Integrative Biological Hydrogen Production: An Overview

Biological hydrogen (H₂) production by dark and photo-fermentative organisms is a promising area of research for generating bioenergy. A large number of organisms have been widely studied for producing H₂ from diverse feeds, both as pure and as mixed cultures. However, their H₂ producing efficiencies have been found to vary (from 3 to 8 mol/mol hexose) with physiological conditions, type of organisms and composition of feed (starchy waste from sweet potato, wheat, cassava and algal biomass). The present review deals with the possibilities of enhancing H₂ production by integrating metabolic pathways of different organisms-dark fermentative bacteria (from cattle dung, activated sludge, Caldicellulosiruptor, Clostridium, Enterobacter, Lactobacillus, and Vibrio) and photo-fermentative bacteria (such as Rhodobacter, Rhodobium and Rhodopseudomonas). The emphasis has been laid on systems which are driven by undefined dark-fermentative cultures in combination with pure photo-fermentative bacterial cultures using biowaste as feed. Such an integrative approach may prove suitable for commercial applications on a large scale.     

Are research efforts on Animalia in the South Pacific associated with the conservation status or population trends?

Analyses of knowledge gaps can highlight imbalances in research, encouraging greater proportionality in the distribution of research efforts. In this research we used generalized linear mixed models (GLMM) with the aim to determine if research efforts for the period 2005–2015 for terrestrial vertebrates of Amphibia, Aves, Mammalia and Reptilia in the South Pacific region were correlated with conservation status (critically endangered (CR), endangered (EN), vulnerable (VU), least concern (LC) and near threatened (NT)) or population trends (increasing, stable, decreasing and unknown) through the International Union for Conservation of Nature (IUCN) database. Our results showed that research distribution was uneven across different classes. Out of 633623 investigated papers, the average number of publications per species was 43.7, 306.7, 717.6 and 115.3 for Amphibia (284 species), Aves (1306 species), Mammalia (243 species) and Reptilia (400 species), respectively. Consistently, the lower publication effort on Amphibia compared to other taxonomic classes was revealed as significant by GLMM analysis. There was no significant differences in research effort among levels of conservation status. However, we found significantly different publication efforts among population trends of all examined species in that species with “unknown” population trends gained significantly lower researchers’ attention compared to species with “decreasing” trend. Results also indicated that, although it was not significant, the highest attention is given to species with “increasing” population trend over all taxonomic classes. Using the Information Theoretic approach we also generated a set of competing models to identify most important factors influencing research efforts, revealing that the highest ranked model included taxonomic class and population trend.     

Differential climate–growth relationships in Abies alba Mill. and Fagus sylvatica L. in Mediterranean mountain forests

Pointer year analysis, simple correlations, and response functions were combined in a dendroecological study to evaluate climate–growth relationships over the last century in two Abies alba Mill. and Fagus sylvatica L. mixed stands in Southern Italy mountainous areas. Analyses revealed species-specific attributes at the two study sites, i.e. Molise and Basilicata. Growth divergence between the two species emerged based on three primary climatic drivers, including drought stress and spring warmer temperatures during the current growing season for F. sylvatica, and water availability in the previous growing season for A. alba. However, despite the microclimatic differences between the two study sites, F. sylvatica showed similar climate–growth patterns, while differences were indicated for A. alba, due to its minor susceptibility to drought stress during the current growing season at the Basilicata site. Indeed, at the southernmost geographic limits of A. alba drought avoidance mechanisms were confirmed, consistent with traits considered diagnostic for the species in the Mediterranean region.     

A Note on Sire Evaluation with Uncertain Paternity

We consider sire evaluation for situations in which paternity is uncertain. We show how mixed models equations can be used to obtain the best linear unbiased predictors for sire evaluation in such situations.     

Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications

CXXC domains have traditionally been considered as CpG specific DNA binding domains that are repelled by cytosine modifications. This view has recently been challenged by the demonstration that CXXC domain of TET3 has relaxed sequence specificity and binds with the highest affinity to symmetric DNA duplex containing 5caCpG. Here, we present a comparative analysis of the MLL1-CXXC and TET3-CXXC sequence specificity and tolerance to cytosine modifications (5-methyl, 5-hydroxymethyl, 5-formyl, 5-carboxyl) in CpG and non-CpG context. For the first time, we take into consideration possible interference from cytosine bases elsewhere in the sequence. We show that despite similar overall structure, MLL1-CXXC has greater sequence and modification specificity than TET3-CXXC. MLL1-CXXC is specific only for CpG and does not tolerate any cytosine modifications. In contrast, TET3-CXXC does not require the CpG context of cytosine bases. Methyl-, formyl- and carboxyl-modifications are tolerated by TET3-CXXC, but only preceding G. Based on our and other data we propose a parsimonious model of MLL1-CXXC and TET3-CXXC DNA binding. This model explains why the binding of modified DNA duplexes by TET3-CXXC requires in some cases a register shift and is therefore context-dependent.     

Episodic development of Cambrian eocrinoid-sponge meadows in the Iberian Chains (NE Spain)

Summary The Lower-Middle Cambrian transition in the Iberian Chains (NE Spain) records a transgressive deposition from peritidal to open-shelf environments. This overall trangressive trend took place across an interval of syndepositional tectonic processes. which have been illustrated during late Bilbilian to Leonian times. The scarcity of building organisms in this areas seems to be directly related to a rhythmic influence of fine terrigenous decantation, which inhibited and interrupted the carbonate production. Only in the more proximal and quiet environments, the episodic establishment of stromatolitic boundstones is evidence. Eocrinoid-sponge meadows were developed in shallow subtidal environments, and were completed by the presence of trilobites, inarticulate brachiopods, hyoliths and Chancelloriid sclerites. The biggest accumulation rates associated to these complex meadow communities seem to be reflected by differential synsedimentary faulting processes.     

Mechanisms of liquid flux across pulmonary alveolar epithelial cell monolayers

Summary Active transport of sodium by pulmonary alveolar epithelial cells (AEC) is believed to be an important component of edema clearance in the normal and injured lung. Data supporting this premise have come from measurements of sodium movement across AEC monolayers or from perfused lung model systems. However, direct measurement of fluid flux across AEC monolayers has not been reported. In the present work, AEC were studied with an experimental system for the measurement of fluid flux (Jv) across functionally intact cell monolayers. Primary adult rat type II alveolar epithelial cells were cultured on 0.8 μm nuleopore filters previously coated with gelatin and fibronectin. Intact monolayers were verified by high electrical resistance (> 1000 Θ) at 4–5 d of primary culture. At the same time interval, transmission electron microscopy revealed cells with type I cell-like morphology throughout the monolayer. These were characterized by both adherens and tight junctional attachments. Fluid flux across the monolayers was measured volumetrically over a period of 2 h in the presence of HEPES-buffered DMEM containing 3% fatty acid-free bovine serum albumin. Flux (Jv) was inhibited 39% by 1 × 10⁻⁴ M ouabain (P < 0.01) and 27% by 5 × 10⁻⁴ M amiloride (P < 0.05). These data support the concept that AEC Na⁺/K⁺-ATPase and Na⁺ transport systems are important determinants of AEC transepithelial fluid movement in vitro.     

Soil disturbance regime in relation to micro-scale landforms and its effects on vegetation structure in a hilly area in Japan

To clarify vegetation-landform relationships, we examined the soil disturbance regime in relation to micro-scale landforms and its effects on vegetation structure in a mixed temperate forest in a hilly area in northeastern Japan. Soil profiles in each micro-landform unit were surveyed to elucidate the effects of soil disturbances on the vegetation structure. The hilly area studied consisted of an upper and a lower hillslope area divided by an erosion front, which differed considerably with respect to vegetation structure. In the upper hillslope area, canopy was closed and dominated by Pinus densiflora and Quercus serrata. In the lower hillslope area, on the other hand, canopy was less closed and shrubs, ferns, and herbaceous species were abundant. The species composition changed gradually from the crest slope to the upper sideslope to the head hollow in the upper hillslope area. However, micro-landforms in the lower hillslope area seemed to have less effect on the vegetation structure. This may be because the lower hillslope area, in contrast to the upper hillslope area, has suffered from soil disturbances, and hence shrubs, ferns, and herbs have developed irrespective of micro-landforms. Thus, vegetation can be quite different depending on whether or not sites have suffered from soil disturbance. In disturbed stands, it is suggested that the frequency and intensity of disturbance are more important for species composition than the type of soil disturbance.     

固氮树种在混交林中的作用研究Ⅱ,固氮树木叶部N,P养分动态特征

研究了２３种固氮与非固氮树种叶部Ｎ,Ｐ含量的季节变化,输出率以及叶片衰老过程中Ｎ,Ｐ输出过程,结果表明,供试树种叶部Ｎ,Ｐ含量均存在着明显的季节变化,平均变化率为２１～２３％,最大变化率出现在叶片衰老期,在衰老期内不同树种表现出不同的Ｎ,Ｐ动态特征,固氮树种表现出输出率,落叶中Ｎ含量是非固氮树种的１．６～３．７倍,固氮树种生长季叶部Ｎ含量在２．５％左右。     

Two-stage functional mixed models for evaluating the effect of longitudinal covariate profiles on a scalar outcome

The Daily Hormone Study, a substudy of the Study of Women's Health Across the Nation (SWAN) consisting of more than 600 pre- and perimenopausal women, includes a scalar measure of total hip bone mineral density (BMD) together with repeated measures of creatinine-adjusted follicle stimulating hormone (FSH) assayed from daily urine samples collected over one menstrual cycle. It is of scientific interest to investigate the effect of the FSH time profile during a menstrual cycle on total hip BMD, adjusting for age and body mass index. The statistical analysis is challenged by several features of the data: (1) the covariate FSH is measured longitudinally and its effect on the scalar outcome BMD may be complex; (2) due to varying menstrual cycle lengths, subjects have unbalanced longitudinal measures of FSH; and (3) the longitudinal measures of FSH are subject to considerable among- and within-subject variations and measurement errors. We propose a measurement error partial functional linear model, where repeated measures of FSH are modeled using a functional mixed effects model and the effect of the FSH time profile on BMD is modeled using a partial functional linear model by treating the unobserved true subject-specific FSH time profile as a functional covariate. We develop a two-stage nonparametric regression calibration method using period smoothing splines. Using the connection between smoothing splines and mixed models, we show that a key feature of our approach is that estimation at both stages can be conveniently cast into a unified mixed model framework. A simple testing procedure for constant functional covariate effect is also proposed. The proposed methods are evaluated using simulation studies and applied to the SWAN data.