Vertical distribution of organic constituents in an Antarctic lake: Lake Vanda

Vertical distribution of organic constituents, i.e. total organic carbon (TOC), extractable organic carbon with ethyl acetate (EOC), hydrocarbons, phytol, sterols, fatty acids and phenolic acids in Lake Vanda was studied to elucidate their features in relation to the stratification of lake water and the distribution of lake organisms. The concentrations of TOC, EOC and sterols increased with depth and attained the maximum values of 25 and 1.5 mgC l^–1 and 1.4 g l^–1 in the bottom, respectively, while those of fatty acids showed the maximum value of 61 g l^–1 at a depth of 55.4 m, along with the highest value of the ratio of unsaturated (UC₁₆, uC₁₈) to saturated (C₁₆, C₁₈) acids (8.5) and with the highest carbon preference index (35). Hydrocarbons were only found in the bottom layers (60.4 and 65.9 m) and bottom sediment. These results suggest strongly that the vertical distribution of lake organisms and their activity are quite different due to depth. In the bottom warm anoxic layers the degradation of organic materials must have occurred significantly and thus refractory organic materials should be concentrated.     

A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis

As zinc is an essential trace metal ion for all living cells, cells elaborate a variety of strategies to cope with zinc starvation. In Bacillus subtilis, genes encoding ribosomal proteins L31 and S14 are duplicated into two types: one type contains a zinc-binding motif (RpmE or RpsN), whereas the other does not (YtiA or YhzA). We have previously shown that displacement of RpmE (L31) by YtiA from already assembled ribosomes is controlled by zinc, and this replacement could contribute to zinc mobilization under zinc-limiting conditions. We propose here that the switch between the two types of S14 has a different significance. rpsN is indispensable for growth and depletion of RpsN results in defective 30S subunits. YhzA can functionally replace RpsN to allow continued ribosome assembly under zinc-limiting conditions. Unlike YtiA, YhzA appeared in the ribosome at a slower rate consistent with incorporation into newly synthesized, rather than pre-existing ribosomes. These results raise the possibility that YhzA is involved in a fail-safe system for the de novo synthesis of ribosomes under zinc-limiting conditions.     

PNA monomers fully compatible with standard Fmoc-based solid-phase synthesis of pseudocomplementary PNA

Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies.     

Spatial and temporal changes in genetic structure and diversity of isolated white-spotted charr (Salvelinus leucomaenis) populations

Hydrobiologia - In Japan, numerous artificial dams constructed for erosion control or hydroelectric power generation have affected almost all rivers and resulted in isolation and fragmentation of...     

Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46

We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38-46. The pipeline integrates programs developed in our group as well as other existing scoring functions. The core of the pipeline is the LZerD protein-protein docking algorithm. If templates of the target complex are not found in PDB, the first step of our docking prediction pipeline is to run LZerD for a query protein pair. Meanwhile, in the case of human group prediction, we survey the literature to find information that can guide the modeling, such as protein-protein interface information. In addition to any literature information and binding residue prediction, generated docking decoys were selected by a rank aggregation of statistical scoring functions. The top 10 decoys were relaxed by a short molecular dynamics simulation before submission to remove atom clashes and improve side-chain conformations. In these CAPRI rounds, our group, particularly the LZerD server, showed robust performance. On the other hand, there are failed cases where some other groups were successful. To understand weaknesses of our pipeline, we analyzed sources of errors for failed targets. Since we noted that structure refinement is a step that needs improvement, we newly performed a comparative study of several refinement approaches. Finally, we show several examples that illustrate successful and unsuccessful cases by our group.     

Preventive Effect of Betaine Against Cognitive Impairments in Amyloid β Peptide-Injected Mice Through Sirtuin1 in Hippocampus

In the pathophysiology of Alzheimer’s disease, the deposition of amyloid β peptide (Aβ) is associated with oxidative stress, leading to cognitive impairment and neurodegeneration. We have already reported that betaine (glycine betaine), an osmolyte and methyl donor in cells, prevents the development of cognitive impairment in mice with intracerebroventricular injection of Aβ_25–35, an active fragment of Aβ, associated with oxidative stress in the hippocampus, but molecular mechanisms of betaine remain to be determined. Here, to investigate a key molecule underlying the preventive effect of betaine against cognitive impairments in Aβ_25–35-injected mice, cognitive tests and qPCR assays were performed in Aβ_25–35-injected mice with continuous betaine intake, in which intake was started a day before Aβ_25–35 injection, and then continued for 8 days. The Aβ_25–35 injection impaired short-term and object recognition memories in the Y-maze and object recognition tests, respectively. PCR assays revealed the down-regulation of Sirtuin1 (SIRT1), a NAD⁺-dependent deacetylase that mediates metabolic responses, in the hippocampus of Aβ_25–35-injected mice, whereas betaine intake prevented memory deficits as well as the decrease of hippocampal SIRT1 expression in Aβ_25–35-injected mice. Further, sirtinol, an inhibitor of the Sirtuin family, blocked the preventive effect of betaine against memory deficits. On the other hand, resveratrol, the potent compound that activates SIRT1, also prevented memory impairments in Aβ_25–35-injected mice, suggesting that SIRT1 plays a causative role in the preventive effect of betaine against memory deficits caused by Aβ exposure.

     

Sudachitin, a polymethoxyflavone from Citrus sudachi, suppresses lipopolysaccharide-induced inflammatory responses in mouse macrophage-like RAW264 cells

Although some polymethoxyflavones possess several important biological properties, including neuroprotective, anticancer, and anti-inflammatory ones, sudachitin, a polymethoxyflavone from Citrus sudachi, has been little studied. In this study, we found that sudachitin inhibited nitric oxide production by suppressing the expression of inducible nitric oxide synthase in lipopolysaccharide-stimulated macrophages, indicating that sudachitin has an anti-inflammatory effect.     

Enhanced Stomatal Conductance by a Spontaneous Arabidopsis Tetraploid,Me-0, Results from Increased Stomatal Size and Greater Stomatal Aperture

The rate of gas exchange in plants is regulated mainly by stomatal size and density. Generally, higher densities of smaller stomata are advantageous for gas exchange; however, it is unclear what the effect of an extraordinary change in stomatal size might have on a plant’s gas-exchange capacity. We investigated the stomatal responses to CO₂ concentration changes among 374 Arabidopsis (Arabidopsis thaliana) ecotypes and discovered that Mechtshausen (Me-0), a natural tetraploid ecotype, has significantly larger stomata and can achieve a high stomatal conductance. We surmised that the cause of the increased stomatal conductance is tetraploidization; however, the stomatal conductance of another tetraploid accession, tetraploid Columbia (Col), was not as high as that in Me-0. One difference between these two accessions was the size of their stomatal apertures. Analyses of abscisic acid sensitivity, ion balance, and gene expression profiles suggested that physiological or genetic factors restrict the stomatal opening in tetraploid Col but not in Me-0. Our results show that Me-0 overcomes the handicap of stomatal opening that is typical for tetraploids and achieves higher stomatal conductance compared with the closely related tetraploid Col on account of larger stomatal apertures. This study provides evidence for whether larger stomatal size in tetraploids of higher plants can improve stomatal conductance.Gas exchange is a vital activity for higher plants that take up atmospheric CO₂ and release oxygen and water vapor through epidermal stomatal pores. Gas exchange affects CO₂ uptake, photosynthesis, and biomass production (Horie et al., 2006; Evans et al., 2009; Tanaka et al., 2014). Stomatal conductance (gs) is used as an indicator of gas-exchange capacity (Franks and Farquhar, 2007). Maximum stomatal conductance (gsmax) is controlled mainly by stomatal size and density, two parameters that change with environmental conditions and are negatively correlated with each other (Franks et al., 2009).Given a constant total stomatal pore area, large stomata are generally disadvantageous for gas exchange compared with smaller stomata, because the greater pore depth in larger stomata increases the distance that gas molecules diffuse through. This increased distance is inversely proportional to g_smax (Franks and Beerling, 2009). The fossil record indicates that ancient plants had small numbers of large stomata when atmospheric CO₂ levels were high, and falling atmospheric [CO₂] induced a decrease in stomatal size and an increase in stomatal density to increase g_s for maximum carbon gain (Franks and Beerling, 2009). The positive relationship between a high g_s and numerous small stomata also holds true among plants living today under various environmental conditions (Woodward et al., 2002; Galmés et al., 2007; Franks et al., 2009). Additionally, the large stomata of several plant species (e.g. Vicia faba and Arabidopsis [Arabidopsis thaliana]) are often not effective for achieving rapid changes in g_s, due to slower solute transport to drive movement caused by their lower membrane surface area-to-volume ratios (Lawson and Blatt, 2014).Stomatal size is strongly and positively correlated with genome size (Beaulieu et al., 2008; Franks et al., 2012; Lomax et al., 2014). Notably, polyploidization causes dramatic increases in nucleus size and stomatal size (Masterson, 1994; Kondorosi et al., 2000). In addition to the negative effects of large stomata on gas exchange (Franks et al., 2009), polyploids may have another disadvantage; del Pozo and Ramirez-Parra (2014) showed that artificially induced tetraploids of Arabidopsis have a reduced stomatal density (stomatal number per unit of leaf area) and a lower stomatal index (stomatal number per epidermal cell number). Moreover, tetraploids of Rangpur lime (Citrus limonia) and Arabidopsis have lower transpiration rates and changes in the expression of genes involved in abscisic acid (ABA), a phytohormone that induces stomatal closure (Allario et al., 2011; del Pozo and Ramirez-Parra, 2014). On the other hand, an increase in the ploidy level of Festuca arundinacea results in an increase in the CO₂-exchange rate (Byrne et al., 1981); hence, polyploids may not necessarily have a reduced gas-exchange capacity.Natural accessions provide a wide range of information about mechanisms for adaptation, regulation, and responses to various environmental conditions (Bouchabke et al., 2008; Brosché et al., 2010). Arabidopsis, which is distributed widely throughout the Northern Hemisphere, has great natural variation in stomatal anatomy (Woodward et al., 2002; Delgado et al., 2011). Recently, we investigated leaf temperature changes in response to [CO₂] in a large number of Arabidopsis ecotypes (374 ecotypes; Takahashi et al., 2015) and identified the Mechtshausen (Me-0) ecotype among ecotypes with low CO₂ responsiveness; Me-0 had a comparatively low leaf temperature, implying a high transpiration rate. In this study, we revealed that Me-0 had a higher g_s than the standard ecotype Columbia (Col), despite having tetraploid-dependent larger stomata. Notably, the g_s of Me-0 was also higher than that of tetraploid Col, which has stomata as large as those of Me-0. This finding resulted from Me-0 having a higher g_s-to-g_smax ratio due to more opened stomata than tetraploid Col. In addition, there were differences in ABA responsiveness, ion homeostasis, and gene expression profiles in guard cells between Me-0 and tetraploid Col, which may influence their stomatal opening. Despite the common trend of smaller stomata with higher gas-exchange capacity, the results with Me-0 confirm the theoretical possibility that larger stomata can also achieve higher stomatal conductance if pore area increases sufficiently.