SPART: A versatile and standardized data exchange format for species partition information

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the “inferred species”. The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.     

Biodiesel production from seed oil of Cleome viscosa L

Edible oil seed crops, such as rapeseed, sunflower, soyabean and safflower and non-edible seed oil plantation crops Jatropha and Pongamia have proved to be internationally viable commercial sources of vegetable oils for biodiesel production. Considering the paucity of edible oils and unsustainability of arable land under perennial plantation of Jatropha and Pongamia in countries such as India, the prospects of seed oil producing Cleome viscosa, an annual wild short duration plant species of the Indogangetic plains, were evaluated for it to serve as a resource for biodiesel. The seeds of C. viscosa resourced from its natural populations growing in Rajasthan, Haryana and Delhi areas of Aravali range were solvent extracted to obtain the seed oil. The oil was observed to be similar in fatty acid composition to the non-edible oils of rubber, Jatropha and Pongamia plantation crops and soybean, sunflower, safflower, linseed and rapeseed edible oil plants in richness of unsaturated fatty acids. The Cleome oil shared the properties of viscosity, density, saponification and calorific values with the Jatropha and Pongamia oils, except that it was comparatively acidic. The C. viscosa biodiesel had the properties of standard biodiesel specified by ASTM and Indian Standard Bureau, except that it had low oxidation stability. It proved to be similar to Jatropha biodiesel except in cloud point, pour point, cold filter plugging point and oxidation stability. In view of the annual habit of species and biodiesel quality, it can be concluded that C. viscosa has prospects to be developed into a short-duration biodiesel crop.     

Lupeol prevents acetaminophen-induced in vivo hepatotoxicity by altering the Bax/Bcl-2 and oxidative stress-mediated mitochondrial signaling cascade

AimsLupeol, a triterpene, possesses numerous pharmacological activities, including anti-malarial, anti-arthritic and anti-carcinogenic properties. The present study was conducted to explore the hepatoprotective potential of lupeol against acetaminophen (AAP)-induced hepatotoxicity in Wistar rats.Main methodsRats were given a prophylactic treatment of lupeol (150 mg/kg body weight, p.o., for 30 consecutive days) with a co-administration of AAP (1 g/kg body weight). The modulatory effects of lupeol on AAP-induced hepatotoxicity were investigated by assaying oxidative stress biomarkers, serum liver toxicity markers, pro/anti apoptotic proteins, DNA fragmentation and by the histopathological examination of the liver.Key findingsLupeol significantly prevented hepatic damage as evident from the histopathological studies and significant decline in serum trans-aminases. The alterations in cellular redox status (p < 0.01) and antioxidant enzyme activities together with the enhanced lipid peroxidation and protein carbonyl levels were also observed in the AAP-treated rats. In addition, significant ROS generation and mitochondrial depolarization were observed in this group. Co-administration of lupeol significantly decreased the level of serum transaminases, MDA and protein carbonyl content. It also prevented ROS generation and mitochondrial depolarization. Furthermore, lupeol enhanced the mitochondrial antioxidant and redox status and inhibited DNA damage and cell death by preventing the downregulation of Bcl-2, upregulation of Bax, release of cytochrome c and the activation of caspase 9/3.SignificanceThe conclusion of this study is that lupeol when co-administered with AAP effectively reduces oxidative stress and prevents AAP-induced hepatotoxicity by inhibiting critical control points of apoptosis.     

Sesamol alleviates diet-induced cardiometabolic syndrome in rats via up-regulating PPARγ, PPARα and e-NOS

Increased oxidative stress and inflammation in obesity are the central and causal components in the pathogenesis and progression of cardiometabolic syndrome (CMetS). The aim of the study was to determine the potential role of sesamol (a natural powerful antioxidant and anti-inflammatory phenol derivative of sesame oil) in chronic high-cholesterol/high-fat diet (HFD)–induced CMetS in rats and to explore the molecular mechanism driving this activity. Rats were fed with HFD (55% calorie from fat and 2% cholesterol) for 60 days to induce obesity, dyslipidemia, insulin resistance (IR), hepatic steatosis and hypertension. On the 30th day, rats with total cholesterol >150 mg/dl were considered hypercholesterolemic and administered sesamol 2, 4 and 8 mg/kg per day for the next 30 days. Sesamol treatment decreased IR, hyperinsulinemia, hyperglycemia, dyslipidemia, TNF-α, IL-6, leptin, resistin, highly sensitive C-reactive protein (hs-CRP), hepatic transaminases and alkaline phosphatase, along with normalization of adiponectin, nitric oxide and arterial pressures in a dose-dependent fashion. Increased TBARS, nitrotyrosine and decreased antioxidant enzyme activities were also amended in HFD rats. Similarly, sesamol normalized hepatic steatosis and ultrastructural pathological alteration in hepatocytes, although the effect was more pronounced at 8 mg/kg. Furthermore, hepatic PPARγ, PPARα and e-NOS protein expressions were increased, whereas LXRα, SERBP-1c, P-JNK and NF-κB expression were decreased by sesamol treatment. These results suggest that sesamol attenuates oxidative stress, inflammation, IR, hepatic steatosis and hypertension in HFD-fed rats via modulating PPARγ, NF-κB, P-JNK, PPARα, LXRα, SREBP-1c and e-NOS protein expressions, thereby preventing CMetS. Thus, the present study demonstrates the therapeutic potential of sesamol in alleviating CMetS.     

Intraoperative squash cytology: accuracy and impact on immediate surgical management of central nervous system tumours

N. Krishnani, N. Kumari, S. Behari, C. Rana and P. Gupta
Intraoperative squash cytology: diagnostic accuracy and its impact on immediate surgical management of central nervous system tumours Objective: To assess the diagnostic accuracy of squash cytology, reasons for deferment, disagreement and partial agreement, and assess its impact on immediate surgical management of central nervous system tumours. Study design: All cases of squash cytology received from January 2007 to July 2010 were reviewed and correlated with final histopathological diagnoses. Deferments, disagreements and partial disagreements were reviewed to look for possible reasons. The impact of disagreements and partial agreements on immediate surgical management was evaluated in consultation with neurosurgeons. Results: Overall accuracy (including complete and partial agreement) for squash smear diagnosis of 334 cases was 94.9% while complete agreement was 79.9%, excluding deferred cases. Disagreement was seen in 17 cases and 31 cases were deferred for final histopathology diagnosis. Good correlation was seen in astrocytoma, meningioma, schwannoma, medulloblastoma, pituitary adenoma and metastatic carcinoma, whereas poor correlation was seen in oligodendroglioma, ependymoma and lymphoma. Among 17 cases with disagreement and 50 cases with partial agreement, an adverse impact on immediate surgical management was found in six (35.3%) cases and one (2.0%) case, respectively. The sensitivity and specificity of squash for diagnosis of neoplastic lesions were 98.7% and 87.5%, respectively. Conclusion: Squash cytology is a rapid, reliable, simple technique for intraoperative consultation in neurosurgical practice with high overall accuracy. Causes causing an adverse impact on surgical management were rare and potential avoidable reasons for them were identified.     

Chlorpyrifos bioremediation in <Emphasis Type="Italic">Pennisetum</Emphasis> rhizosphere by a novel potential degrader <Emphasis Type="Italic">Stenotrophomonas maltophilia</Emphasis> MHF ENV20

Rhizoremediation is a specific type of phytoremediation involving both plants and their rhizosphere associated microbes. In the present study Pennisetum pedicellatum and rhizosphere associated degrading strains were evaluated for chlorpyrifos remediation. Time-course pot experiments were conducted in greenhouse with P. pedicellatum grown in soil amended with chlorpyrifos at the concentrations of 10, 25, 50, 75 and 100 mg/kg for 60 days. The half life of chlorpyrifos varied from 19.25 to 13.02 days in planted treatments. Residual concentrations of chlorpyrifos were negatively correlated with abundance of degrading microorganisms in rhizosphere. The isolated species of Bacillus, Rhodococcus and Stenotrophomonas were evaluated for their degrading potential in mineral medium. A novel isolated strain of potential degrader Stenotrophomonas maltophilia named as MHF ENV20 showed better survival and degradation at high concentration of chlorpyrifos. Degradation of chlorpyrifos by strain MHF ENV20, 100, 50 and 33.3% degradation within the time period of 48 h (h), 72 and 120 h at 50,100 and 150 mg/kg concentrations, further the gene encoding the organophosphorous hydrolase (mpd) was amplified using PCR amplification strategy and predesigned primers. Our findings indicate that rhizosphere remediation is effective bioremediation technique to remove chlorpyrifos residues from soil. P. pedicellatum itself, in addition to the rhizosphere bacterial consortium, seemed to play an important role in reducing chlorpyrifos level in soil. High chlorpyrifos tolerance and rhizospheric degradation capability of P. pedicellatum, makes this plant suitable for decontamination and remediation of contaminated sites. The ability to survive at higher concentration of chlorpyrifos and enhanced degrading potential due to presence of mpd gene make S. maltophilia MHF ENV20 an ideal candidate for its application in chlorpyrifos remediation.     

Genomic and proteomic studies on the effects of the insect growth regulator diflubenzuron in the model beetle species Tribolium castaneum

Several benzoylphenyl urea-derived insecticides such as diflubenzuron (DFB, Dimilin) are in wide use to control various insect pests. Although this class of compounds is known to disrupt molting and to affect chitin content, their precise mode of action is still not understood. To gain a broader insight into the mechanism underlying the insecticidal effects of benzoylphenyl urea compounds, we conducted a comprehensive study with the model beetle species and stored product pest Tribolium castaneum (red flour beetle) utilizing genomic and proteomic approaches. DFB was added to a wheat flour-based diet at various concentrations and fed to larvae and adults. We observed abortive molting, hatching defects and reduced chitin amounts in the larval cuticle, the peritrophic matrix and eggs. Electron microscopic examination of the larval cuticle revealed major structural changes and a loss of lamellate structure of the procuticle. We used a genomic tiling array for determining relative expression levels of about 11,000 genes predicted by the GLEAN algorithm. About 6% of all predicted genes were more than 2-fold up- or down-regulated in response to DFB treatment. Genes encoding enzymes involved in chitin metabolism were unexpectedly unaffected, but many genes encoding cuticle proteins were affected. In addition, several genes presumably involved in detoxification pathways were up-regulated. Comparative 2D gel electrophoresis of proteins extracted from the midgut revealed 388 protein spots, of which 7% were significantly affected in their levels by DFB treatment as determined by laser densitometry. Mass spectrometric identification revealed that UDP-N-acetylglucosamine pyrophosphorylase and glutathione synthetase were up-regulated. In summary, the red flour beetle turned out to be a good model organism for investigating the global effects of bioactive materials such as insect growth regulators and other insecticides. The results of this study recapitulate all of the different DFB-induced symptoms in a single model insect, which have been previously found in several different insect species, and further illustrate that DFB treatment causes a wide range of effects at the molecular level.     

Race Profiling and Molecular Diversity Analysis of Fusarium oxysporum f.sp. ciceris Causing Wilt in Chickpea

Seventy isolates of Fusarium oxysporum f.sp. ciceris (Foc) causing chickpea wilt representing 13 states and four crop cultivation zones of India were analysed for their virulence and genetic diversity. The isolates of the pathogen showed high variability in causing wilt incidence on a new set of differential cultivars of chickpea, namely C104, JG74, CPS1, BG212, WR315, KWR108, GPF2, DCP92‐3, Chaffa and JG62. New differential cultivars for each race were identified, and based on differential responses, the isolates were characterized into eight races of the pathogen. The same set of isolates was used for molecular characterization with four different molecular markers, namely random amplified polymorphic DNA, universal rice primers, simple sequence repeats and intersimple sequence repeats. All the four sets of markers gave 100% polymorphism. Unweighted paired group method with arithmetic average analysis grouped the isolates into eight categories at genetic similarities ranging from 37 to 40%. The molecular groups partially corresponded to the states of origin/chickpea‐growing region of the isolates as well as races of the pathogen characterized in this study. The majority of southern, northern and central Indian populations representing specific races of the pathogen were grouped separately into distinct clusters along with some other isolates, indicating the existence of variability in population predominated by a single race of the pathogen. The present race profiling for the Indian population of the pathogen and its distribution pattern is entirely new. The knowledge generated in this study could be utilized in resistance breeding programme. The existence of more than one race, predominated by a single one, in a chickpea cultivation zone as supported by the present molecular findings is also a new information.