Crystal structure of class I acetohydroxy acid isomeroreductase from Pseudomonas aeruginosa

Acetohydroxy acid isomeroreductase (AHIR) is a key enzyme in the biosynthesis of branched-chain amino acids. We have determined the first crystal structure of a class I AHIR from Pseudomonas aeruginosa at 2.0 A resolution. Its dodecameric architecture of 23 point group symmetry is assembled of six dimeric units and dimerization is essential for the formation of the active site. The dimeric unit of P.aeruginosa AHIR partially superimposes with a three-domain monomer of spinach AHIR, a class II enzyme. This demonstrates that the so-called plant-specific insert in the middle of spinach AHIR is structurally and functionally equivalent to the C-terminal alpha-helical domain of P.aeruginosa AHIR, and the C-terminal alpha-helical domain was duplicated during evolution from the shorter, class I AHIRs to the longer, class II AHIRs. The dimeric unit of P.aeruginosa AHIR possesses a deep figure-of-eight knot, essentially identical with that in the spinach AHIR monomer. Thus, our work lowers the likelihood of the previous proposal that "domain duplication followed by exchange of a secondary structure element can be a source of such a knot in the protein structure" being correct.     

Industrial attributes of β-glucanase produced by Bacillus sp. CSB55 and its potential application as bio-industrial catalyst

Bioprocess and Biosystems Engineering - The β-glucanase produced from Bacillus sp. CSB55 not only depicts the potent industrial characteristics but also relates as bio-industrial catalyst...     

Renal actions of dendroaspis natriuretic peptide in rabbits

Dendroaspis natriuretic peptide (DNP) is one of four members of the natriuretic peptide family sharing functional and structural properties. The purpose of the present study was to elucidate the physiological role of DNP on renal functions and its cellular mechanism in the rabbit kidney. DNP (5 μg/kg/min) infused intravenously increased urine volume and urinary excretion of electrolytes. These renal actions induced by DNP were more pronounced than those caused by atrial natriuretic peptide (ANP). We compared profiles of (125)I-ANP and (125)I-DNP by reverse-phase HPLC during incubation in rabbit plasma at 37°C for 1, 2, and 4h. While (125)I-ANP was quickly degraded within 1h, (125)I-DNP was still stable in plasma for 4h. DNP induced the greatest cyclic guanosine monophosphate (cGMP) production in the glomeruli in a dose-dependent manner, when compared to other renal structures including cortical tubules, outer medullary tubules, and inner medullary tubules. Affinity cross-linking analysis revealed NPR-A is selective receptor for DNP in glomeruli. Forskolin, a stimulator of adenylyl cyclase, significantly decreased cGMP production in the renal glomeruli but not in the renal medulla. In summary, DNP is a more effective activator of renal functions than ANP, possibly because of the degradation resistance of DNP against the endogenous peptidases in plasma or tissues. These findings suggest that DNP plays a pivotal role as a renal regulating peptide via specific natriuretic peptide receptors with a guanylyl cyclase domain.     

Cell separation from high cell density broths of Alcaligenes eutrophus by using a coagulant

Summary Alcaligenes eutrophus was successfully recovered from high cell density broths by pre-treatment with polyaluminium hydroxide chloride silicate as a coagulant at 36–90 mg Al/l. The optimum pH range for cell coagulation was 10–12. Subsequent centrifugation (45×g) and filtration (pore size 0.5 mm) gave a cell recovery of higher than 90%. The energy demand for cell recovery with the coagulant was only 3–11% of that without it.     

High-performance data mining with intelligent SSD

An intuitive way to process the big data efficiently is to reduce the volume of data transferred over the storage interface to a host system. This is the reason that the notion of intelligent SSD (iSSD) was proposed to give processing power to SSD. There is rich literature on iSSD, however, its real implementation has not been provided to the public yet. Most prior work aims to quantify the benefits of iSSD with analytical modeling. In this paper, we first develop on iSSD simulator and present the potential of iSSD in data mining through the iSSD simulator. Our iSSD simulator performs on top of the gem 5 simulator and fully simulates all the processes of data mining algorithms running in iSSD with cycle-level accuracy. Then, we further addresse how to exploit all the computing resources for efficient processing of data mining algorithms. These days, CPU, GPU, and SSD are recently equipped together in most computing environment. If SSD is replaced with iSSD later on, we have a new computing environment where the three computing resources collaborate one another to process big data quite effectively. For this, scheduling is required to decide which computing resource is going to run for which function at which time. In our heterogeneous scheduling, types of computing resources, memory sizes in computing resources, and inter-processor communication times including IO time in SSD are considered. Our scheduling results show that processing in the collaborative environment outperforms that in the traditional one by up to about 10 times.     

Postconditioning for salvage of ischemic skeletal muscle from reperfusion injury: efficacy and mechanism

We tested our hypothesis that postischemic conditioning (PostC) is effective in salvage of ischemic skeletal muscle from reperfusion injury and the mechanism involves inhibition of opening of the mitochondrial permeability transition pore (mPTP). In bilateral 8x13 cm pig latissimus dorsi muscle flaps subjected to 4 h ischemia, muscle infarction increased from 22+/-4 to 41+/-1% between 2 and 24 h reperfusion and remained unchanged at 48 (38+/-6%) and 72 (40+/-1%) h reperfusion (P<0.05; n=4 pigs). PostC induced by four cycles of 30-s reperfusion/reocclusion at the onset of reperfusion after 4 h ischemia reduced muscle infarction from 44+/-2 to 22+/-2% at 48 h reperfusion. This infarct protective effect of PostC was mimicked by intravenous injection of the mPTP opening inhibitor cyclosporin A or NIM-811 (10 mg/kg) at 5 min before the end of 4 h ischemia and was abolished by intravenous injection of the mPTP opener atractyloside (10 mg/kg) at 5 min before PostC (P<0.05; n=4-5 pigs). PostC or intravenous cyclosporin A injection at 5 min before reperfusion caused a decrease in muscle myeloperoxidase activity and mitochondrial free Ca2+ concentration and an increase in muscle ATP content after 4 h ischemia and 2 h reperfusion compared with the time-matched controls. These effects of PostC were abolished by intravenous injection of atractyloside at 5 min before PostC (P<0.05; n=6 pigs). These observations support our hypothesis that PostC is effective in salvage of ischemic skeletal muscle from reperfusion injury and the mechanism involves inhibition of opening of the mPTP.     

CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination

At least 25 inherited disorders in humans result from microsatellite repeat expansion. Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however, cis-elements and trans-factors regulating the instability process remain undefined. Genomic fragments from the human spinocerebellar ataxia type 7 (SCA7) locus, containing a highly unstable CAG tract, were previously introduced into mice to localize cis-acting “instability elements,” and revealed that genomic context is required for repeat instability. The critical instability-inducing region contained binding sites for CTCF—a regulatory factor implicated in genomic imprinting, chromatin remodeling, and DNA conformation change. To evaluate the role of CTCF in repeat instability, we derived transgenic mice carrying SCA7 genomic fragments with CTCF binding-site mutations. We found that CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues, and that CpG methylation of CTCF binding sites can further destabilize triplet repeat expansions. As CTCF binding sites are associated with a number of highly unstable repeat loci, our findings suggest a novel basis for demarcation and regulation of mutational hot spots and implicate CTCF in the modulation of genetic repeat instability.     

Dendrochronological analysis of the canopy history of two Ohio old-growth forests

This study examined the temporal patterns of establishment, suppression, and release of major tree species in two old-growth Ohio forest remnants as a means to determine the past disturbance history of these forests. Increment cores were taken from a total of 154 trees from two well-drained, upland plots and two poorly-drained, bottomland plots in each of the two forested areas. Acer saccharum and Fagus grandifolia exhibited multiple episodes of suppression and release prior to becoming canopy trees, and could tolerate suppressions as long as 84 years. In contrast, Quercus macrocarpa, Q. muehlenbergii, Prunus serotina, and Acer saccharinum rerely exhibited any tolerance to suppression and appeared to have entered the canopy after single disturbances had opened large areas of canopy. There was clear synchrony in the temporal pattern of establishment and final release from suppression among trees from bottomland plots scattered throughout the stands, indicating that relatively large disturbances were important in these poorly-drained areas. In contrast, there was little synchrony among trees from well-drained upland plots, except in a single instance where selective cutting of Quercus trees opened the canopy. Thus, the canopy of upland site was likely subjected only to small disturbances resulting from the death of one or a few trees. At the whole of forest level, there was evidence of episodic recruitment of canopy trees in both forests. Establishment of Fraxinus spp. and Quercus spp. were particularly episodic, and few Fraxinus or Quercus trees alive today established during the last century. These data suggest that large disturbances have affected canopy dynamics of both upland and bottomland areas prior to 1900 and in bottomland forests through this century. In contrast, disturbances in upland areas during this century have been restricted to small, treefall-generated canopy gaps.