Minor- and trace-element intra-shell variations in Santonian inoceramids (Basque-Cantabrian Basin,northern Spain): diagenetic and primary causes

Santonian deep- and platform-marine facies inoceramids from the Basque-Cantabrian Basin show clear saw-toothed intra-shell variations with respect to Mg/Ca, Sr/Ca, Na/Ca, Ba/Ca, Fe/Ca and Mn/Ca ratios. Under cathodoluminescence, the most luminescent zones in all the inoceramids present lower Mg/Ca and Sr/Ca (up to 48% and 35% lower values, respectively) and higher Fe/Ca and Mn/Ca ratios (up to 362% and 819% higher values, respectively), which is indicative of diagenetic modification. In contrast, the least luminescent zones show higher Mg/Ca and Sr/Ca ratios and lower Fe/Ca and Mn/Ca. These findings, along with the presence of frequent, well-correlated Mg/Ca, Sr/Ca and Na/Ca ratios, inversely related to Fe/Ca and Mn/Ca, in the weakest luminescent zones suggest major retention of the primary intra-shell variations in these zones. Moreover, Ba/Ca profiles, not connected with the general cathodoluminescence behaviour of the shells, also point towards partial retention of the primary patterns. The saw-toothed intra-shell variations are thought to be caused by the distinct geochemical signals acquired originally by the inoceramid alternating clear and dark growth lines. The deposition of the growth lines and thus the saw-toothed intra-shell variations may be mainly related to periodically changing palaeoenvironmental conditions, such as seawater temperature variations and phytodetritus rainfall. This interpretation is supported by the appearance of highly similar chemical saw-toothed variations in the extant shallow-marine Atrina rigida shell.     

Organic phosphorus in soil water under a European beech (Fagus sylvatica L.) stand in northeastern Bavaria, Germany: seasonal variability and changes with soil depth

Organically bound phosphorus (P) is a mobile form of phosphorus in many soils and thus its dynamics relevant for the leaching and cycling of this element. Despite its importance, little is known about the chemical composition of dissolved organic P. We studied the concentrations, fluxes, and chemical composition of organic P in forest floor leachates and soil solutions in a Rendzic Leptosol under a 90-year-old European beech (Fagus sylvatica L.) forest over a 27-month period (1997–1999). The chemical composition of organic P was analysed using XAD-8 fractionation and ³¹P-nuclear magnetic resonance (NMR) spectroscopy. Organic P was the dominant P form in forest floor leachates as well as in porewaters of the mineral soil. The largest concentrations of organic P were observed during summer and peaked (330–400 g dissolved organic P l^–1) after rain storms following short dry periods, concurrently with the concentrations of organic carbon (OC). Because of high rainfall, fluxes of organic P (and C) were greatest in autumn although concentrations of organic C and P were lower than in summer. In forest floor leachates, the hydrophilic fraction of dissolved organic matter contained 83 ± 13% of the bulk organic P. In soil solutions from 90 cm depth, organic P was almost exclusively in the hydrophilic fraction. Because of the low retention of the hydrophilic fraction of dissolved organic matter in the mineral soils, concentrations of organic P in soil water remained almost constant with depth. Consequently, organic P contributed > 95% of the total P leached into deeper subsoils. The overall retention of organic P in the weakly developed mineral soils was little and so the average annual fluxes of organic P in subsoils at 90 cm depth (38 mg m^–2) comprised 67% of those from the forest floors (57 mg m^–2) during the study period. Hence, organic P proved to be mobile in the studied soil. ³¹P-NMR spectroscopy confirmed the dominance of organic P species in soil water. Signals due to inorganic P occurred only in spectra of samples collected in winter and spring months. Spectra of samples from summer and autumn revealed traces of condensed phosphates. Due to low P contents, identification of organic P species in samples from winter and spring was not always possible. In summer and autumn, monoester and diester phosphates were the dominant organic species and varied little in their relative distributions. The distribution of organic species changed little from forest floor leachates to the subsoil solutions indicating that the composition of P-containing compounds was not influenced by sorptive interactions or biological transformation.     

Human sequence variation and mutation databases

This paper aims to give an overview of current resources onhuman sequence variations and give an idea about the directionin which these services are moving.      

A study of factors that may influence the determination of copper, iron, and zinc in human milk during sampling and in sample individuals

The aim of this study was to establish the possible effects of the sampling protocol (between-breast, within-feed, and diurnal differences) and the mother’s personal factors (age, parity, iron supple-mentation, smoking habits, and lactation period) on the copper, iron, and zinc contents in human milk. One hundred thirty-six human milk samples identified by their origin and sampling conditions were analyzed. The samples were obtained from the 2nd to 15th d postpartum from 62 women. The data on the individuals required for the study were available. Mineral determinations were analyzed by flame atomic absorption spectrometry following a standarized protocol. The results showed that iron contents were higher in hind-milk samples and at the nighttime feeding and depended on the breast from which the sample was taken. The copper and zinc concentrations showed no significant variations. There was no significant relationship among the mothers’ age, parity, smoking habits, iron supplementation, and copper content. Milk from older women had lower zinc contents than that of younger women. Increased amounts of iron were found in multiparous women. Between colostrum and transitional milk, a sharp decrease in zinc content was observed, whereas copper and iron contents remained constant. All of these results make it clear that standardized sampling protocols are needed in order to obtain comparable values.     

Short-term variations in the abundance and cell volume of bacterioplankton in an artificial tropical lake

Circadian and spatial fluctuations in bacterioplankton abundance and cell volume were examined, for the first time, in the Municipal Lake located in the down town area of Yaoundé (Capital of Cameroon, Central Africa, ca 3° 52′ N, 11° 31′ E). Bacterial cell volumes (range, 0.05 to 0.2 μm3) were consistent with those reported for other aquatic systems while bacterial densities (0.8 to 2 × 108 cells ml-1) were among the highest values reported in pelagic systems. These variables and chlorophyll a and dissolved oxygen concentrations within a single depth-zone varied from 13 to 61%, while water temperature fluctuated only from 2 to 6%. Spatial fluctuations of physical-chemical and biological variables were generally higher during the day-time than during the night-time. A significant diel variation was provided for bacterial cell volume in the surface waters where synchronized cell division was occurring during the night. The measured bacterial abundances in this study were 4 to 17 fold higher than values known from other lakes of similar trophic status, and both cell abundance and volume were not correlated with chlorophyll. We conclude that this was due to the dependence of bacterial populations to different sources of allochthonous substrates, including untreated sewage from the major influents of the lake, resuspension of benthic material, and substrate releasing from macrophytes which are prevalent in the littoral zone of the lake. This revised version was published online in September 2006 with corrections to the Cover Date.     

Self-organization and productivity in semi-arid ecosystems: implications of seasonality in rainfall

Spatial self-organization including striking vegetation patterns observed in arid ecosystems has been studied in models with uniform rainfall. In this paper, we present a fully seasonal rainfall model that produces vegetation patterns found in nature by including the natural adaptation of plants to scarcity of water and the consequent seasonal variation in their growth and metabolic rate. We present results for the mean-field and spatially extended versions of the model. We find that the patterns depend on the duration of the wet season even with fixed total annual precipitation (PPT) showing how seasonality affects spatial self-organization. We observe that the productivity can vary for fixed PPT as a function of the duration thereby providing another source of observed variations. We compute the maximum vegetation cover as function of PPT and find that the behavior is consistent with observations. We comment on the implications for regime shifts due to increased interannual fluctuations caused by climatic changes. Our specific model calculations provide more general conclusions for ecosystems with competition for scarce resources due to seasonal variations in the resource, especially for self-organization and productivity.     

基于空间距离指数的青藏高原生态敏感性综合评价及时空演变分析

生态敏感性是生态系统对外界压力的适应性及遭受破坏的恢复力,开展生态敏感性评价是识别区域生态环境问题的有效手段之一。根据青藏高原的区域特性和主要生态环境问题,在定量构建土地荒漠化敏感性、水土流失敏感性、滑坡灾害敏感性和冻融侵蚀敏感性的基础上,通过空间距离指数法对青藏高原生态敏感性进行综合评价,并采用空间自相关分析和生态敏感性变化模式分析,探讨其时空演变特征和保护管理区划。结果表明：（1）青藏高原综合生态敏感性由西北向东南递减,极度和重度敏感区主要集中在西北部和高大山脉区,不敏感区主要集中在东南部;（2）2000-2018年间青藏高原综合生态敏感性指数值从1.49上升到1.51,表明该区域生态敏感性逐步下降,生态环境改善明显;（3）青藏高原生态敏感性存在显著的空间正相关,低-低聚集网格数量波动上升,从2000年的7277增至2018年7357,表明青藏高原部分地区的生态环境仍存在着一定恶化的风险;（4）根据区域生态敏感性变化模式分析,将青藏高原划分为严格保护区、生态退化区、潜在治理区、生态改善区和综合发展区五个区域,并提出了相应保护与管理对策。研究结果可以为青藏高原生态保护和可持续发展提供参考,从而有效推动保护管理措施的制定。     

Reproductive biology of the horned viper,Cerastes cerastes gasperettii in the central region of Saudi Arabia

The reproductive biology of the horned viper, Cerastes cerastes gasperettii, in Riyadh region of Saudi Arabia was investigated over a period of one year. Study of reproductive cycle of male and female C. c. gasperettii revealed that the breeding season is relatively short (April and May). Thereafter females laid eggs by mid of July and hatching probably had taken place by the end of September. No activity was observed during winter, this may indicate just a single clutch per year. Relative testis weight to body weight was drastically increased (X¯ = 0.88%) during the peak of reproductive activity (May) where maximal expansion of seminiferous tubules was also attained during April and May (X¯ = 209 μm and 191 μm, respectively). Likewise, the ovarian activity was the highest during May where ovarian parameters were greater in terms of relative ovarian weight to body weight and ova diameter being 0.46% and 2.29 mm, respectively. Fat body weight was increased drastically just before the peak of reproductive activity then started to decline during June. It could be concluded that the harsh desert conditions and similar environments certainly affect reproductive activity of Saudi Arabian reptiles including snakes.     

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.