FISH ASSEMBLAGE RESPONSES TO DIFFERENT SECONDARY CHANNEL DESIGNS IN THE LOWER MISSISSIPPI RIVER,U.S.A.:A TEMPLATE FOR RIVER RESTORATION

The lower Mississippi River(LMR) has been heavily modified for multiple human purposes such as navigation, flood control, and bank stabilization. However, the LMR simultaneously supports a diverse fish fauna that includes recreational and commercial fisheries. Due to river training and diversion structures constructed during the past 80 years, the historic characteristics of the LMR have been drastically altered and have likely influenced fishes and fisheries in the system. One common restoration measure used throughout the LMR has been to "notch" wing-dike structures that close secondary(side) river channels. Dike notching allows year-round flows through secondary channels, which enhances habitat diversity and promotes biological productivity at the ecosystem scale. Although notching is presumed good for LMR fishes and other biota, few studies have examined its effects on fish assemblages. In this study, fish assemblages were sampled at seven LMR secondary channels spanning from river kilometer(rkm) 628(Louisiana-Mississippi, U.S.A.) upstream to rkm 1504(Missouri-Kentucky, U.S.A.). Four secondary channels were termed "permanent"(i.e.,with notched dikes) while three secondary channels were termed "temporary"(i.e., without notched dikes).Fishes were sampled by boat-mounted electrofishing conducted during falling and low stages from1995—1997. Fish assemblages differed between permanent and temporary secondary channels, and varied somewhat between falling and low stages. Gizzard shad(Dorosoma cepedianum), threadfin shad(D. petenense), and white bass(Morone chrysops) demonstrated consistent preferences for low-current conditions associated with temporary secondary channels. Conversely, blue catfish(Ictalurus furcatus), flathead catfish(Pylodictis olivaris), and freshwater drum(Aplodinotus grunniens) were more associated with permanent secondary channels. Future restoration strategies in the LMR should consider dike notching and resultant maintenance of permanent secondary channels in selected river reaches. However, temporary secondary channels also contain unique fish species, and also appear to be important sites of riverine primary production. Restoration strategies should consider a balance of both secondary channel types, which should support the greatest biodiversity for the LMR ecosystem.     

Applications of stem cells and bioprinting for potential treatment of diabetes

Currently, there does not exist a strategy that can reduce diabetes and scientists are working towards a cure and innovative approaches by employing stem cellbased therapies. On the other hand, bioprinting technology is a novel therapeutic approach that aims to replace the diseased or lost β-cells, insulin-secreting cells in the pancreas, which can potentially regenerate damaged organs such as the pancreas. Stem cells have the ability to differentiate into various cell lines including insulinproducing cells. However, there are still barriers that hamper the successful differentiation of stem cells into β-cells. In this review, we focus on the potential applications of stem cell research and bioprinting that may be targeted towards replacing the β-cells in the pancreas and may offer approaches towards treatment of diabetes. This review emphasizes on the applicability of employing both stem cells and other cells in 3 D bioprinting to generate substitutes for diseased β-cells and recover lost pancreatic functions. The article then proceeds to discuss the overall research done in the field of stem cell-based bioprinting and provides future directions for improving the same for potential applications in diabetic research.     

Behavioral and neural auditory thresholds in a frog

Vocalizations play a critical role in mate recognition and mate choice in a number of taxa, especially, but not limited to, orthopterans, frogs, and birds. But receivers can only recognize and prefer sounds that they can hear. Thus a fundamental question linking neurobiology and sexual selection asks-what is the threshold for detecting acoustic sexual displays? In this study, we use 3 methods to assess such thresholds in tdngara frogs: behavioral responses, auditory brainstem responsesz and multi unit electrophysiological recordi ngs from the midbrain.We show that thresholds are lowest for multiunit recordings (ca. 45 dB SPL), and then for behavioral responses (ca. 61 dB SPL), with auditory brainstem responses exhibiting the highest thresholds (ca. 71 dB SPL). We discuss why these estimates differ and why, as with other studies, it is unlikely that they should be the same. Although all of these studies estimate thresholds they are not measuring the same thresholds;behavioral thresholds are based on signal salienee whereas the 2 neural assays estimate physiological thresholds. All 3 estimates, however, make it clear that to have an appreciation for detection and salienee of acoustic signals we must listen to those signals through the ears of the receivers.     

中国省级行政区生态环境可持续性评价

从自然条件、人类胁迫、生态环境效应和社会响应4个主题出发,构建了包含28个指标的中国省级行政区生态环境可持续性评价指标体系,并通过专家调查和层次分析法为各主题层中的指标赋权.分别用各主题层中的指标和对应的权重,采用加权平均法构建自然条件(NSI)、人类胁迫(HPI)、生态环境效应(EEI)和社会响应(SRI)4个分指数,然后用这4个分指数通过灰色关联法构建综合生态环境可持续性指数(CEI),对我国各省级行政区生态环境可持续性进行评价.同时论文通过主成分分析法和相关分析法分析造成各指数地域差异的主导因素和评价中指标赋权的合理性.最后以4个分指数作为变量,采用快速样本聚类法对我国31个省级行政区进行聚类分析.评价结果表明,2003年我国各生态环境指数存在显著的地域差异.自然条件从东南到西北呈明显的由优到劣的过渡趋势,降雨量、年均气温、森林覆盖率和水网密度4个指标是导致地域差异的主导因素;人类胁迫东部发达地区明显高于西部和中部地区,同一个地区经济发展水平存在显著的正相关;生态环境效应西北地区最为显著,同各地区自然条件存在显著的负相关,在人类活动干扰下,自然条件差的地区更容易发生生态损害与退化;社会响应无明显的地域分析规律,各地区经济发展水平对其有一定影响,但并非决定性因素.区域综合生态环境可持续性由区域NSI、HPI、EEI和SRI共同决定,综合评价得到2003年我国各省级行政区生态环境可持续性排序情况,其中生态环境可持续性最强的几个地区为海南、云南、广西、江西等地,最弱的几个地区为内蒙古、宁夏、上海、西藏、新疆等地.最后,聚类分析把我国31个省级行政区聚为生态环境特点各异的六大类,可以促进我国生态环境的分类管理.     

A lubricant boundary condition for a biological body lined by a thin heterogeneous biofilm

We study the asymptotic behavior of an incompressible viscous fluid flow in a biological body lined by a thin biological film with a cellular microstructure,varying thickness,and a heterogeneous viscosity regulated by a time random process.Let ting the thickness of the film tend to zero,we derive an effective biological slip boundary condition on the boundary of the body.This law relates the tangential fluxes to the tangential velocities via a proportional coefficient corresponding to the energy of some local problem.This law describes the ability of the biological film to function as a lubricant reducing friction at the wall of the body.The tangential velocities are functions of the random trajectories of a finely concentrated biological particle.     

猛犸雪原

正我对东北的了解和向往,最早来自上世纪70年代初期读过的描写北大荒知青生活的小说《征途》。我最感兴趣的是书中描述的东北的自然风光和动物植物:"遮天蔽日的红松林,尽管被大雪覆盖,但远远望去,依然是郁郁苍苍。朔风吹过,发出万马奔腾的松涛声。那一望无际的桦树林,好像千百株银枝玉树,俊秀挺拔地屹立在冰天雪地中";"咱这疙瘩呀,是‘棒打獐子瓢舀鱼,雉鸡飞到饭锅里’。汽车在公路上撞死几个挡道的狍子,跟你们南方碾死一条蛇一样不稀     

我国近代发酵工业的先驱——金培松

金培松(又名金柏卿,英文名Pei-sung King)1906年10月30日生于浙江省东阳后岑山村.童年时他是在农村渡过,牛角挂书,放牛识字.1919年进入东阳县长山小学,1923年高小毕业,入东阳县城初级中学,3年后毕业,考入浙江省立第一中学高中部,1年后因家庭经济困难辍学,1927年9月以高中肄业学历被上海劳动大学农学院农艺化学系录取,1931年毕业.     

Species Account of Anura ns from the Western Slope of Mt. Kita nglad,Mindanao Island,Philippines

The Mt. Kitanglad Range is one of the country’s important key biodiversity sites;however, information about anuran diversity in this protected area remains depauperate. Herein we provided accounts of anuran species from high-elevation forests, in three sites of the western slope of Mt. Kitanglad range. The combined belt-transect sampling and microha bitat searches accounted for 13 species representing five families. The most represented family was Rhacophoridae with five representative species of the genus Philautus. Twelve out of the 13 species documented in the current survey are endemic. Four previously unaccounted species(Pelophr yne brevipes, Pulchrana grandocula, Sanguirana mearnsi, and Philautus surrufus) were added and brought the total anurans known from Mt. Kitanglad to 26 species. Most of the species were also recorded in forested sites, suggestive of their lesser affinity to non-forested ecosystems. The additional species detected during our survey may also imply that full understanding of anuran diversity of Mt. Kitanglad remains far from complete.     

2008年春鄱阳湖区斑背大尾莺状况

2008年1月下旬至2月上旬在中国南方广大地区发生冻雨雪灾害,给在鄱阳湖区越冬的斑背大尾莺(Locustella pryeri)带来不利影响,据3月上旬的调查,原本在江西鄱阳湖南矶湿地国家级自然保护区内广泛分布的斑背大尾莺已变得十分稀少.     

Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions

? Plants and animals possess very different developmental processes, yet share conserved epigenetic regulatory mechanisms, such as histone modifications. One of the most important forms of histone modification is methylation on lysine residues of the tails, carried out by members of the SET protein family, which are widespread in eukaryotes. ? We analyzed molecular evolution by comparative genomics and phylogenetics of the SET genes from plant and animal genomes, grouping SET genes into several subfamilies and uncovering numerous gene duplications, particularly in the Suv, Ash, Trx and E(z) subfamilies. ? Domain organizations differ between different subfamilies and between plant and animal SET proteins in some subfamilies, and support the grouping of SET genes into seven main subfamilies, suggesting that SET proteins have acquired distinctive regulatory interactions during evolution. We detected evidence for independent evolution of domain organization in different lineages, including recruitment of new domains following some duplications. ? More recent duplications in both vertebrates and land plants are probably the result of whole-genome or segmental duplications. The evolution of the SET gene family shows that gene duplications caused by segmental duplications and other mechanisms have probably contributed to the complexity of epigenetic regulation, providing insights into the evolution of the regulation of chromatin structure.     

Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes

Chaperonins are oligomeric protein-folding complexes which are divided into two distantly related structural classes. Group I chaperonins (called GroEL/cpn60/hsp60) are found in bacteria and eukaryotic organelles, while group II chaperonins are present in archaea and the cytoplasm of eukaryotes (called CCT/TriC). While archaea possess one to three chaperonin subunit-encoding genes, eight distinct CCT gene families (paralogs) have been characterized in eukaryotes. We are interested in determining when during eukaryotic evolution the multiple gene duplications producing the CCT subunits occurred. We describe the sequence and phylogenetic analysis of five CCT genes from TRICHOMONAS: vaginalis and seven from GIARDIA: lamblia, representatives of amitochondriate protist lineages thought to have diverged early from other eukaryotes. Our data show that the gene duplications producing the eight CCT paralogs took place prior to the organismal divergence of TRICHOMONAS: and GIARDIA: from other eukaryotes. Thus, these divergent protists likely possess completely hetero-oligomeric CCT complexes like those in yeast and mammalian cells. No close phylogenetic relationship between the archaeal chaperonins and specific CCT subunits was observed, suggesting that none of the CCT gene duplications predate the divergence of archaea and eukaryotes. The duplications producing the CCTdelta and CCTepsilon subunits, as well as CCTalpha, CCTbeta, and CCTeta, are the most recent in the CCT gene family. Our analyses show significant differences in the rates of evolution of archaeal chaperonins compared with the eukaryotic CCTs, as well as among the different CCT subunits themselves. We discuss these results in light of current views on the origin, evolution, and function of CCT complexes.     

Extensive concerted evolution of rice paralogs and the road to regaining independence

Many genes duplicated by whole-genome duplications (WGDs) are more similar to one another than expected. We investigated whether concerted evolution through conversion and crossing over, well-known to affect tandem gene clusters, also affects dispersed paralogs. Genome sequences for two Oryza subspecies reveal appreciable gene conversion in the approximately 0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, approximately 8% of japonica paralogs produced 5-7 MYA on chromosomes 11 and 12 have been affected by gene conversion and several reciprocal exchanges of chromosomal segments, while approximately 70-MY-old "paleologs" resulting from a genome duplication (GD) show much less conversion. Sequence similarity analysis in proximal gene clusters also suggests more conversion between younger paralogs. About 8% of paleologs may have been converted since rice-sorghum divergence approximately 41 MYA. Domain-encoding sequences are more frequently converted than nondomain sequences, suggesting a sort of circularity--that sequences conserved by selection may be further conserved by relatively frequent conversion. The higher level of concerted evolution in the 5-7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization.     

Nebulin: A Study of Protein Repeat Evolution

Protein domain repeats are common in proteins that are central to the organization of a cell, in particular in eukaryotes. They are known to evolve through internal tandem duplications. However, the understanding of the underlying mechanisms is incomplete. To shed light on repeat expansion mechanisms, we have studied the evolution of the muscle protein Nebulin, a protein that contains a large number of actin-binding nebulin domains.Nebulin proteins have evolved from an invertebrate precursor containing two nebulin domains. Repeat regions have expanded through duplications of single domains, as well as duplications of a super repeat (SR) consisting of seven nebulins. We show that the SR has evolved independently into large regions in at least three instances: twice in the invertebrate Branchiostoma floridae and once in vertebrates.In-depth analysis reveals several recent tandem duplications in the Nebulin gene. The events involve both single-domain and multidomain SR units or several SR units. There are single events, but frequently the same unit is duplicated multiple times. For instance, an ancestor of human and chimpanzee underwent two tandem duplications. The duplication junction coincides with an Alu transposon, thus suggesting duplication through Alu-mediated homologous recombination.Duplications in the SR region consistently involve multiples of seven domains. However, the exact unit that is duplicated varies both between species and within species. Thus, multiple tandem duplications of the same motif did not create the large Nebulin protein.Finally, analysis of segmental duplications in the human genome reveals that duplications are more common in genes containing domain repeats than in those coding for nonrepeated proteins. In fact, segmental duplications are found three to six times more often in long repeated genes than expected by chance.     

Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases

Eukaryotes and archaea both possess multiple genes coding for family B DNA polymerases. In animals and fungi, three family B DNA polymerases, alpha, delta, and epsilon, are responsible for replication of nuclear DNA. We used a PCR-based approach to amplify and sequence phylogenetically conserved regions of these three DNA polymerases from Giardia intestinalis and Trichomonas vaginalis, representatives of early-diverging eukaryotic lineages. Phylogenetic analysis of eukaryotic and archaeal paralogs suggests that the gene duplications that gave rise to the three replicative paralogs occurred before the divergence of the earliest eukaryotic lineages, and that all eukaryotes are likely to possess these paralogs. One eukaryotic paralog, epsilon, consistently branches within archaeal sequences to the exclusion of other eukaryotic paralogs, suggesting that an epsilon-like family B DNA polymerase was ancestral to both archaea and eukaryotes. Because crenarchaeote and euryarchaeote paralogs do not form monophyletic groups in phylogenetic analysis, it is possible that archaeal family B paralogs themselves evolved by a series of gene duplications independent of the gene duplications that gave rise to eukaryotic paralogs.      

Identification of a novel non-structural maintenance of chromosomes (SMC) component of the SMC5-SMC6 complex involved in DNA repair

Structural maintenance of chromosomes (SMC) proteins play central roles in chromosome organization and dynamics. They have been classified into six subtypes, termed SMC1 to SMC6, and function as heterodimer components of large protein complexes that also include several non-SMC proteins. The SMC2-SMC4 and SMC1-SMC3 complexes are also known as condensin and cohesin, respectively, but the recently identified SMC5 and SMC6 complex is less well characterized. Here, we report that NSE1 from Saccharomyces cerevisiae encodes a novel non-SMC component of the SMC5(Yol034wp)-SMC6(Rhc18p) complex corresponding to the 2-3-MDa molecular mass. Nse1p is essential for cell proliferation and localizes primarily in the nucleus. nse1 mutants are highly sensitive to DNA-damaging treatments and exhibit abnormal cellular morphologies, suggesting aberrant mitosis as a terminal morphological phenotype. These results are consistent with the reported features of the Schizosaccharomyces pombe SMC6 gene, rad18, which is thought to be involved in recombinational DNA repair. We conclude that Nse1p and the SMC5-SMC6 heterodimer together form a high molecular mass complex that is conserved in eukaryotes and required for both DNA repair and proliferation.     

The evolution of ADAM gene family in eukaryotes

The ADAM (A Disintegrin And Metalloprotease) gene family encodes proteins with adhesion and proteolytic functions. ADAM proteins are associated with diseases like cancers. Twenty ADAM genes have been identified in humans. However, little is known about the evolution of the family. We analyzed the repertoire of ADAM genes in a vast number of eukaryotic genomes to clarify the main gene copy number expansions. For the first time, we provide compelling evidence that early-branching green algae (Mamiellophyceae) have ADAM genes, suggesting that they originated in the last common ancestor of eukaryotes, before the split of plants, fungi and animals. The ADAM family expanded in early metazoans, with the most significative gene expansion happening during the first steps of vertebrate evolution. We concluded that most of mammal ADAM diversity can be explained by gene duplications in early bone fish. Our data suggest that ADAM genes were lost early in green plant evolution.     

Gene copy number variation and its significance in cyanobacterial phylogeny

ABSTRACT: BACKGROUND: In eukaryotes, variation in gene copy numbers is often associated with deleterious effects, but may also have positive effects. For prokaryotes, studies on gene copy number variation are rare. Previous studies have suggested that high numbers of rRNA gene copies can be advantageous in environments with changing resource availability, but further association of gene copies and phenotypic traits are not documented. We used one of the morphologically most diverse prokaryotic phyla to test whether numbers of gene copies are associated with levels of cell differentiation. RESULTS: We implemented a search algorithm that identified 44 genes with highly conserved copies across 22 fully sequenced cyanobacterial taxa. For two very basal cyanobacterial species, Gloeobacter violaceus and a thermophilic Synechococcus species, distinct phylogenetic positions previously found were supported by identical protein coding gene copy numbers. Furthermore, we found that increased ribosomal gene copy numbers showed a strong correlation to cyanobacteria capable of terminal cell differentiation. Additionally, we detected extremely low variation of 16S rRNA sequence copies within the cyanobacteria. We compared our results for 16S rRNA to three other eubacterial phyla (Chroroflexi, Spirochaetes and Bacteroidetes). Based on Bayesian phylogenetic inference and the comparisons of genetic istances, we could confirm that cyanobacterial 16S rRNA paralogs and orthologs show significantly stronger conservation than found in other eubacterial phyla. Conclusions: A higher number of ribosomal operons could potentially provide an advantage to terminally differentiated cyanobacteria. Furthermore, we suggest that 16S rRNA gene copies in cyanobacteria are homogenized by both concerted evolution and purifying selection. In addition, the small ribosomal subunit in cyanobacteria appears to evolve at extraordinary slow evolutionary rates, an observation that has been made previously for morphological characteristics of cyanobacteria.     

Structure and DNA-binding activity of the Pyrococcus furiosus SMC protein hinge domain

Structural Maintenance of Chromosomes (SMC) proteins are essential for a wide range of processes including chromosome structure and dynamics, gene regulation, and DNA repair. While bacteria and archaea have one SMC protein that forms a homodimer, eukaryotes possess three distinct SMC complexes, consisting of heterodimeric pairs of six different SMC proteins. SMC holocomplexes additionally contain several specific regulatory subunits. The bacterial SMC complex is required for chromosome condensation and segregation. In eukaryotes, this function is carried out by the condensin (SMC2-SMC4) complex. SMC proteins consist of N-terminal and C-terminal domains that fold back onto each other to create an ATPase "head" domain, connected to a central "hinge" domain via a long coiled-coil region. The hinge domain mediates dimerization of SMC proteins and binds DNA. This activity implicates a direct involvement of the hinge domain in the action of SMC proteins on DNA. We studied the SMC hinge domain from the thermophilic archaeon Pyrococcus furiosus. Its crystal structure shows that the SMC hinge domain fold is largely conserved between archaea and bacteria as well as eukarya. Like the eukaryotic condensin hinge domain, the P. furiosus SMC hinge domain preferentially binds single-stranded DNA (ssDNA), but its affinity for DNA is weaker than that of its eukaryotic counterpart, and point mutations reveal that its DNA-binding surface is more confined. The ssDNA-binding activity of its hinge domain might play a role in the DNA-loading process of the prokaryotic SMC complex during replication.