On computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble

Abstract

In the present paper, computational efficiency of the hybrid Monte Carlo (HMC) method applied to the multicanonical ensemble is studied; the HMC is an equation of motion guided Monte Carlo method. As in the standard HMC for the canonical ensemble, the multicanonical HMC calculations with high acceptance ratio show better efficiency; about 60% acceptance yields the best performance for the system examined.     

Germination stimulant from root exudates of Vigna unguiculata

Root exudate of Vigna unguiculata was extracted from a soil system consisting of charcoal and vermiculite. Germination stimulating activity for Striga gesnerioides was found in extracts of the soil system, and an active compound was isolated. The chemical structure of the active ingredient was determined to be (+)-4-O-acetylorobanchol, based on analysis of the spectral data of 1-D and 2-D NMR together with nuclear Overhauser effect (NOE) experiments. Application of the active compound to the seeds of S. gesnerioides at a concentration of 0.35 × 10⁻⁹ mol/disk led to 69% germination. The germination observed with application of GR-24, a positive control, at 0.57 × 10⁻¹⁰ mol/disk was 80%.     

8-Nitroguanine formation in oral leukoplakia, a premalignant lesion.

Oral leukoplakia is a premalignant lesion associated with development of oral cancer. To clarify the mechanism of development of oral carcinogenesis from leukoplakia, we examined DNA damage in oral epithelium of biopsy specimens of patients with leukoplakia by immunohistochemical methods. Histological changes, such as epithelial dysplasia and infiltration of inflammatory cells were observed in oral tissues of leukoplakia patients. A double immunofluorescence labeling study demonstrated that the accumulation of mutagenic 8-nitroguanine, an indicator of nitrative DNA damage, and 8-oxo-7,8-dihydro-2'-deoxyguanosine, an indicator of oxidative DNA damage, was apparently observed in the oral epithelium of patients with leukoplakia, whereas little or no immunoreactivity was observed in normal oral mucosa. Expression of inducible nitric oxide synthase (iNOS) was also observed in oral epithelium of leukoplakia patients. Immunoreactivity of 3-nitrotyrosine, an indicator of nitrative stress, was observed in oral epithelial cells and colocalized with 8-nitroguanine. Moreover, proliferating cell nuclear antigen and p53 were expressed in 8-nitroguanine-positive epithelial cells in the basal layer. These results suggest that iNOS-mediated nitrative stress contributes to development of oral carcinogenesis from leukoplakia through DNA damage as well as oxidative stress.     

Interferon-β Produces Synergistic Combinatory Anti-Tumor Effects with Cisplatin or Pemetrexed on Mesothelioma Cells

Interferons (IFNs) have been tested for the therapeutic effects in various types of malignancy, but mechanisms of the anti-tumors effects and the differential biological activities among IFN members are dependent on respective cell types. In this study, we examined growth inhibitory activities of type I and III IFNs on 5 kinds of human mesothelioma cells bearing wild-type p53 gene, and showed that type I IFNs but not type III IFNs decreased the cell viabilities. Moreover, growth inhibitory activities and up-regulated expression levels of the major histocompatibility complexes class I antigens were greater with IFN-β than with IFN-α treatments. Cell cycle analyses demonstrated that type I IFNs increased S- and G2/M-phase populations, and subsequently sub-G1-phase fractions. The cell cycle changes were also greater with IFN-β than IFN-α treatments, and these data collectively showed that IFN-β had stronger biological activities than IFN-α in mesothelioma. Type I IFNs-treated cells increased p53 expression and the phosphorylation levels, and activated apoptotic pathways. A combinatory use of IFN-β and cisplatin or pemetrexed, both of which are the current first-line chemotherapeutic agents for mesothelioma, produced synergistic anti-tumor effects, which were also evidenced by increased sub-G1-phase fractions. These data demonstrated firstly to our knowledge that IFN-β produced synergistic anti-tumor effects with cisplatin or pemetrexed on mesothelioma through up-regulated p53 expression.     

Mineral Metabolism Markers Are Associated with Myocardial Infarction and Hemorrhagic Stroke but Not Ischemic Stroke in Hemodialysis Patients: A Longitudinal Study

Background/Aims

The associations between phosphate, calcium, and intact parathyroid hormone (PTH) levels and composite cardiovascular end points have been studied. This study examined the associations of these markers with myocardial infarction (MI) and stroke separately.

Methods

This is a longitudinal study on 65,849 hemodialysis patients from the Japan Renal Data Registry. Patients with prior events at baseline were excluded. Predictors were phosphate, albumin-corrected calcium, intact PTH, and calcium times phosphate product levels. Outcome was the first episode of MI or stroke during a 1-year observation period. Data were analyzed using multiple logistic regression analyses, adjusted for potential confounders.

Results

There were 1,048, 651, and 2,089 events of incident MI, hemorrhagic, and ischemic stroke, respectively. Incident MI was associated with phosphate levels ≥6.5 mg/dL (odds ratio 1.49; confidence interval 1.23–1.80) compared with phosphate levels of 4.7–5.4 mg/dL and intact PTH levels>500 pg/mL (1.35; 1.03–1.79) compared with intact PTH levels of 151–300 pg/mL. Higher albumin-corrected calcium level was positively associated with MI (p = 0.04 by trend analysis). Hemorrhagic stroke was associated only with intact PTH levels>500 pg/mL (1.54; 1.10–2.17). Incident ischemic stroke had no association with phosphate, calcium, or intact PTH levels. The association of calcium times phosphate product with outcomes was essentially the same pattern as that of phosphate and outcomes.

Conclusions

MI was associated with phosphate, calcium, and intact PTH levels, whereas hemorrhagic stroke was associated only with intact PTH. Ischemic stroke was not associated with any of them. The potential distinct beneficial effect on MI and stroke by managing bone and mineral disease should be investigated in future studies.     

Zoledronic acid induces apoptosis and S-phase arrest in mesothelioma through inhibiting Rab family proteins and topoisomerase II actions

Zoledronic acid (ZOL), a nitrogen-containing bisphosphonate, produced anti-tumor effects through apoptosis induction or S-phase arrest depending on human mesothelioma cells tested. An addition of isoprenoid, geranylgeraniol but not farnesol, negated these ZOL-induced effects, indicating that the ZOL-mediated effects were attributable to depletion of geranylgeranyl pyrophosphates which were substrates for prenylation processes of small guanine-nucleotide-binding regulatory proteins (small G proteins). ZOL-treated cells decreased a ratio of membrane to cytoplasmic fractions in RhoA, Cdc42 and Rab6 but less significantly Rac1 proteins, indicating that these proteins were possible targets for ZOL-induced actions. We further analyzed which small G proteins were responsible for the three ZOL-induced effects, caspase-mediated apoptosis, S-phase arrest and morphological changes, using inhibitors for respective small G proteins and siRNA for Cdc42. ZOL-induced apoptosis is due to insufficient prenylation of Rab proteins because an inhibitor of geranlygeranyl transferase II that was specific for Rab family proteins prenylation, but not others inhibitors, activated the same apoptotic pathways that ZOL did. ZOL suppressed an endogenous topoisomerase II activity, which was associated with apoptosis and S-phase arrest in respective cells because we detected the same cell cycle changes in etoposide-treated cells. Inhibitors for geranlygeranyl transferase I and for RhoA produced morphological changes and disrupted actin fiber structures, both of which were similar to those by ZOL treatments. These data demonstrated that anti-tumor effects by ZOL were attributable to inhibited functions of respective small G proteins and topoisomerase II activity, and suggested that cellular factors were involved in the differential cell cycle changes.Bisphosphonates (BPs), synthetic analogues of pyrophosphates, are clinically in use for diseases with excessive bone absorption such as osteoporosis and malignancy-associated hypercalcemia. BPs administered in vivo are accumulated in the bone matrix and inhibit activities of osteoclasts.¹ The first generation of BPs, without nitrogen in the structure, is converted into cytotoxic non-hydrolyzable ATP analogues and achieves cytotoxic effects thorough decreased mitochondrial membrane potentials.^2,3 The second and the third generations, containing nitrogen, inhibit farnesyl pyrophosphate synthetase, a key enzyme in the mevalonate pathways, and deplete isoprenoid pools, which subsequently results in decreased prenylation of small guanine-nucleotide-binding regulatory proteins (small G proteins) (Supplementary Figure S1).⁴Isoprenoid lipids, farnesyl pyrophosphate and geranylgeranyl pyrophosphate, are substrates for prenylation processes that mediate farnesylation and geranylgeranylation of small G proteins, respectively.^5,6 Ras family proteins are either farnesylated by farnsyl transferase or geranylgeranylated by geranylgeranyl transferase I. In contrast, the majority of Rho family proteins and Rab family proteins are geranylgeranylated by geranylgeranyl transferase I and II, respectively. These lipid modifications are essential for most of small G proteins to bind to cytoplasmic and organelle membranes where prenylated small G proteins become functional, whereas unprenylated small G proteins remain in the cytoplasm and non-functional.⁵The nitrogen-containing BPs (N-BPs) also induce cytotoxicity to osteoclasts, which is favorable for enhanced bone mineralization, and recent studies also showed that N-BPs had cytotoxic activities on tumors such as breast and prostate cancer.^7,8 These cytotoxic actions are attributable to a number of mechanisms including apoptosis induction and anti-angiogenesis,^9,10 but it is not well investigated as to which small G proteins produce the cytotoxic effects.We recently showed that zoledronic acid (ZOL), which is one of the N-BPs to inhibit farnesyl pyrophosphate synthetase, produced cytotoxic activities to human mesothelioma.¹¹ ZOL treatments induced apoptotic cell death or S-phase arrest in cell cycle, and moreover caused morphological changes from fibroblast-like to spherical shapes. In the present study, we examined what kinds of small G proteins are responsible to these ZOL-mediated effects using inhibitors or small interfering RNA (siRNA) for the respective small G proteins and for prenylating enzymes.     

On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates

As a group closely related to chordates, hemichordate acorn worms are in a key phylogenic position for addressing hypotheses of chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the chordate notochord, crowning this animal group “hemichordates.” Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord‐forming region in acorn worm juveniles is expressed in the club‐shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to chordate organs deriving from the anterior pharynx rather than to the notochord. genesis 52:925–934, 2014. © 2014 Wiley Periodicals, Inc.     

Ranges of diurnal variation and the pattern of body temperature, blood pressure and heart rate in laboratory beagle dogs.

Ranges in diurnal variation and the patterns of body temperature (T), blood pressure (BP), heart rate (HR) and locomotor activity (LA) in 61 laboratory beagle dogs were analyzed using a telemetry system. Body temperature, BP, HR and LA increased remarkably at feeding time. Locomotor activity increased sporadically during the other periods. Body temperature was maintained at the higher value after feeding but had decreased by 0.2 C by early the next morning. Blood pressure fell to a lower value after feeding but had increased by 2.8% by early the next morning. Heart rate decreased progressively after feeding and was 14.5% lower the next morning. This study determined that in laboratory beagles the ranges of diurnal variation and patterns of T, BP and HR are significantly different from those reported in humans and rodents, and that over 24 hr these physiological changes were associated with their sporadic wake-sleep cycles of the dogs.     

Molecular studies of hemichordate development: a key to understanding the evolution of bilateral animals and chordates

SUMMARY Using the Hawaiian acorn worm, Ptychodera flava, we began molecular studies on the development of hemichordates, a phylum previously unstudied at this level. Here we review results garnered from the examination of a few specific genes selected to help understand the evolution of vertebrate structures. These studies suggest new ideas about the evolution of developmental mechanisms in the deuterostomes. In a seminal observation, we noted an unexpected zone of expression of the Brachyury gene in the early anterior embryonic ectoderm where the mouth will form. Typically, the Brachyury gene is closely linked to development of the notochord and is expressed around the blastopore and in the posterior mesoderm in most animals. This first expression of Brachyury at the blastopore may represent a regulatory program associated with organizing the original animal head and gut opening, as suggested by the expression of Brachyury during hypostome formation in hydra. We believe that the anterior expression of Brachyury in deuterostomes represents the cooption of the program for organizing the original animal gut opening to form the deuterostome mouth. Recent data from the trochophore larva of a polychaete show that an anterior zone of expression of Brachyury is produced in this protostome by splitting of the Brachyury field during the formation of a gut with a mouth and anus by the lateral fusion of the sides of the blastopore. The ability to initiate independently a secondary regulatory program to organize the new mouth leading to an anterior field of Brachyury expression may be a signal event in the evolution of the deuterostomes. We also noted that the P. flava homolog of T‐brain/Eomes, a gene closely related by sequence and expression around the blastopore to Brachyury and associated with development of the vertebrate brain, also exhibits early posterior expression around the blastopore and a field of de novo anterior ectoderm expression during later embryogenesis. The tissue in the zone of de novo anterior ectoderm expression of Pf‐Tbrain produces the apical organ, a larval neural structure that has been touted as an evolutionary precursor of the chordate dorsal brain. The gene regulatory mechanisms responsible for initiating the anterior zone of de novo expression of T‐brain may represent a cooption to specify early neuroectoderm of the regulatory program evolved first to drive anterior Brachyury expression for deuterostome mouth formation. It will be interesting to examine the possibilities that an ability to initiate the de novo anterior expression of the program that includes T‐brain may be a key event in the evolution of the developmental mechanisms leading to the chordate dorsal nervous system.