TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery

Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general. An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. We proposed an objective protocol for target prioritisation using TargetMine and set up a benchmarking procedure to evaluate its performance. The results show that the protocol can identify known disease-associated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine.nibio.go.jp/.     

RLIP76, a glutathione-conjugate transporter, plays a major role in the pathogenesis of metabolic syndrome

Purpose

Characteristic hypoglycemia, hypotriglyceridemia, hypocholesterolemia, lower body mass, and fat as well as pronounced insulin-sensitivity of RLIP76^−/− mice suggested to us the possibility that elevation of RLIP76 in response to stress could itself elicit metabolic syndrome (MSy). Indeed, if it were required for MSy, drugs used to treat MSy should have no effect on RLIP76^−/− mice.

Research Design and Methods

Blood glucose (BG) and lipid measurements were performed in RLIP76^+/+ and RLIP76^−/− mice, using Ascensia Elite Glucometer® for glucose and ID Labs kits for cholesterol and triglycerides assays. The ultimate effectors of gluconeogenesis are the three enzymes: PEPCK, F-1,6-BPase, and G6Pase, and their expression is regulated by PPARγ and AMPK. The activity of these enzymes was tested by protocols standardized by us. Expressions of RLIP76, PPARα, PPARγ, HMGCR, pJNK, pAkt, and AMPK were performed by Western-blot and tissue staining.

Results

The concomitant activation of AMPK and PPARγ by inhibiting transport activity of RLIP76, despite inhibited activity of key glucocorticoid-regulated hepatic gluconeogenic enzymes like PEPCK, G6Pase and F-1,6-BP in RLIP76^−/− mice, is a salient finding of our studies. The decrease in RLIP76 protein expression by rosiglitazone and metformin is associated with an up-regulation of PPARγ and AMPK.

Conclusions/Significance

All four drugs, rosiglitazone, metformin, gemfibrozil and atorvastatin failed to affect glucose and lipid metabolism in RLIP76^−/− mice. Studies confirmed a model in which RLIP76 plays a central role in the pathogenesis of MSy and RLIP76 loss causes profound and global alterations of MSy signaling functions. RLIP76 is a novel target for single-molecule therapeutics for metabolic syndrome.     

Modulation of antioxidant enzyme activities, platelet aggregation and serum prostaglandins in rats fed spray-dried milk containing n-3 fatty acid

Spray-dried milk enriched with n-3 fatty acids from linseed oil (LSO) or fish oil (FO) were fed to rats to study its influence on liver lipid peroxides, hepatic antioxidant enzyme activities, serum prostaglandins and platelet aggregation. Significant level of α linolenic acid, eicosapentaenoic acid and docosahexaenoic acid were accumulated at the expense of arachidonic acid in the liver of rats fed n-3 fatty acid enriched formulation. The linseed oil and fish oil enriched formulation fed group had 44 and 112% higher level of lipid peroxides in liver homogenate compared to control rats fed groundnut oil enriched formulation. Catalase activity in liver homogenate was increased by 37 and 183% respectively in linseed oil and fish oil formulation fed rats. The glutathione peroxidase activity decreased to an extent of 25–36% and glutathione transferase activity increased to an extent of 34–39% in rats fed n-3 fatty acids enriched formulation. Feeding n-3 fatty acid enriched formulation significantly elevated the n-3 fatty acids in platelets and increased the lipid peroxide level to an extent of 4.2 to 4.5-fold compared to control. The serum thromboxane B₂ level was decreased by 35 and 42% respectively in linseed oil and fish oil enriched formulation fed rats, whereas 6-keto-prostaglandin F1α level was decreased by 17 and 23% respectively in linseed oil and fish oil enriched formulation fed rats. The extent and rate of platelet aggregation was decreased significantly in n-3 fatty acids enriched formulation fed rats. This indicated that n-3 fatty acids enriched formulation beneficially reduces platelet aggregation and also enhances the activities of hepatic antioxidant enzymes such as catalase and glutathione transferase.     

Plant water status,H<Subscript>2</Subscript>O<Subscript>2</Subscript> scavenging enzymes,ethylene evolution and membrane integrity of <Emphasis Type="Italic">Cicer arietinum</Emphasis> roots as affected by salinity

The chickpea genotype, CSG-8962 was raised in screenhouse to study salinity induced changes in ethylene evolution, antioxidative defence system and membrane integrity in relation to changes in plant water and mineral content. At vegetative stage (60 d after sowing), the plants were exposed to single saline irrigation (0, 2.5, 5.0 and 10.0 dS m^–1). Sampling was done 3 d after saline treatments. The other sets of treated plants were re-irrigated with water and sampled after further 3 d. The _w of leaf and _s of leaf and roots decreased from –0.47 to –0.61 MPa, –0.67 to –1.23 MPa and from –0.57 to –0.95 MPa, respectively, with increasing salinity. Similarly, RWC of leaf and roots reduced from 87.5 to 72.3 % and 96.7 to 84.35 %, respectively. The decline in s of roots was mainly due to accumulation of proline and total soluble sugar. With salinity, increase in ethylene evolution, 1-aminocyclopropane-1-carboxylic acid (ACC) content and ACC oxidase activity was reported. Similarly, marked increase in H₂O₂ content (20 – 182 %) and lipid peroxidation (43 – 170 %) was observed. The defense mechanism activated in roots was confirmed by the increased activities of superoxide dismutase (SOD), peroxidase (POX), ascorbate peroxidase (APX), glutathione transferase (GTase), glutathione reductase (GR) and catalase (CAT) but ascorbic acid (AA) content was decreased. About 3-fold increase in Na⁺/K⁺ ratio and 2.5 fold increase in Cl^– content was observed. Upon desalinization, a partial recovery was observed in most of the parameters studied.     

Biologically active novel conformational state of botulinum, the most poisonous poison

Botulinum neurotoxins (serotypes A-G), the most toxic substances known to humankind, cause flaccid muscle paralysis by blocking acetylcholine release at nerve-muscle junctions through a very specific and exclusive endopeptidase activity against SNARE proteins of presynaptic exocytosis machinery. We have examined polypeptide folding of the endopeptidase moiety of botulinum neurotoxin/A (the light chain) under conditions of its optimal enzymatic activity and have found that one of its stable conformational states is a molten-globule, which retains over 60% of its optimal enzyme activity. More importantly, we have discovered that the light chain acquires a novel pre-imminent molten-globule enzyme conformation at the physiologically relevant temperature, 37 degrees C. The pre-imminent molten-globule enzyme form also exhibited the maximum endopeptidase activity against its intracellular substrate, SNAP-25 (synaptosomal associated protein of 25 kDa). These findings will not only open new avenues to design effective diagnostics and antidotes against botulism but also provide new information on enzymatically active molten-globule or molten-globule like structures.     

Eugenol--the active principle from cloves inhibits 5-lipoxygenase activity and leukotriene-C4 in human PMNL cells

Polymorphonuclear leukocytes (PMNL) play an important role in the modulation of inflammatory conditions in humans. PMNL cells recruited at the site of inflammation, release inflammatory mediators such as leukotrienes, proteolytic enzymes and reactive oxygen species. Among these, leukotrienes are implicated in pathophysiology of allergic and inflammatory disorders like asthma, allergic rhinitis, arthritis, inflammatory bowel disease and psoriasis. 5-lipoxygenase (5-LO) is the key enzyme in biosynthetic pathway of leukotrienes. Our earlier studies showed that spice phenolic active principles significantly inhibit 5-LO enzyme in human PMNLs. In this study we have further characterized the inhibitory mechanism of eugenol, the active principle of spice-clove on 5-LO enzyme and also its effect on leukotriene C((4)) (LTC(4)). Substrate dependent enzyme kinetics showed that the inhibitory effect of eugenol on 5-LO was of a non-competitive nature. Further, eugenol was found to significantly inhibit the formation of LTC(4) in calcium ionophore A23187 and arachidonic acid (AA) stimulated PMNL cells. These data clearly suggest that eugenol inhibits 5-LO by non-competitive mechanism and also inhibits formation of LTC(4) in human PMNL cells and thus may have beneficial role in modulating 5-LO pathway in human PMNL cells.     

Water relations, activities of antioxidants, ethylene evolution and membrane integrity of pigeonpea roots as affected by soil moisture

The plants of pigeonpea (Cajanus cajan L.) cv. H77-216 were subjected to moderate [soil moisture content (SMC) = 7.3 ± 0.5 %] and severe (SMC = 4.3 ± 0.5 %) drought by withholding the irrigation at vegetative stage (45 d after sowing). The control plants were maintained at SMC of 11.0 ± 0.5 %. Half of the stressed plants were re-irrigated and their recovery was studied after 2 d. Leaf water potential, osmotic potential, and relative water content of leaf and root decreased significantly while a sharp rise in proline and total soluble sugars contents were noticed. Drought induced a significant increase in 1-aminocyclopropane 1-carboxylic acid (ACC) content and ACC oxidase activity which caused a considerable increase in ethylene evolution. Malondialdehyde content and relative stress injury were increased under drought whereas reverse was true for ascorbic acid content. The membrane integrity of roots decreased during stress and recovered on rehydration. The specific activity of total superoxide dismutase, ascorbate peroxidase, glutathione reductase, and glutathione transferase decreased to 37 – 78 %, 17 – 62 %, 29 – 36 % and 57 – 79 % at moderate and severe drought, respectively. The increase in activity of catalase and peroxidase could not overcome the accumulation of H₂O₂ content in the roots.     

Lipocalin 2 Regulates Inflammation during Pulmonary Mycobacterial Infections

Pulmonary tuberculosis (TB), caused by the intracellular bacteria Mycobacterium tuberculosis, is a worldwide disease that continues to kill more than 1.5 million people every year worldwide. The accumulation of lymphocytes mediates the formation of the tubercle granuloma in the lung and is crucial for host protection against M.tuberculosis infection. However, paradoxically the tubercle granuloma is also the basis for the immunopathology associated with the disease and very little is known about the regulatory mechanisms that constrain the inflammation associated with the granulomas. Lipocalin 2 (Lcn2) is a member of the lipocalin family of proteins and binds to bacterial siderophores thereby sequestering iron required for bacterial growth. Thus far, it is not known whether Lcn2 plays a role in the inflammatory response to mycobacterial pulmonary infections. In the present study, using models of acute and chronic mycobacterial pulmonary infections, we reveal a novel role for Lcn2 in constraining T cell lymphocytic accumulation and inflammation by inhibiting inflammatory chemokines, such as CXCL9. In contrast, Lcn2 promotes neutrophil recruitment during mycobacterial pulmonary infection, by inducing G-CSF and KC in alveolar macrophages. Importantly, despite a common role for Lcn2 in regulating chemokines during mycobacterial pulmonary infections, Lcn2 deficient mice are more susceptible to acute M.bovis BCG, but not low dose M.tuberculosis pulmonary infection.     

Type 2 diabetic obese db/db mice are refractory to myocardial ischaemic post-conditioning in vivo: potential role for Hsp20, F1-ATPase δ and Echs1

Ischaemic post-conditioning (PostC) is a clinically relevant cardioprotective modality that has been confirmed in many species including human. It remains unknown if PostC can still protect heart in Type 2 diabetes, a rapidly growing disease in the world. This study investigated the efficacy of PostC in the leptin receptor-deficient db/db mice, which possess Type 2 diabetic characteristics including obesity, hyperglycaemia and hyperleptinaemia. Adult male C57BL/6J wild-type (WT) and db/db mice were anaesthetized, mechanically ventilated and subjected to left coronary artery occlusion for 30 min. followed by 24 hrs of reperfusion. For the PostC groups, the hearts underwent six cycles of 10 sec. of reperfusion and 10 sec. of re-occlusion at the onset of reperfusion. The mice were sacrificed at the end of 24 hrs reperfusion for infarct size measurement. PostC significantly reduced infarct size in WT mice (n = 6/group; P < 0.05), but not in the db/db mice. To identify alterations in protein expression by PostC, proteomic analyses were performed in the heart samples using two-dimensional differential in-gel electrophoresis with three CyDye labelling, followed by mass spectrometry. The results show that mitochondrial proteins (F(1)-ATPase γ and Echs1) were down-regulated by PostC in WT heart. Such change was absent in the db/db heart. On the other hand, PostC reduced Hsp20 in the diabetic heart. In summary, PostC fails to protect Type 2 diabetic mice against ischaemia-reperfusion injury. The potential protein targets for the loss of PostC may include F(1)-ATPase γ, Echs1 and Hsp20 that could regulate cellular ATP consumption/production and defense response to ischaemic stress.     

Cerebrovascular Hemodynamics During the Practice of Bhramari Pranayama,Kapalbhati and Bahir-Kumbhaka: An Exploratory Study

Various pranayama techniques are known to produce different physiological effects. We evaluated the effect of three-different pranayama techniques on cerebrovascular hemodynamics. Eighteen healthy volunteers with the mean?±?standard deviation age of 23.78?±?2.96 years were performed three-different pranayama techniques: (1) Bhramari, (2) Kapalbhati and (3) Bahir-Kumbhaka in three-different orders. Continuous transcranial Doppler (TCD) monitoring was performed before, during and after the pranayama techniques. TCD parameters such as peak systolic velocity, end diastolic velocity (EDV), mean flow velocity (MFV) and pulsatility index (PI) of right middle cerebral artery were recorded. Practice of Kapalbhati showed significant reductions in EDV and MFV with significant increase in PI while, Bahir-Kumbhaka showed significant increase in EDV and MFV with significant reduction in PI. However, no such significant changes were observed in Bhramari pranayama. Various types of pranayama techniques produce different cerebrovascular hemodynamic changes in healthy volunteers.