), in leaves of lower, middle and upper canopies of plants. The concentration of ICP was tested through Enzyme-linked Immunosorbent Assay and found significantly variable (P < 0.01) between and within accessions. The highest mean expression was observed in Accession-2 and Accession-4, while the lowest in Accession-21 and Accession-19. Among fresh leaf tissues from different parts of the plant, the highest mean expression was recorded at 60 days after sowing in upper canopy leaves of cotton accessions, which decreased in lower parts of the plant with the lowest mean expression in lower canopy leaves. Laboratory bioassays, to calculate lethal dose, for H. armigera showed that LD50 and LD95 were 0.62 µg/g and 1.59 µg/g of fresh tissue weight, respectively. A strong positive correlation also exists between the levels of Cry1Ac protein and insect mortality (r = 0.84). These findings suggested the future risk of cultivation of Bt cotton, carrying single Cry1Ac gene, in Pakistan, as resistance surging in H. armigera against Cry protein. These results may also have significant implications for the resistance management in Bt crops, especially cotton, in future.

Modulation of agronomic and nutritional response of Pleurotus eryngii strains by utilizing glycine betaine enriched cotton waste.

BACKGROUND: This study aimed to evaluate the possibility of cotton waste enrichment with glycine betaine (GB) for production of two strains (P9, P10) of king oyster (Pleurotus eryngii). Cotton waste was used as (100%) control (T0 = cotton waste) and augmented with various combinations of GB, (T1 = 2 mmol L-1 , T2 = 4 mmol L-1 , T3 = 6 mmol L-1 , T4 = 8 mmol L-1 and T5 = 10 mmol L-1 ). The response of king oyster to GB was evaluated by earliness, yield, biological efficiency (BE), minerals (nitrogen, phosphorus, potassium, zinc (Zn), copper (Cu), magnesium (Mg), manganese (Mn), iron (Fe), sodium (Na), calcium (Ca)), total sugars, total soluble solids, reducing sugars, non-reducing sugars, ascorbic acid, proximate (crude protein, carbohydrates, crude fibers, ash, fats) content of fruiting body and Fourier-transform infrared (FTIR) spectroscopy analysis compared with the control substrate (cotton waste). RESULTS: The earliness, yield, and BE were higher as compared to control substrate and increased with an augmentation in the concentration of GB within the cotton waste. Two strains showed (on dry weight basis) 33.9-54.9 mg g-1 nitrogen, 6.8-12.5 mg g-1 phosphorus, 16.9-25.1 mg g-1 potassium, 40.5-64.2 mg kg-1 Zn, 17.1-37.3 mg kg-1 Cu, 1174-1325 mg kg-1 Mg, 20.1-29.1 mg kg-1 Mn, 129-265 mg kg-1 Fe, 779-835 mg kg-1 Ca), 6.3%-11.3% total sugars, 7.3-14.9 °Brix total soluble solids, 2.1-7.3% reducing sugars, 10.4-18.1% crude protein, 3.6-4.4% crude fiber and 5.6-16.7 mg (100 g)-1 on various concentration of GB enrich cotton waste. Cotton waste enriched with GB significantly affected nutritional profile of king oyster mushroom. CONCLUSION: The results revealed that GB enriched cotton waste can be used as an innovative substrate to enhance the yield and quality of king oyster mushroom. © 2019 Society of Chemical Industry.

Comparative analysis of resistance gene analogues encoding NBS-LRR domains in cotton.

BACKGROUND: Plant production is severely affected by biotic and abiotic stresses R-genes exhibit resistance against a range of diseases and pathogens in plants. The nucleotide binding site and leucine rich repeat (NBS-LRR) class of R-genes is the most comprehensively studied in terms of sequence evolution and genome distribution. The differential response for resistance against biotic and abiotic stress has been observed in cultivated and wild relatives of the genus Gossypium. RESULTS: Efforts have been made to address the recent evolution of NBS-LRR sequences within Gossypium hirsutum and resistance gene analogue (RGA) sequences derived from G. arboreum and G. raimondii. The % identity and phylogenetic analysis of NBS-LRR-encoded RGAs from tetraploid New World cotton and its diploid ancestors G. raimondii and G. arboreum suggest that the evolution of NBS-LRR-encoding sequences in G. hirsutum occurred by gradual accumulation of mutants that led to positive selection and a slow rate of divergence within distinct R-gene families. CONCLUSION: The allotetraploid genome of cotton, after separating from its diploid parents, experienced polyploidisation, natural and artificial selection, hybrid necrosis, duplication and recombination which became the reason to shed off and evolve new genes for its survival. These driving forces influenced the development of genomic architecture that make it susceptible to diseases and pathogens as compared to donor parents.

Molecular markers and cotton genetic improvement: current status and future prospects.

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.

TPD1-like Gene as a Suitable Marker for Early Sex Determination in Date Palm (Phoenix dactylifera L.).

Date palm (Phoenix dactylifera L.) is a considerably beneficial and economically profitable fruit crop. Female date palm plants produce fruit that is rich in fiber and sugar. Date palm is propagated by two means: suckers and seed. The propagation of date palm through seeds is very necessary for germplasm conservation and breeding. The late reproductive age (4-5 years) and dioecious nature of date palm make genetic improvement and breeding difficult. Early sex determination is the only way to improve breeding by selecting experimental male and female plants at the seedling stage. The primers for Tapetum Determinant 1 (TPD1-like) were designed using Amplify software. The DNA amplification of selected date palm suckers of three genotypes (Ajwa, Amber, and Medjool) was observed through PCR. Expression profiling of selected genotypes was carried out through semi-q PCR and RT-PCR by using the cDNA of suckers and unknown seedlings. Different in silico analyses were performed for the gene and protein characterization and identification of cis-acting elements in the promoter region. The promoter was identified along with the protein's properties and functionality. The expression of TPD1-like gene was found in the leaves of three selected genotypes of male sucker and in some plants of selected unknown seedlings that are considered male plants, and no expression was observed in female suckers and unknown seedlings that are considered female plants. The findings suggested that the TPD1-like gene has the potential for sex differentiation at the seedling stage, as the TPD1-like gene is essential to the specialization of tapetal cells and plays a critical role in plant reproduction.

Pharmacological activities of Artemisia absinthium and control of hepatic cancer by expression regulation of TGFß1 and MYC genes.

Plant derived compounds have always been an important source of medicines and have received significant attention in recent years due to their diverse pharmacological properties. Millions of plant-based herbal or traditional medicines are used to cure various types of cancers especially due to activation of proliferative genes. The aim of the present study was to characterize the altered and attenuated gene expression of the selected growth factor namely Transforming growth factor Beta -1 (TGFß1) and MYC in human hepatoma-derived (Huh7) liver cancer cell lines in response to extracts of Artemisia absinthium dissolved in selected organic solvents. Ethanolic, methanolic and acetone extract of different plant parts (leaf, stem and flowers) was used to access the antiproliferative activity by MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assay. Quantitative Real-Time RT-PCR revealed that the transcript levels of TGFß1 are induced in the samples treated with methanolic extract of Artemisia absinthium. Furthermore, reduced expression levels of MYC gene was noticed in cancerous cells suggesting antiproliferative properties of the plant. This study further highlights the resistance profile of various microbes by antimicrobial susceptibility test with plant extracts. In addition, antidiabetic effect of Artemisia absinthium have also shown positive results. Our study elucidates the potentials of Artemisia absinthium as a medicinal plant, and highlights the differential expression of genes involved in its mitogenic and anti-proliferative activity with a brief account of its pharmacological action.

Characterization, antioxidant activity, and mineral profiling of Auricularia cornea mushroom strains.

Background: Mushrooms are considered as next-generation healthy food components. Owing to their low-fat content, high-quality proteins, dietary fiber, and rich source of nutraceuticals. They are ideally preferred in formulation of low-caloric functional foods. In this view, the breeding strategies of mushroom Auricularia cornea (A. cornea) focusing on high yield and higher quality with rich nutritional values and health benefits are still needed. Materials and methods: A total of 50 strains of A. cornea were used to analyze the bio efficiency and the time required for fruiting body formation following the cultivation experiment. The calorimetric method was used to evaluate the antioxidant activity and quantify the crude polysaccharides and minerals content thereafter. Results: The results showed that the time required for fruiting body formation and biological efficiency varied significantly among the selected strains. Noticeably, the wild domesticated strain Ac13 of A. cornea mushroom showed the shortest fruit development time (80 days). Similarly, the hybrid strains including Ac3 and Ac15 possessed the highest biological efficiency (82.40 and 94.84%). Hybrid strains Ac18 (15.2%) and cultivated strains Ac33 (15.6%) showed the highest content of crude polysaccharides, while cultivated strains Ac1 and Ac33, demonstrated the highest content of total polysaccharides in the fruiting body (216 mg. g-1 and 200 mg. g-1). In the case of mineral content, the highest zinc contents were observed from the cultivated strain Ac46 (486.33 mg·kg-1). The maximum iron content was detected from the hybrid strain Ac3 (788 mg·kg-1), and the wild domesticated strain Ac28 (350 mg·kg-1). The crude polysaccharides of the A. cornea strain showed significant antioxidant potential, and the ability of Ac33 and Ac24 to scavenge DPPH radicals and ABTS, which was significantly improved compared to other strains, respectively. Principal component analysis was applied to examine the agronomic traits and chemical compounds of various strains of A. cornea mushrooms. The results revealed that cultivated, wild domesticated, and hybrid strains of A. cornea exhibited distinct characteristics in terms of growth, yield, and nutritional properties. Conclusion: The crude polysaccharides from A. cornea mushroom strains act as natural antioxidants, the wild, hybrid, and commercial A. cornea mushroom strains can achieve rapid growth, early maturation, and high yields. The evaluation of biochemical indexes and nutritional characteristics of strains with excellent traits provided a scientific basis for initiating high-quality breeding, provided germplasm resources for the production of "functional food" with real nutritional and health value.

Discovery of rare mutations in populations: TILLING by sequencing.

Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.

In-situ stabilization of potentially toxic elements in two industrial polluted soils ameliorated with rock phosphate-modified biochars.

The present study was aimed at determining the efficacy of rock phosphate (RP) 3% loaded in a green coconut shell, chicken manure, and vegetable waste to make green coconut-modified biochar (GMB), chicken manure modified-biochar (CMB), and vegetable waste-modified biochar (VMB) in the fixation of Cr, Pb, Cu, Zn, Ni, and Cd in Sharafi goth and Malir polluted soils. The impact of RP impregnated with organic waste material to produce modified biochars (MBs) on stabilizing PTEs from polluted soils and reducing their uptake by mustard plant has not yet been thoroughly investigated. All modified BCs in 0.5, 1, and 2% doses were used to stabilize Cr, Pb, Cu, Zn, Ni, and Cd in two polluted soils and to reduce their uptake by the mustard plant. The obtained results revealed that the maximum mustard fresh biomass was 17.8% higher with GMB 1% in Sharafi goth polluted soil and 25% higher with VMB 0.5% in Malir polluted soil than in the control treatment. After applying modified BCs, immobilization of Cr, Pb, Cu, Ni, and Cd was observed in both soils and it reduced the uptake of these elements by mustard plants. On the other hand, although Zn mobilization increased by 0.38% for CMB 0.5% and by 5.9% for VMB 0.5% in Sharafi goth polluted soil, as well as by 3.15% for GMB 1%, 6.34% for GMB 2%, and 4.78% for VMB 0.5% in Malir polluted soil, this was due to changes in soil pH and OM. It was found that GMB 1%, CMB 0.5%, and VMB 0.5% have the potential to increase Zn uptake by mustard, while VMB 2% can reduce the element uptake by the plant. Redundancy analysis showed that soil chemical parameters were negatively correlated with PTEs in both soils and reduced their uptake by mustard. The present study revealed that MBs can stabilize PTEs in industrial and wastewater soils polluted with multiple metals and reduce their uptake by plants.

Double flap patch closure of VSD with elevated pulmonary vascular resistance: an experience at AFIC/NIHD.

OBJECTIVE: To determine the 30 days outcome measured in terms of morbidity and mortality in cases of ventricular septal defect (VSD) with increased pulmonary vascular resistance (PVR) managed with double flap patch closure. STUDY DESIGN: Case series. PLACE AND DURATION OF STUDY: Armed Forces Institute of Cardiology (AFIC/NIHD), Rawalpindi, from December 2005 to December 2008. METHODOLOGY: Forty patients with VSD having PVR 9.58 + 4.33 wood units underwent double flap patch closure. The patch was fenestrated as one half of the expected aortic annulus diameter. A separate flap patch 5 mm larger than fenestration was attached to superior upper one third margins of fenestration. The patch was placed with flap to open towards the left ventricular apex. Modified ultra filtration (MUF) was employed in every case and sildenafil was given postoperatively. RESULTS: The age of patients ranged from 1 to 28 years with a mean of 6.66 + 5.70 years. There were 22 males and 18 females. All patients were weaned off from inotropic and ventilatory support as earlier as possible postoperatively with intensive care unit (ICU) stay of 77.15 + 54.56 hours. Postoperative pulmonary artery pressures were reduced to 42.63 + 10.86 mmHg as compared to pre-operative pulmonary artery pressures of 88.3 + 15.2 mmHg. Postoperatively 11 patients with suprasystemic pulmonary artery pressures and desaturation went into pulmonary hypertensive crisis in which immediate 2D echo evidenced the functioning flap valve with right to left shunt. There was only one death (early) out of 40 patients with an overall mortality of 2.5% along with limited morbidity. CONCLUSION: Double flap patch is an inexpensive, easy to construct technique with low morbidity and mortality in cases of VSD with raised PVR.

Comparative Profiling of Button Mushroom, Agaricus bisporus (Agaricomycetes), Possessing Textural, Antibacterial, Elemental, and Antioxidant Properties in Diverse Collections from China.

Button mushroom (Agaricus bisporus) is cultured commercially and consumed worldwide for its unique flavor, texture, and culinary qualities. The objective of this study was to assess the textural profile together with the phenolic content and antioxidant, antibacterial, and elemental composition of wild and commercially cultivated A. bisporus from China. Of the six mushroom strains studied, both cultivated strains CCMJ1013 (fresh: 85.8 N/m2; stored: 57.9 N/m2) and CCMJ1343 (fresh: 94.7 N/m2; stored: 52.9 N/m2) recorded elevated hardness. Our results revealed that wild A. bisporus strain CCMJ1363 contained the highest phenolic content (7.840 mg gallic acid equivalents [GAE]/g), followed by CCMJ1361 (7.125 mg GAE/g) and CCMJ1351 (6.709 mg GAE/g). Antioxidant activity was elevated in CCMJ1351 (inhibition concentration at 50% inhibition [IC50] = 1.04 mg/mL) followed by CCMJ1361 (IC50 = 1.67 mg/mL) in the 1,1-diphenyl-2-picrylhydrazyl assay, whereas CCMJ1351 showed the maximum antioxidant activity (353.54 mg Trolox equivalents/g) in the ferric reducing antioxidant power assay. The maximum 2,2'-azobis(2-amidinopropane) di-hydrochloride-induced erythrocyte hemolysis inhibition was found in wild A. bisporus CCMJ1363 (86.09% inhibition) followed by CCMJ1351 (84.45% inhibition). In terms of antibacterial activity, only a wild A. bisporus strain (CCMJ1361) showed antibacterial activity against pathogenic bacteria (Bacillus coli and Staphylococcus aureus). Wild strain CCMJ1110 contained the highest level of zinc and magnesium; CCMJ1361 showed higher levels of calcium and iron, and CCMJ1363 contained a comparatively higher composition of nitrogen, sodium, and aluminum. Therefore, the current study lays a foundation for creating high-performance, culinary-quality, and stress-resistant germplasms in breeding for A. bisporus strains.

Fabrication of a lead ion selective membrane based on a polycarbazole Sn(iv) arsenotungstate nanocomposite and its ion exchange membrane (IEM) kinetic studies.

A polycarbazole-Sn(iv) arsenotungstate (Pcz-SnAT) nanocomposite cation exchanger membrane (CEM) was prepared via the casting solution technique utilizing polycarbazole-Sn(iv) arsenotungstate and PVC (polyvinyl chloride) as a binder. The synthesis of the Pcz-SnAT membrane was confirmed via various characterization methods such as EDX, SEM, TGA, XRD, and FTIR spectroscopy. This membrane having a 4.5 : 1 composition ratio of composite by PVC exhibited the most effective outcomes for swelling, thickness, porosity, and water content. Our research indicates that the present ion selective membrane electrode is selective towards Pb(ii) ions, with the detection limit ranging from 1 × 10-7 mol L-1 to 1 × 10-1 mol L-1 where 20 s is the response time and 3-7 is the working value pH. The mechanism of the Pcz SnAT ion exchange membrane was obtained by kinetic studies by utilizing the equation given by Nernst Planck at 40-80 °C. As a result, activation energy and thermodynamic studies were done. The analytical utility of this electrode is conventional by utilizing it as an electrode indicator within the potentiometric titration.

Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map.

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

Novel mutant camelina and jatropha as valuable feedstocks for biodiesel production.

Novel mutant camelina has become a crop of interest inspired by its short growing season, low harvesting costs and high oil composition. Despite those advantages, limited research has been done on novel mutant lines to determine applicability for biodiesel production. Jatropha is an extremely hardy, frugal and high oil yielding plant species. The major aim of the present study was not only to compare biodiesel production from jatropha and camelina but was also to test the efficacy of camelina mutant lines (M6 progenies) as superior feedstock. The biodiesel yield from camelina oil and jatropha oil was 96% and 92%, respectively. The gas chromatographic analysis using flame ionization detector (GC-FID) showed that mutant camelina oil biodiesel sample contain major amount of oleic acid (46.54 wt%) followed by linolenic acid (20.41 wt%) and linoleic acid (16.55 wt%). Jatropha biodiesel found to contain major amount of oleic acid (45.03 wt%) followed by linoleic acid (25.07 wt%) and palmitic acid (19.31 wt%). The fuel properties of produced biodiesel were found in good agreement with EN14214 and ASTM D6751 standards. The mutant camelina lines biodiesel have shown comparatively better fuel properties than jatropha. It has shown low saponification value (120.87-149.35), high iodine value (130.2-157.9) and better cetane number (48.53-59.35) compared to jatropha biodiesel which have high saponification value (177.39-198.9), low iodine value (109.7-123.1) and lesser cetane number (47.76-51.26). The results of the present student of utilizing novel mutant camelina lines for biodiesel production are quite promising and are helpful in turning out the outcomes of the previous studies suggesting that C. sativa biodiesel presents serious drawbacks for biodiesel applications.

Coronary endarterectomy for severe diffuse coronary artery disease.

OBJECTIVE: To determine the outcome of Coronary Endarterectomy (CE) in patients undergoing Coronary Artery Bypass Graft (CABG) surgery for diffuse Coronary Artery Disease (CAD), in terms of postoperative mortality and morbidity, relief from angina and survival at one year. STUDY DESIGN: A case series. PLACE AND DURATION OF STUDY: Department of Cardiac Surgery, Armed Forces Institute of Cardiology and National Institute of Heart Diseases, Rawalpindi, from January 2003 to November 2005. METHODOLOGY: Included in the study were all patients with such diffuse CAD that conventional bypass grafting was not possible. Those with the diseased coronary artery supplying an akinetic myocardium and a fixed perfusion defect on perfusion scan, or with poor left ventricular function (ejection fraction<30%) in association with severe chronic hepatic disease and deranged liver function tests, permanent severe immune deficiency state, or poor results at lung function tests were excluded. Cardiopulmonary Bypass (CPB) was used in all patients. All patients were followed up for a mean time of one year, for assessment of postoperative mortality and morbidity, relief from angina and survival. RESULTS: Fifty five patients (3.2%) underwent CE of at least one major coronary artery for severe diffuse atheromatous disease. The mean age was 53.9+/-9.5 years. Twenty six (47.3%) had previous Myocardial Infarction (MI), 16 (29.1%) had unstable angina, 12 (21.8%) had poor Left Ventricular (LV) function, 5 (9.1%) underwent emergency CABG surgery for impending infarction, 39 (70.9%) had angina Canadian Cardiovascular Society (CCS) class II/III, 11 (20%) had critical left main stem disease and 12 (21.8%) required Intra-Aortic Balloon Pump (IABP) for hemodynamic support. There were 2 (3.6%) early deaths and 2 (3.6%) cases of non-fatal infarctions. Three (5.4%) patients had low Cardiac Output (CO) after operation. At one year follow-up, there were no late deaths and 43 patients (91.5% of those reporting for follow-up) did not have angina. CONCLUSION: CE acted as an adjunct to CABG surgery with acceptable operative risks and satisfactory results at one year in terms of mortality and angina relief.

Haemodynamic response to induction, laryngoscopy and tracheal intubation in diabetic and non-diabetic patients.

OBJECTIVE: Presence of autonomic neuropathy in diabetic patients can alter the haemodynamic response to induction and tracheal intubation. This trial was conducted to compare this response in 30 non-diabetic (control group) and 30 diabetic patients including both insulin and non-insulin dependent. METHODS: A prospective, age matched case controlled study was conducted at the Aga Khan University Hospital, for one year. After pre-medication with tablet midazolam 7.5 mgs orally, patients received pethidine 0.8 mg kg(-1), thiopentone sodium 4 to 5 mg kg(-1) for induction and vecuronium 0.1 mg kg(-1) to facilitate tracheal intubation. Following manual ventilation with isoflurane 0.8% in oxygen 33% and nitrous oxide 66%, laryngoscopy and tracheal intubation was performed. Blood pressure (systolic, diastolic and mean) and heart rate responses were measured for 10 minutes. RESULTS: The systolic arterial pressure dropped by 9% after induction and rose by 16% after intubation in nondiabetics compared to 12% drop after induction and a rise of 10% after intubation in diabetics. No difference was seen in diastolic blood pressure which increased by 27% in ND compared to 22% in DB groups. The heart rate rose by 27% in non-diabetics compared to 17% in diabetics after intubation. CONCLUSION: The systolic, diastolic and mean blood pressure response was similar in the two groups. A greater fall in SAP was observed post intubation in the DB group. A significant difference was observed in the heart rate response which was less in the diabetic group.

Placing epicardial pacing wires in isolated coronary artery bypass graft surgery--a procedure routinely done but rarely beneficial.

BACKGROUND: After Coronary Artery Bypass Graft (CABG) surgery, temporary epicardial pacing wires are placed on heart to meet unforeseen complications like bradyarrhythmias or asystoles. This step needs additional time, resources and has potential to cause complication. Even having less complications, is this additional step in elective CABG surgery necessary? Some important predictive factors in patients who require this pacing wire placement have to be isolated. The objective of the study was to avoid this step if not required especially in elective CABG surgery. METHODS: This prospective observational study involved 1047 consecutive patients undergoing CABG at our institution from May 2006 to April 2008. Patient who did not receive pacing wire (230), Preoperative pacemaker (2), CABG with valvular surgery (10), CABG with Ischemic VSD or MR surgery (3), off-pump CABG (21), or incomplete follow-up (11) were excluded from the study. Patients who received pacing wire (770) were divided in two groups. Group A, consisted of patients who did not require pacing postoperatively 748 (97.1%), and Group B, who required pacing postoperatively 22 (2.9%). Both groups were compared in demographic, preoperative, per-operative and postoperative variables. The incidence of pacing during the postoperative period was recorded. Predictors for postoperative pacing were determined using medical records and the AFIC/NIHD cardiac surgery database. RESULTS: In the postoperative period, 22 of 770 patients (2.9%) required pacing. Analysis identified age (p = 0.02), preoperative arrhythmia, especially Bundle Branch Block (p = 0.000), pacing utilized at separation from bypass (p = 0.000) and use of antiarrhythmics on leaving the operating room (p = 0.015) as predictors of the need for postoperative pacing. Diabetes, considered one of the major factor requiring pacing was not significant in our study (p = 0.379). Preoperative arrhythmias, pacing utilized to separate from bypass and use of antiarrhythmics on leaving the operating room were found to be three most significant risk factors. If the patients with any of these three risk factors are excluded, only 1.11% (8/716) of them would have required pacing. CONCLUSIONS: Procedure of routine use of temporary epicardial pacing after elective CABG surgery has negligible role, rather has additional cost and potential of rare complications. Diabetes is not a risk factor for post operative pacing.