Influence of dam removal on trichopteran assemblages in the lowland Drzewiczka River,Poland

The aim of this study is to assess the response of Trichoptera in a patchy tailwater stretch of the Drzewiczka River (Poland) to dam removal as compared to the previous pulse discharge disturbance. The study was carried out in the river at the end of a whitewater slalom canoeing track located downstream of the dam reservoir called Drzewieckie Lake (area 0.84 km²). Between February and April 2002, the dam reservoir was gradually emptied before its dredging, and the Drzewiczka River recovered its natural discharge (1.7–4.5 m³ s⁻¹) for several years (temporary renaturisation). Altogether, 120 monthly samples of macroinvertebrates and their environments were collected in two sampling cycles, S1 in 2000–2001 during high discharge fluctuations (2.1–12.0 m³ s⁻¹ daily) and S2 in 2002–2003 during renaturisation after emptying the reservoir, from the following five habitats: H_P—pool habitat, H_S—stagnant habitat, H_M—macrophyte habitat, H_B—bank habitat and H_R—riffle habitat. On the basis of trichopteran abundance, the patterns in their assemblages were recognised with use of a self-organising map that was a Kohonen artificial neural network. The obtained classification of trichopteran samples was found to be based in general on the spatial criterion, i.e. dependent on habitats, irrespective of which sampling cycle the samples originated from, which clearly showed that the habitat mosaic of the river bed was observed both in S1 and S2. In addition, a very important function was noted for riparian and land plants, which developed intensively at the bottom of the Drzewieckie Reservoir immediately after it was emptied. They restricted extensive transport of reservoir sediments to the downstream river reach, thus reducing differences between S1 and S2 in the tailwater. It is also worth noting that in S1, in comparison to S2, Cyrnus trimaculatus, Mystacides azurea and Lype reducta flowing downstream from the reservoir were observed more frequently in the river, which confirmed that impoundments can be conducive to the presence of certain species downstream of dams. Summing up, although artificial short-term flow fluctuations usually diminish the quality and quantity of benthos, the article presents a case in which they were small and short enough to allow the formation of a mosaic of bed patches and positively affected certain parameters of macrobenthic communities according to the intermediate disturbance hypothesis. Handling editor: David Dudgeon     

What You Should Know About Land-Cover Data

ABSTRACT Wildlife biologists are using land-characteristics data sets for a variety of applications. Many kinds of landscape variables have been characterized and the resultant data sets or maps are readily accessible. Often, too little consideration is given to the accuracy or traits of these data sets, most likely because biologists do not know how such data are compiled and rendered, or the potential pitfalls that can be encountered when applying these data. To increase understanding of the nature of land-characteristics data sets, I introduce aspects of source information and data-handling methodology that include the following: ambiguity of land characteristics; temporal considerations and the dynamic nature of the landscape; type of source data versus landscape features of interest; data resolution, scale, and geographic extent; data entry and positional problems; rare landscape features; and interpreter variation. I also include guidance for determining the quality of land-characteristics data sets through metadata or published documentation, visual clues, and independent information. The quality or suitability of the data sets for wildlife applications may be improved with thematic or spatial generalization, avoidance of transitional areas on maps, and merging of multiple data sources. Knowledge of the underlying challenges in compiling such data sets will help wildlife biologists to better assess the strengths and limitations and determine how best to use these data.     

Bottom water oxygenation history in southeastern Arabian Sea during the past 140 ka: Results from redox-sensitive elements

The concentrations of multiple redox-sensitive elements such as Re, U, Mo, Cd, V, Sb, and Tl were determined in sediments from the southeastern Arabian Sea (9°21′N: 71°59′E) to understand the bottom water oxygenation history throughout the past 140 ka. The enrichment of redox-sensitive elements (Re, U, Cd and Sb) above average crustal abundances suggests that the Last Glacial Maxima (17.48 ka), stadials of Marine Isotope Stage (MIS)-5 (5b and 5d) and Glacial Termination (GT)-II (133 ka) were associated with suboxic bottom water conditions. Sediments deposited during these suboxic conditions show the highest Re content (up to 54 ppb normalized to a carbonate free basis) which is highly enriched over average continental crust (0.4 ppb) and these sediments appear to be the major sink for the global mass balance estimation. Marine Isotope Stages 1, 3, 4 and interstadials of MIS-5 (5a, 5c & 5e) were all associated with near-oxic conditions. Overall, the lack of enrichment of Mo and V above crustal abundance, and a high Re/Mo (ppm/ppm) ratio (avg. 18.2 × 10^− 3) suggest that sediments of the southeastern Arabian Sea never contained free H₂S during the last 140 ka. These changes in the bottom water oxygen content can be related to the oceanic circulation pattern during this time and in part are reflected in relationships between the timing of redox changes and paleoproductivity proxies.     

海马位置细胞对空间信息的处理

海马位置细胞接收各种来源的空间信息后,可对这些信息进行加工处理,在海马内形成认知地图或加强联合皮层内细胞集群的突触联系以形成对空间位置的永久记忆。海马内的空间信息输出后,在伏核（nucleus accumbens,NAC）。内与其它来源的信息进行整合,最终通过运动环路形成目标指向性行为。     

Nucleotide sequence analysis of the cloned salmon preproinsulin cDNA

A cDNA library was constructed using polyadenylated RNA from salmon (Oncorhynchus keta) Brockmann bodies, plasmid vector pBR322, and in vitro recombinant DNA techniques. Insulin-related clones were identified with a cDNA probe generated from the same RNA and enriched for insulin sequences. Two recombinants were shown to contain the nucleotide sequence of the entire coding region and parts of the 5' and 3' untranslated regions. The salmon preproinsulin mRNA is about 760 nucleotides long, 315 of which code for the protein, while about 190 and 200 nucleotides belong to the 5' and 3' flanking regions, respectively. Comparison of the nucleotide sequences of salmon insulin mRNA with those from other species reveals that sequence conservation is limited to the regions coding for the B and A peptides and two segments of the signal peptide. The C-peptide region exhibits no significant sequence homology with the C-peptides of other vertebrates. The 5' and 3' untranslated regions of the salmon preproinsulin mRNA are homologous only with the anglerfish mRNA, whereas there is no evident homology with those of birds and mammals. In addition to establishing the sequence of the preproinsulin mRNA, cloned salmon insulin cDNA provides a specific probe for the analysis and isolation of genomic DNA fragments containing insulin genes.     

Chloroplast DNA differences between cultivated hop,Humulus lupulus and the related species H. japonicus

Chloroplast DNA (cpDNA) of Humulus Lupulus and H. japonicus was examined by restriction endonuclease analysis with BamHI, BanI, BclI, BstEII, DraI, EcoRI, EcoRV, HindIII, KpnI, PaeR7I, PstI, PvuII, SalI and XhoI. The restriction fragment patterns showed that the cpDNAs shared a large number of restriction sites. However, the chloroplast genomes of the two species could be distinguished by differences in restriction site and restriction fragment patterns in the PstI, PvuII, BclI, EcoRV, DraI and HindIII digests. On the basis of the complexity of restriction enzyme patterns, the enzymes PstI, PvuII, SalI, KpnI and XhoI were selected for mapping the chloroplast genomes. Single and double restriction enzyme digests of cpDNA from the two species were hybridized to cpDNA probes of barley and tobacco. The data obtained from molecular hybridization experiments were used to construct the cleavage site maps. Except for the PstI digest, the arrangement of cpDNA restriction sites was found to be the same for both species. An extra PstI site was present in H. lupulus. Three small insertions/deletions of about 0.8 kbp each were detected in the chloroplast genomes of the two species. Two of these insertions/deletions were present in the large and one in the small singlecopy region of the chloroplast genome. The cpDNA of Humulus was found to be a circular molecule of approximately 148 kbp that contains two inverted repeat regions of 23 kbp each, a small and a large single -copy region of approximately 20 kbp and 81 kbp, respectively. The chloroplast genome of hop has the same physical and structural organization as that found in most angiosperms.     

重要花卉植物高密度遗传连锁图谱构建研究进展

遗传连锁图谱是以遗传标记间重组频率为基础的染色体或基因组内位点相对位置的线性排列图,高密度遗传图谱构建可实现物理图谱和遗传图谱的整合,对促进基因图位克隆具有重要作用。利用遗传图谱可有效地提高育种效率和改良品种。重要花卉植物高遗传图谱精密度尚无法满足精细定位研究的要求,百合、紫薇、郁金香、向日葵等重要花卉高密度遗传图谱构建研究较少,制约了花卉植物分子育种研究进程。概述了高密度遗传图谱构建流程及作图方法,综述了牡丹、梅花、月季、菊花、兰花、荷花、桂花等重要花卉植物遗传图谱构建研究进展,讨论了重要花卉植物高密度遗传图谱构建存在的主要问题,对今后重要花卉植物遗传图谱构建研究的发展方向及其在育种中的应用前景进行了展望,以期为花卉植物基因定位、辅助基因组组装、比较基因组学、基因克隆、分子标记辅助育种等提供参考。     

Fine Mapping of Xa2, a Bacterial Blight Resistance Gene in Rice

The rice bacterial blight resistance gene, Xa2, confers resistance to T7147 of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae. It is located on the long arm of chromosome 4. Here, we report the fine mapping of Xa2 by genetic recombination analysis with simple sequence repeat (SSR) markers according to the genome sequence. Two F₂ populations are constructed to localize Xa2. In a primary analysis with 136 random F₂ plants of Zhenzhuai/IRBB2, it was found that Xa2 was located in approximately 20 cM region. To accurately determine the locus of Xa2, 120 new SSR markers were developed in this region by screening the sequence. Twelve new SSR markers were successfully used in genetic recombination analysis in IR24/IRBB2 population, while 20 in ZZA/IRBB2 population. We found that the nearest SSR markers to Xa2 are HZR950-5 and HZR970-4, which cover approximately 190-kb region. The sequence analysis of this 190-kb region revealed the presence of a homologous sequence of leucine rich repeat (LRR)-kinase. These results are very useful for transferring or pyramiding Xa2 by molecular marker-assistant selection in rice breeding programs and for cloning Xa2 by map-based cloning in combination with a long-range PCR strategy. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

A Study on Protein Residue Contacts Prediction by Recurrent Neural Network

1IntroductionThe three-dimensional(3D)structure of a proteinis perhaps the most important of all its features,since itdetermines completely how the protein functions andinteracts with other molecules.Most biological mech-anisms at the protein level are based on shape-complementarity,so that proteins present particularconcavities and convexities that allow them to bind toeach other and formcomplexstructures,and tendon.Forthis reason,for instance,the drug design problem con-sists primarily in th…     

High‐resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two‐speed genome evolution

Recombination is a major evolutionary force, increasing genetic diversity and permitting efficient coevolution of fungal pathogen(s) with their host(s). The ascomycete Fusarium graminearum is a devastating pathogen of cereal crops, and can contaminate food and feed with harmful mycotoxins. Previous studies have suggested a high adaptive potential of this pathogen, illustrated by an increase in pathogenicity and resistance to fungicides. In this study, we provide the first detailed picture of the crossover events occurring during meiosis and discuss the role of recombination in pathogen evolution. An experimental recombinant population (n = 88) was created and genotyped using 1306 polymorphic markers obtained from restriction site‐associated DNA sequencing (RAD‐seq) and aligned to the reference genome. The construction of a high‐density linkage map, anchoring 99% of the total length of the reference genome, allowed the identification of 1451 putative crossovers, positioned at a median resolution of 24 kb. The majority of crossovers (87.2%) occurred in a relatively small portion of the genome (30%). All chromosomes demonstrated recombination‐active sections, which had a near 15‐fold higher crossover rate than non‐active recombinant sections. The recombination rate showed a strong positive correlation with nucleotide diversity, and recombination‐active regions were enriched for genes with a putative role in host–pathogen interaction, as well as putative diversifying genes. Our results confirm the preliminary analysis observed in other F. graminearum strains and suggest a conserved ‘two‐speed’ recombination landscape. The consequences with regard to the evolutionary potential of this major fungal pathogen are also discussed.