A plant oxysterol, 28-homobrassinolide binds HMGCoA reductase catalytic cleft: stereoselective avidity affects enzyme function

Understanding the influence of ubiquitously present plant steroids on mammalian cell biology is currently of interest. Feedback inhibition of HMGCoA reductase (HMGCR) catalytic activity in the transformation of HMG-CoA to mevalonate is a significant regulatory step in sterol biosynthetic pathway. To assess the role of dietary steroids in this biochemical transformation, the phytosteroid isoform 28-homobrassinolide (28-HB), 90 % pure, obtained from Godrej Agrovet (India) was used to determine its effect on mammalian HMG-CoA reductase. Photometric assay of pure human and select rat tissue HMGCR post 28-HB oral feed, PCR-HMGCR gene expression, and in silico docking of 28-HB and HMGCoA on HMGCR protein template were carried out. Using an oral feed regimen of pure 28-HB, we noted a decrease of 16 % in liver, 17.1 % in kidney and 9.3 % in testicular HMGCR enzyme activity, 25 % in HMGCR gene expression and 44 % in the activity of pure human HMGCR due to this plant oxysterol. In silico docking studies yielded binding metrics for 28-HB-HMGCR lower than for HMGCoA-HMGCR, indicating stronger binding of HMGCR by this ligand. 28-HB exerts differential effects on rat tissue HMGCR, down regulates liver HMGCR gene expression and significantly inhibits HMGCR activity.     

Use of <Emphasis Type="Italic">Cupriavidus basilensis</Emphasis>-aided bioabatement to enhance fermentation of acid-pretreated biomass hydrolysates by <Emphasis Type="Italic">Clostridium beijerinckii</Emphasis>

Lignocellulose-derived microbial inhibitors (LDMICs) prevent efficient fermentation of Miscanthus giganteus (MG) hydrolysates to fuels and chemicals. To address this problem, we explored detoxification of pretreated MG biomass by Cupriavidus basilensis ATCC^®BAA-699 prior to enzymatic saccharification. We document three key findings from our test of this strategy to alleviate LDMIC-mediated toxicity on Clostridium beijerinckii NCIMB 8052 during fermentation of MG hydrolysates. First, we demonstrate that growth of C. basilensis is possible on furfural, 5-hydroxymethyfurfural, cinnamaldehyde, 4-hydroxybenzaldehyde, syringaldehyde, vanillin, and ferulic, p-coumaric, syringic and vanillic acid, as sole carbon sources. Second, we report that C. basilensis detoxified and metabolized ~98 % LDMICs present in dilute acid-pretreated MG hydrolysates. Last, this bioabatement resulted in significant payoffs during acetone-butanol-ethanol (ABE) fermentation by C. beijerinckii: 70, 50 and 73 % improvement in ABE concentration, yield and productivity, respectively. Together, our results show that biological detoxification of acid-pretreated MG hydrolysates prior to fermentation is feasible and beneficial.     

Exotic fish species in a global biodiversity hotspot: observations from River Chalakudy,part of Western Ghats,Kerala, India

We record here the occurrence of five exotic fish species viz Oreochromis mossambicus, Gambusia affinis, Osphronemus goramy, Xiphophorus maculatus and Poecilia reticulata in the Chalakudy River, part of the Western Ghats, a global biodiversity hotspot in Kerala, India. O. mossambicus was ubiquitous in occurrence with large shoals being encountered at all sampling sites spread along the downstream-upstream gradient of the river, including at an altitude of 1050 m ASL. Osphronemus goramy was recorded from the downstream region of the river while Gambusia affinis was recorded from three sampling sites located downstream as well as midstream. Xiphophorus maculatus was collected from a second order stream flowing through a tea plantation at an altitude of 1050 m ASL. Samples of brooders and early fry of Poecilia reticulata indicate that the fish has already established a breeding population in the river. Possible threats to the indigenous fish fauna of the Chalakudy River as a result of the invasion and proliferation of these exotics is discussed.     

Alkali and alkaline earth metals in decomposing macrophytes in a wetland system

The foraging habitat selections of brown-eared pheasant (Crossoptilon mantchuricum) and the common pheasant (Phasianus colchicus) were studied in Huanglongshan Nature Reserve Shaanxi, China. Foraging habitat characteristics were measured on the basis of expected differences between species at 183 sites from November to December 2006 and January 2007. The results showed that both species selected foraging habitats with altitude (<1200 m), conifer forest, half sunny and half shady slope, sunny slope, density of trees (<5 individuals/100 m²), cover of shrub (>50%), visibility class (<10%) and distance to water source (<300 m). However, the brown-eared pheasant selected habitats with cover of trees (30–50%), middle or lower slope location, distance to edge of woods (<300 m) and human disturbance (<500 m), and the selection on density of shrub was not observed, compared to the selections on cover of trees (<30%), lower slope location, distance to edge of woods (<500 m) and human disturbance (<300 m), and density of shrub (>500 individuals/100 m²) for common pheasant. We also found that the common pheasant avoid predators by concealment whereas brown-eared pheasant evade predations by running away strategy.     

XenLoop: a transparent high performance inter-VM network loopback

Advances in virtualization technology have focused mainly on strengthening the isolation barrier between virtual machines (VMs) that are co-resident within a single physical machine. At the same time, a large category of communication intensive distributed applications and software components exist, such as web services, high performance grid applications, transaction processing, and graphics rendering, that often wish to communicate across this isolation barrier with other endpoints on co-resident VMs. State of the art inter-VM communication mechanisms do not adequately address the requirements of such applications. TCP/UDP based network communication tends to perform poorly when used between co-resident VMs, but has the advantage of being transparent to user applications. Other solutions exploit inter-domain shared memory mechanisms to improve communication latency and bandwidth, but require applications or user libraries to be rewritten against customized APIs—something not practical for a large majority of distributed applications. In this paper, we present the design and implementation of a fully transparent and high performance inter-VM network loopback channel, called XenLoop, in the Xen virtual machine environment. XenLoop does not sacrifice user-level transparency and yet achieves high communication performance between co-resident guest VMs. XenLoop intercepts outgoing network packets beneath the network layer and shepherds the packets destined to co-resident VMs through a high-speed inter-VM shared memory channel that bypasses the virtualized network interface. Guest VMs using XenLoop can migrate transparently across machines without disrupting ongoing network communications, and seamlessly switch between the standard network path and the XenLoop channel. In our evaluation using a number of unmodified benchmarks, we observe that XenLoop can reduce the inter-VM round trip latency by up to a factor of 5 and increase bandwidth by a up to a factor of 6.

Nitrooxyethylation reverses the healing-suppressant effect of Ibuprofen

Nonsteroidal antiinflammatory drugs like ibuprofen impede tissue repair by virtue of retarding inflammation. The present study was undertaken to explore if linking of nitrooxyethyl ester to ibuprofen reverses its healing-depressant propensity. Nitrooxyethyl ester of ibuprofen (NOE-Ibu) was synthesized in our laboratory through a well-established synthetic pathway. NOE-Ibu was screened for its influence on collagenation, wound contraction and epithelialization phases of healing, and scar size of healed wound in three wound models, namely, incision, dead space, and excision wounds. Besides, its influence on the oxidative stress (levels of GSH and TBARS) was also determined in 10-day-old granulation tissue. NOE-Ibu was further screened for its antiinflammatory activity in rat paw edema model. NOE-Ibu promoted collagenation (increase in breaking strength, granulation weight, and collagen content), wound contraction and epithelialization phases of healing. NOE-Ibu also showed a significant antioxidant effect in 10-day-old granulation tissue as compared to ibuprofen. Results vindicate that the esterification of ibuprofen with nitrooxyethyl group reverses the healing-suppressant effect of ibuprofen. The compound also showed equipotent antiinflammatory activity as ibuprofen.     

Interaction of foot-and-mouth disease virus with dendritic cells

Despite several decades of investigation, the manner in which foot-and-mouth disease virus (FMDV) interacts with the innate and adaptive immune compartments is not completely understood. The importance of elucidating this relationship is emphasized by the inability of current FMDV vaccines to provide long-term protection and the recent outbreaks of FMDV in formerly disease-free countries. Dendritic cells (DCs) are professional antigen-presenting cells that have evolved to monitor the environment and provide a link between the innate and adaptive immune systems. Comprehending the cross-talk between DC and FMDV will provide valuable information towards understanding the host response to the virus and will aid in the design of effective tools and vaccines to block virus spread.     

Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P

The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg²⁺-dependent cleavage of the 5′ leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) cooperate to recognize different parts of the pre-tRNA. While ∼250–500 mM Mg²⁺ renders the archaeal RPR active without RNase P proteins (RPPs), addition of all RPPs lowers the Mg²⁺ requirement to ∼10–20 mM and improves the rate and fidelity of cleavage. To understand the Mg²⁺- and RPP-dependent structural changes that increase activity, we used pre-tRNA cleavage and ensemble FRET assays to characterize inter-domain interactions in Pyrococcus furiosus (Pfu) RPR, either alone or with RPPs ± pre-tRNA. Following splint ligation to doubly label the RPR (Cy3-RPR_{C domain} and Cy5-RPR_{S domain}), we used native mass spectrometry to verify the final product. We found that FRET correlates closely with activity, the Pfu RPR and RNase P holoenzyme (RPR + 5 RPPs) traverse different Mg²⁺-dependent paths to converge on similar functional states, and binding of the pre-tRNA by the holoenzyme influences Mg²⁺ cooperativity. Our findings highlight how Mg²⁺ and proteins in multi-subunit RNPs together favor RNA conformations in a dynamic ensemble for functional gains.     

Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection

RNase P is a catalytic ribonucleoprotein primarily involved in tRNA biogenesis. Archaeal RNase P comprises a catalytic RNase P RNA (RPR) and at least four protein cofactors (RPPs), which function as two binary complexes (POP5•RPP30 and RPP21• RPP29). Exploiting the ability to assemble a functional Pyrococcus furiosus (Pfu) RNase P in vitro, we examined the role of RPPs in influencing substrate recognition by the RPR. We first demonstrate that Pfu RPR, like its bacterial and eukaryal counterparts, cleaves model hairpin loop substrates albeit at rates 90- to 200-fold lower when compared with cleavage by bacterial RPR, highlighting the functionally comparable catalytic cores in bacterial and archaeal RPRs. By investigating cleavage-site selection exhibited by Pfu RPR (±RPPs) with various model substrates missing consensus-recognition elements, we determined substrate features whose recognition is facilitated by either POP5•RPP30 or RPP21•RPP29 (directly or indirectly via the RPR). Our results also revealed that Pfu RPR + RPP21•RPP29 displays substrate-recognition properties coinciding with those of the bacterial RPR-alone reaction rather than the Pfu RPR, and that this behaviour is attributable to structural differences in the substrate-specificity domains of bacterial and archaeal RPRs. Moreover, our data reveal a hierarchy in recognition elements that dictates cleavage-site selection by archaeal RNase P.