Seasonal impact of waterfowl on communities of macrophytes in a shallow lake

From 2005 to 2007, we established bird-proof enclosures in a small, shallow and semi-permanent lake, lacking fish, at Brown Moss, Shropshire, UK, to investigate the effects of aquatic birds on seasonal growth of submerged and emergent macrophytes. The highest density of birds on the lake was in winter (110 individuals ha⁻¹) and the lowest in summer 2005 (6 ha⁻¹). Plant growth varied with season but there were significantly different (F = 8.03, p < 0.05, df = 1) standing crops of macrophytes between bird-proof enclosures (proportion of volume occupied, 0.47 ± 0.04) and control treatments (0.36 ± 0.11). Different densities of birds occurred in different areas and this was reflected in their effects. Ducks, mainly mallard (Anas platyrhynchos, Linnaeus), and teal (Anas crecca, Linnaeus), damaged plants by direct consumption, uprooting and trampling, whereas larger birds, such as mute swan (Cygnus olor, Gmelin), were able to remove Typha latifolia (Linnaeus). In summer, grazing pressure was reduced as the population of birds declined. Waterfowl caused seasonal impacts on the re-development of the water plant community. However, waterfowl herbivory had low potential to shift a macrophyte-dominated state into a phytoplankton-dominated state because aquatic plants could recover, during the growing season, when bird populations declined.     

Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean

GAs are plant hormones that play fundamental roles in plant growth and development. GA2ox, GA3ox, and GA20ox are three key enzymes in GA biosynthesis. These enzymes belong to the 2OG-Fe (II) oxygenase superfamily and are independently encoded by different gene families. To date, genome-wide comparative analyses of GA oxidases in plant species have not been thoroughly carried out. In the present work, 61 GA oxidase family genes from rice (Oryza sativa), Arabidopsis, and soybean (Glycine max) were identified and a full study of these genes including phylogenetic tree construction, gene structure, gene family expansion and analysis of functional motifs was performed. Based on phylogeny, most of the GA oxidases were divided into four subgroups that reflected functional classifications. Intron/intron average length of GA oxidase genes in rice analysis revealed that GA oxidase genes in rice experienced substantial evolutionary divergence. Segmental duplication events were mainly found in soybean genome. However, in rice and Arabidopsis, no single expansion pattern exhibited dominance, indicating that GA oxidase genes from these species might have been subjected to a more complex evolutionary mechanism. In addition, special functional motifs were discovered in GA20ox, GA3ox, and GA2ox, which suggested that different functional motifs are associated with differences in protein function. Taken together our results suggest that GA oxidase family genes have undergone divergent evolutionary routes, especially at the monocot-dicot split, with dynamic evolution occurring in Arabidopsis thaliana and soybean.     

Adult human CD133/1 kidney cells isolated from papilla integrate into developing kidney tubules

Approximately 60,000 patients in the United States are waiting for a kidney transplant due to genetic, immunologic and environmentally caused kidney failure. Adult human renal stem cells could offer opportunities for autologous transplant and repair of damaged organs. Current data suggest that there are multiple progenitor types in the kidney with distinct localizations. In the present study, we characterize cells derived from human kidney papilla and show their capacity for tubulogenesis. In situ, nestin⁺ and CD133/1⁺ cells were found extensively intercalated between tubular epithelia in the loops of Henle of renal papilla, but not of the cortex. Populations of primary cells from the renal cortex and renal papilla were isolated by enzymatic digestion from human kidneys unsuited for transplant and immuno-enriched for CD133/1⁺ cells. Isolated CD133/1⁺ papillary cells were positive for nestin, as well as several human embryonic stem cell markers (SSEA4, Nanog, SOX2, and OCT4/POU5F1) and could be triggered to adopt tubular epithelial and neuronal-like phenotypes. Isolated papillary cells exhibited morphologic plasticity upon modulation of culture conditions and inhibition of asymmetric cell division. Labeled papillary cells readily associated with cortical tubular epithelia in co-culture and 3-dimensional collagen gel cultures. Heterologous organ culture demonstrated that CD133/1⁺ progenitors from the papilla and cortex became integrated into developing kidney tubules. Tubular epithelia did not participate in tubulogenesis. Human renal papilla harbor cells with the hallmarks of adult kidney stem/progenitor cells that can be amplified and phenotypically modulated in culture while retaining the capacity to form new kidney tubules. This article is part of a Special Issue entitled: Polycystic Kidney Disease.     

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set

The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein β-barrel assembly machine in E. coli. The first 100 residues in BamC were disordered in solution. The Rosetta calculations showed that BamC_101-344 forms two well-defined domains connected by an ∼ 18-residue linker, where the relative orientation of the domains was not defined. Both domains adopt a helix-grip fold previously observed in the Bet v 1 superfamily. ¹⁵N relaxation data indicated a high degree of conformational flexibility for the linker connecting the N-terminal domain and the C-terminal domain in BamC. The results here show that CS-RDC-NOE Rosetta is robust and has a high tolerance for misassigned nuclear Overhauser effect restraints, greatly simplifying NMR structure determinations.     

Role of φ29 connector channel loops in late-stage DNA packaging

Double-stranded DNA bacteriophages and their eukaryotic virus counterparts have 12-fold head-tail connector assemblages embedded at a unique capsid vertex. This vertex is the site of assembly of the DNA packaging motor, and the connector has a central channel through which viral DNA passes during genome packaging and subsequent host infection. Crystal structures of connectors from different phages reveal either disordered residues or structured loops that project into the connector channel. Given the proximity to the translocating DNA substrate, these loops have been proposed to play a role in DNA packaging. Previous models have proposed structural motions in either the packaging ATPase or the connector channel loops as the driving force that translocates the DNA into the prohead. Here, we mutate the channel loops of the Bacillus subtilis bacteriophage φ29 connector and show that these loops have no active role in translocation of DNA. Instead, they appear to have an essential function near the end of packaging, acting to retain the packaged DNA in the head in preparation for motor detachment and subsequent tail assembly and virion completion.     

Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding

M-phase phosphoprotein 8 (MPP8) harbors an N-terminal chromodomain and a C-terminal ankyrin repeat domain. MPP8, via its chromodomain, binds histone H3 peptide tri- or di-methylated at lysine 9 (H3K9me3/H3K9me2) in submicromolar affinity. We determined the crystal structure of MPP8 chromodomain in complex with H3K9me3 peptide. MPP8 interacts with at least six histone H3 residues from glutamine 5 to serine 10, enabling its ability to distinguish lysine-9-containing peptide (QTARKS) from that of lysine 27 (KAARKS), both sharing the ARKS sequence. A partial hydrophobic cage with three aromatic residues (Phe59, Trp80 and Tyr83) and one aspartate (Asp87) encloses the methylated lysine 9. MPP8 has been reported to be phosphorylated in vivo, including the cage residue Tyr83 and the succeeding Thr84 and Ser85. Modeling a phosphate group onto the side-chain hydroxyl oxygen of Tyr83 suggests that the negatively charged phosphate group could enhance the binding of positively charged methyl-lysine or create a regulatory signal by allowing or inhibiting binding of other protein(s).     

Designing connected nature reserve networks using a graph theory approach

Habitat fragmentation has been cited as one of the critical reasons for biodiversity loss. Establishing connected nature reserve networks is an effective way to reduce habit fragmentation. However, the resources devoted to nature reserves have always been scarce. Therefore it is important to allocate our scarce resources in an optimal way. The optimal design of a reserve network which is effective both ecologically and economically has become an important research topic in the reserve design literature. The problem of optimal selection of a subset from a larger group of potential habitat sites is solved using either heuristic or formal optimization methods. The heuristic methods, although flexible and computationally fast, can not guarantee the solution is optimal therefore may lead to scarce resources being used in an ineffective way. The formal optimization methods, on the other hand, guarantees the solution is optimal, but it has been argued that it would be difficult to model site selection process using optimization models, especially when spatial attributes of the reserve have to be taken into account. This paper presents a linear integer programming model for the design of a minimal connected reserve network using a graph theory approach. A connected tree is determined corresponding to a connected reserve. Computational performance of the model is tested using datasets randomly generated by the software GAMS. Results show that the model can solve a connected reserve design problem which includes 100 potential sites and 30 species in a reasonable period of time. As an empirical application, the model is applied to the protection of endangered and threatened bird species in the Cache River basin area in Illinois, US. Two connected reserve networks are determined for 13 bird species.     

神农架川金丝猴冬春季节取食影响因素

以样方调查法和粪便显微组织学分析法确定了冬春季神农架地区川金丝猴的食物组成,分析了主要食源植物的营养成分,探讨了影响川金丝猴冬春季节取食的主要因素.结果表明:在冬季,川金丝猴食物组成与食源植物的粗灰分含量( r=0.709,P=0.015)呈正相关,而与食源植物的相对丰富度(r=0.543,P=0.084)、粗蛋白含量(r=0.036,P=0.916)、粗纤维含量(r=0.458,P=0.156)、粗脂肪含量(r=0.445,P=0.170)、含水量(r=-0.099,P=0.771)和无氮浸出物含量(r=-0.522,P=0.100)均不相关;在春季,与食源植物的相对丰富度(r=0.721,P=0.000)呈正相关,与含水量(r=0.114,P=0.507)、粗脂肪含量(r=0.151,P=0.380)、无氮浸出物含量(r=0.084,P=0.625)、粗蛋白含量(r=-0.275,P=0.105)、粗纤维含量(r=-0.010,P=0.956)和粗灰分含量(r=-0.178,P=0.299)不相关.主成分分析表明,食源植物的粗纤维(0.992)、粗脂肪(0.944)、粗蛋白(0.905)和食物丰富度(0.885)为川金丝猴冬季取食的主要影响因子,粗蛋白(0.946)、无氮浸出物(0.939)、含水量(0.920)和食物丰富度(0.898)为川金丝猴春季取食的主要影响因子.     

江西南矶山国家级自然保护区非繁殖期鸟类多样性研究

2009年10月~2010年3月,采用样点法调查了南矶山自然保护区3种生境鸟类多样性.共记录鸟类106种47 516只,分属10目35科70属.优势种为豆雁Anser fabalis、白骨顶Fulica atra、灰雁Anser anser和丝光椋鸟Sturnus sericeus.国家重点保护鸟类12种,CITES公约收录13种.6个湖泊共记录水鸟47种38 378只,分属6目14科29属.其中,战备湖水鸟种数最多,常湖水鸟个体数最多;白沙湖的多样性指数H′最高,其次为战备湖.