Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis

We used a power spectrum method to identify periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes and genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in eubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worm Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, we speculated that the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated nucleosomes.     

Quantification of galectin-7 and its localization in adult mouse tissues

We developed a method to quantify galectin-7 extracted from adult mouse tissues by Western blot analysis. More than 0.5 ng of galectin-7 per mg of tissue was detectable by this method. The amounts of galectin-7 in tissues were determined as follows: skin, 62 +/- 3 ng/mg; esophagus, 23 +/- 8 ng/mg; stomach, 18 +/- 6 ng/mg; anus, 13 +/- 1 ng/mg; and tongue, 12 +/- 2 ng/mg. This indicates that galectin-7 production coincides with the degree of stratification of the epithelia. Interestingly, we also detected significant amounts of galectin-7, 5.9 plus minus 1.4 and 2.7 +/- 0.6 ng/mg, in the trachea and ovaries, respectively. Moreover, we found that galectin-7 is localized in the pseudostratified epithelium of the trachea and stromal epithelium of the ovaries by immunohistochemistry. Thus, galectin-7 protein might be produced primarily in stratified epithelia, but also in some wet epithelia, and plays a unique role in cell-mucus contact, or the growth of ovarian follicles.     

Pollination partners of Mucuna macrocarpa (Fabaceae) at the northern limit of its range

Mucuna macrocarpa is a plant found in tropical and subtropical regions that requires an “explosive opening.” Explosive opening is the process that exposes the stamen and pistil from the opening of the carina. This process is needed for cross pollination; however, the plant cannot open itself and opening by an animal is needed. The most common opener of Mucuna flowers is several nectar‐eating bats (e.g., Syconycteris), but the flying fox, Pteropus dasymallus, is the only opener of M. macrocarpa on the subtropical island of Okinawajima. Here, we present the explosive openers and possible pollinators in the northernmost and temperate Kamae region, Kyushu, Japan, where nectar‐eating bats are absent. The Japanese macaque, Macaca fuscata, and the Japanese marten, Martes melampus, were the explosive openers observed during our survey in Kamae. Martens opened flowers using their snout in a manner similar to that of the flying fox, whereas macaques opened flowers using their hands. This is the first time that an animal has been observed opening these flowers with its hands rather than snout. In total, 97% (n = 283) of explosively opened flowers were opened by macaques, and the macaque largely contributed to the overall flower opening. Because many pollen grains become attached to the explosive openers, they are considered to be primary pollinators. Furthermore, two bee species, Apis cerana japonica and Bombus ardens ardens, also visited opened flowers and collected pollen, and they were possibly secondary pollinators.     

GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids

Determining the solid–liquid phase transition point by conventional molecular dynamics (MD) simulations is difficult because of the tendency of the system to get trapped in local minimum energy states at low temperatures and hysteresis during cooling and heating cycles. The replica exchange method, used in performing many MD simulations of the system at different temperature conditions simultaneously and performs exchanges of these temperatures at certain intervals, has been introduced as a tool to overcome this local-minimum problem. However, around the phase transition temperature, a greater number of different temperatures are required to adequately find the phase transition point. In addition, the number of different temperature values increases when treating larger systems resulting in huge computation times. We propose a computational acceleration of the replica exchange MD simulation on graphics processing units (GPUs) in studying first-order solid–liquid phase transitions of Lennard-Jones (LJ) fluids. The phase transition temperature for a 108-atom LJ fluid has been calculated to validate our new code. The result corresponds with that of a previous study using multicanonical ensemble. The computational speed is measured for various GPU-cluster sizes. A peak performance of 196.3 GFlops with one GPU and 8.13 TFlops with 64 GPUs is achieved.     

Trophic eggs compensate for poor offspring feeding capacity in a subsocial burrower bug

Various animals produce inviable eggs or egg-like structures called trophic eggs, which are presumed to be an extended maternal investment for the offspring. However, there is little knowledge about the ecological or physiological constraints associated with their evolutionary origin. Trophic eggs of the seminivorous subsocial burrower bug (Canthophorus niveimarginatus) have some unique characteristics. Trophic eggs are obligate for nymphal survival, and first-instar nymphs die without them. To identify the cause of nymphal death, we hypothesized that first-instar nymphs starve to death because they cannot feed on anything but trophic eggs. Although first-instar nymphs fed on artificially exposed endosperm did survive, nymphs that were provided with intact seed were not able to penetrate the seed vessel and starved to death. Another hypothesis that trophic eggs play a role in transferring the midgut symbiont, essential for survival in heteropteran bugs, from mother to offspring was rejected because almost all nymphs had retained the symbiont without feeding on trophic eggs. These results suggest that poor feeding capacity of the offspring is the cause of nymphal death, and the important constraint that promotes the evolution of the curious trophic egg system in C. niveimarginatus.     

A new approach regarding the treatment of preeclampsia and preterm labor

Both preeclampsia and preterm delivery are important complications in pregnancy and are leading causes for maternal and perinatal morbidity and mortality. The underlying molecular mechanisms of both diseases remain unknown, thus treatments (beta2-stimulants and magnesium sulfate) are essentially symptomatic. Both molecules have molecular weights less than 5-8 kDa and cross the placental barrier thus exerting their effects on the fetus. In addition, the fetus produces peptide hormones that are highly vasoactive and uterotonic and increase in response to maternal stress and with continued development. Fetal peptides are also small molecules that inevitably leak across into the maternal circulation. Aminopeptidases such as placental leucine aminopeptidase (P-LAP) and aminopeptidase A (APA) are large molecules that do not cross the placental barrier. We have shown that APA acts as an antihypertensive agent in the pregnant spontaneously hypertensive rat by degrading vasoactive peptides and as a result returns the animal to a normotensive state. We have also noted that P-LAP acts as an anti-uterotonic agent by degrading uterotonic peptides, and as a result prolongs gestation in the pregnant mouse. Thus, P-LAP and APA represent promising agents for the treatment of preeclampsia and preterm labor by degrading bioactive hormones derived from the feto-placental circulation.     

Influence of age on cardiac baroreflex function during dynamic exercise in humans

We investigated the influence of aging on cardiac baroreflex function during dynamic exercise in seven young (22 +/- 1 yr) and eight older middle-aged (59 +/- 2 yr) healthy subjects. Carotid-cardiac baroreflex function was assessed at rest and during moderate-intensity steady-state cycling performed at 50% heart rate reserve (HRR). Five-second pulses of neck pressure and neck suction from +40 to -80 Torr were applied to determine the operating point gain (G(OP)) and maximal gain (G(MAX)) of the full carotid-cardiac baroreflex function curve and examine baroreflex resetting during exercise. At rest, mean arterial pressure (MAP) and heart rate were similar between the younger and older subjects. In contrast, the resting G(OP) and G(MAX) were significantly lower in the older subjects. The increase in MAP from rest to exercise was greater in the older subjects (Delta +20 +/- 2 older vs. Delta +6 +/- 3 younger mmHg; P < 0.001). However, the G(OP) was similar in both groups during exercise because of a reduction in the younger subjects. In contrast, G(MAX) was unchanged from rest and therefore remained lower in older subjects (-0.19 +/- 0.05 older vs. -0.42 +/- 0.05 younger beats.min(-1).mmHg(-1); 50% HRR; P < 0.001). Furthermore, exercise resulted in an upward and rightward resetting of the cardiac baroreflex function curve in both groups. Collectively, these findings suggest that the cardiac baroreflex function curve appropriately resets during exercise in older subjects but operates at a reduced G(MAX) primarily because of age-related reductions in carotid-cardiac control manifest at rest.     

Possible involvement of SDF-1α/CXCR4-DPPIV axis in TGF-β1-induced enhancement of migratory potential in human peritoneal mesothelial cells

We have previously reported that human peritoneal mesothelial cells (HPMCs) express a large amount of dipeptidyl peptidase IV (DPPIV) and that its expression is regulated by a variety of bioactive substances in malignant ascites from ovarian cancer patients. The aim of this study has been to examine the expression and role of the SDF-1α/CXCR4-DPPIV axis in HPMCs. We have demonstrated that the expression levels of DPPIV and E-cadherin in HPMCs decrease, following TGF-β1-induced morphological change, in a time- and concentration-dependent manner. Additionally, we show that both SDF-1α (a chemokine and substrate for DPPIV) and its receptor, CXCR4, are expressed on HPMCs, and that their expression levels are upregulated by TGF-β1 treatment, resulting in an increased migratory potential of HPMCs. Furthermore, the migratory potential of HPMCs is significantly enhanced in the presence of SDF-1α or DPPIV-specific inhibitor in the wound-healing assay. These results suggest that DPPIV and SDF-1α/CXCR4 play crucial roles in regulating the migratory potential of HPMCs, which may be involved in the re-epithelialization of denuded basement membrane at the site of peritoneal injury.