A SERINE KINASE REGULATES INTRACELLULAR-LOCALIZATION OF SPLICING FACTORS IN THE CELL CYCLE

Small nuclear ribonucleoprotein particles (snRNPs) and non-snRNP splicing factors containing a serine/arginine-rich domain (SR proteins) concentrate in 'speckles' in the nucleus of interphase cells(1). It is believed that nuclear speckles act as storage sites for splicing factors while splicing occurs on nascent transcripts(2). Splicing factors redistribute in response to transcription inhibition(3,4) or viral infection(5), and nuclear speckles break down and reform as cells progress through mitosis(6). We have now identified and cloned a kinase, SRPK1, which is regulated by the cell cycle and is specific for SR proteins; this kinase is related to a Caenorhabditis elegans kinase and to the fission yeast kinase Dsk1 (ref. 7). SRPK1 specifically induces the disassembly of nuclear speckles, and a high level of SRPK1 inhibits splicing in vitro. Our results indicate that SRPK1 mag have a central role in the regulatory network for splicing, controlling the intranuclear distribution of splicing factors in interphase cells, and the reorganization of nuclear speckles during mitosis.

九寨沟核心景区湖泊硅藻的组成及其密度与环境因子的关系

九寨沟自然保护区地处四川盆地北部岷山山脉南段，属川西高原气候中的暖温带。保护区内分布着118 个串珠状排列的高山湖泊，核心景区共有湖泊20 个（组），集中在海拔2000 米到3000 米之间。水资源是九寨沟的灵魂，保护水生生态系统是九寨沟生态旅游可持续发展的立足之本。本研究以九寨沟湿地生物多样性保护项目为依托，于2007 年5 月～2008 年4 月对九寨沟核心景区湖泊水体硅藻植物进行调查，分析了其密度与环境因子的相互关系，旨在为九寨沟湖泊生态系统保护提供科学依据和基础资料。主要有以下几点结论： （1）九寨沟硅藻植物丰富，调查统计为2 纲6 目10 科35 属159 种（包括变种和变型），水体硅藻中真性浮游种类较少，着生种类多，羽纹纲的脆杆藻属、舟形藻属、桥弯藻属、异极藻属、曲壳藻属的种类最多，常为优势属组成湖泊硅藻群落，只在长海是小环藻属占绝对优势。 （2）九寨沟水体中硅藻细胞密度不大，多在4×104～30×104 个/L，长海最高，五花海最低。在年变化上，不同的湖泊水体中硅藻的生长高峰季节不尽相同，在夏季、秋末和冬末春初均有可能出现高密度。在空间上，整体看来密度与海拔有一定的正相关，但由于水温不是单一主导因素，密度受多种环境因子影响，在海拔梯度上呈现一定的波浪状变化。 （3）影响九寨沟湖泊水体硅藻细胞密度较重要的环境因子是海拔、水温和pH。硅藻细胞密度年变化幅度大的湖泊水体，年平均细胞密度大。因此，环境因素不太稳定的湖泊水体，更可能出现高的硅藻细胞密度。11 月份响应于水量剧烈的减少，细齿菱形藻大量出现在五彩池成为优势种群，造成水体硅藻细胞密度的大幅增加。 （4）九寨沟湖泊水体水质几乎达到国家地表水I 类标准，但是，硅藻商指数以及代表多样性的Cairns 指数计算的结果不能反映水质的情况，这是由于水质状况不是决定九寨沟湖泊水体中硅藻生存的种类和数量的主要因素。因此在用各种指数分析水质的时候，都应该先判断计算该指数的参数是否主要由水质状况决定，然后再综合理化性质等其他指标分析和比较。 （5）人类的活动对九寨沟湖泊水生态系统有一定的影响。一方面，在低海拔景点人类活动的干扰比海拔高处相对要大，干扰引起低海拔景点湖泊硅藻Cairns指数较高；另一方面，旺季的影响比淡季大，水体中出现了典型富营养种类。因此，应加强低海拔景点和旺季的管理，并限制淡季的人类活动以保证九寨沟生态系统的自我恢复。 Jiuzhaigou nature reserve is located in north Sichuan, at the south section of Minshan Mountain, having a warm temperate climate which belongs to West Sichuan plateau climate. It includes 118 mountain lakes, and 20 of them between 2000 and 3000 altitude degree constitute the core area of Jiuzhaigou. The water is Jiuzhaigou's soul, so it is the basis of sustainable tourism development of Jiuzhaigou to protect the water ecological environment. Research depends on Jiuzhaigou wetland biodiversity protection program in this paper, invested the diatom plants in 17 lakes at the core area from May 2007 to April 2008. The composition and the correlation of diatom density and the environment were studied, which could provide scientific and basic information for the protection of the ecological environment of Jiuzhaigou. The main conclusions were: 1 The diatom species were in abundance, investigation showed that there were 159 species belong to 10 families and 35 genera. Most diatoms were benthos, euplankton were less. Genera Fragilaria, Navicula, Cymbella, Gomphonema and Achnanthes had the most species, which always were the dominant genera. Only in The Long Lake genus Cyclotella possessed a predominant status. 2 The diatom cell density was not very high, always between 4×104 cell/L and 30×104 cell/L, highest in The Long Lake and lowest in The Colorful Lake. In one year's time, diatom in different lakes had different growth type. The maximum could be in summer, late autumn and late winter early spring. The cell density showed a positive correlation to altitude in the whole, but fluctuated in details along altitude because of comprehensive influence by many environmental factors. 3 Altitude, water temperature and pH were the more important factors to determine the cell density. There was a positive correlation between the range of cell density in one year and the average cell density. So high annual cell average density probably will appear in lakes which has an unstable environmental condition. The boom of Denticula elegans in The Jade-Colored Lake in November was corresponding to the large decrease in water quantity. 4 The water quality of Jiuzhaigou was near the National Surface Water Standard rank I, but the Diatom Quotient and the Cairns Index didn't reflect the water quality accordingly. It was because the water quality wasn't the most important factor here which determined the species number and species quantity, so the index based on these items would not reflect it. Therefore, it is recommended that, when we use indices to evaluate the water quality, we should know first whether the water quality is the main determinative factor inflects the items used to compute the indices, and then combined with other chemical indices to analyze and do comparison. 5 The tourists' activities had influenced the water ecosystem of Jiuzhaigou. On the one hand, disturbance was relatively high at the lower altitude, it resulted in higher Cairns index; on the other hand, influence in high season was more severe than in low season, some typical species indicating eutrophication were observed in the water. It is suggested that the management at lower altitude and in high season must be strengthen, and less people activity in low season is necessary to fulfill the recovery of the water ecosystem.

Knockdown and overexpression of Unc-45b result in defective myofibril organization in skeletal muscles of zebrafish embryos

We thank John Stubblefield for editing, Junling Li for the assistance in the Western blot analysis. This research was supported by a training grant from National Institutes of Health (#T32 AR07592) and a research grant MB-8713-08 from United States - Israel Binational Agriculture Research and Development Fund.

Novel antifouling and antimicrobial compound from a marine-derived fungus Ampelomyces sp.

In this study, using a bioassay-guided isolation and purification procedure, we obtained 3-chloro-2,5-dihydroxybenzyl alcohol from a marine-derived Ampelomyces species that effectively inhibited larval settlement of the tubeworm Hydroides elegans and of cyprids of the barnacle Balanus amphitrite. The inhibitive effect on larval settlement was nontoxic and the EC50 of 3-chloro-2,5-dihydroxybenzyl alcohol ranged from 3.19 mu g ml(-1) to 3.81 mu g ml(-1) while the LC50 was 266.68 lambda g ml(-1) for B. amphitrite cyprids; EC50 ranged from 0.67 mu g ml(-1) to 0.78 mu g ml(-1), and LC50 was 2.64 mu g ml(-1) for competent larvae of H. elegans, indicating that inhibitive effect of this compound was nontoxic. At a concentration of 50 mu g per disc, this compound showed strong inhibitive effects on the growth of 13 out of 15 marine bacterial species tested in disc diffusion bioassay. Overall, the high inhibitory activities against bacteria and larval settlement as well as the non- or low-toxic nature of this compound to the barnacle and polychaete larvae suggest this compound could be a potent antifoulant and/or antibiotic.

The Apertospathulidae, a new family of haptorid ciliates (Protozoa, Ciliophora)

We studied the morphology of three rare haptorid ciliates, using live observation and silver impregnation: Apertospathula verruculifera n. sp., Longispatha elegans n. gen., n. sp., and Rhinothrix porculus (Penard, 1922) n. gen., n. comb. Simple ethanol fixation (50-70%, v/v) is recommended to reveal the ciliary pattern of "difficult" ciliates, such as R. porculus, by protargol impregnation. The three genera investigated have a distinct feature in common, viz., a lasso-shaped oral bulge and circumoral kinety, where the right half is slightly to distinctly longer than the left and the circumoral kinety is open ventrally. Thus, they are united in a new spathidiid family, the Apertospathulidae n. fam., which probably evolved from a Bryophyllum-like ancestor by partial reduction of the oral bulge and circumoral kinety. Apertospathula verruculifera has a wart-like process, the palpus dorsalis, at the anterior end of the dorsal brush. The right branch of the circumoral kinety is only slightly longer than the left one. Longispatha elegans has a straight oral bulge and circumoral kinety, the right branch of which extends to the posterior end of the body while the left branch ends in the anterior third of the body. Rhinothrix porculus, a curious ciliate with a snout-like dorsal elongation of the oral bulge, the palpus oralis, has a highly characteristic ciliary pattern: the oral pattern is as in Longispatha, but the bulge and circumoral kinety extend spirally to the posterior end of the body while the somatic kinetics course meridionally. This is achieved by inserting some shortened kinetics in the curves of the oral bulge.

Identification of ribosomal proteins specific to higher eukaryotic organisms

This report describes the identification of a novel protein named PS1D (Genbank accession number ), which is composed of an S1-like RNA-binding domain, a (cysteine)x3-(histidine) CCCH-zinc finger, and a very basic carboxyl domain. PS1D is expressed as two isoforms, probably resulting from the alternative splicing of mRNA. The long PS1D isoform differs from the short one by the presence of 48 additional amino acids at its amino-terminal extremity. Analysis of PS1D subcellular distribution by cell fractionation reveals that this protein belongs to the core of the eukaryotic 60S ribosomal subunit. Interestingly, PS1D protein is a highly conserved protein among mammalians as murine, human, and simian PS1D homologues share more than 95% identity. In contrast, no homologous protein is found in lower eukaryotes such as yeast and Caenorhabditis elegans. These observations indicate that PS1D is the first eukaryotic ribosomal protein that is specific to higher eukaryotes.

Robust test method for time-course microarray experiments.

BACKGROUND: In a time-course microarray experiment, the expression level for each gene is observed across a number of time-points in order to characterize the temporal trajectories of the gene-expression profiles. For many of these experiments, the scientific aim is the identification of genes for which the trajectories depend on an experimental or phenotypic factor. There is an extensive recent body of literature on statistical methodology for addressing this analytical problem. Most of the existing methods are based on estimating the time-course trajectories using parametric or non-parametric mean regression methods. The sensitivity of these regression methods to outliers, an issue that is well documented in the statistical literature, should be of concern when analyzing microarray data. RESULTS: In this paper, we propose a robust testing method for identifying genes whose expression time profiles depend on a factor. Furthermore, we propose a multiple testing procedure to adjust for multiplicity. CONCLUSIONS: Through an extensive simulation study, we will illustrate the performance of our method. Finally, we will report the results from applying our method to a case study and discussing potential extensions.

UNC-6 (netrin) stabilizes oscillatory clustering of the UNC-40 (DCC) receptor to orient polarity.

The receptor deleted in colorectal cancer (DCC) directs dynamic polarizing activities in animals toward its extracellular ligand netrin. How DCC polarizes toward netrin is poorly understood. By performing live-cell imaging of the DCC orthologue UNC-40 during anchor cell invasion in Caenorhabditis elegans, we have found that UNC-40 clusters, recruits F-actin effectors, and generates F-actin in the absence of UNC-6 (netrin). Time-lapse analyses revealed that UNC-40 clusters assemble, disassemble, and reform at periodic intervals in different regions of the cell membrane. This oscillatory behavior indicates that UNC-40 clusters through a mechanism involving interlinked positive (formation) and negative (disassembly) feedback. We show that endogenous UNC-6 and ectopically provided UNC-6 orient and stabilize UNC-40 clustering. Furthermore, the UNC-40-binding protein MADD-2 (a TRIM family protein) promotes ligand-independent clustering and robust UNC-40 polarization toward UNC-6. Together, our data suggest that UNC-6 (netrin) directs polarized responses by stabilizing UNC-40 clustering. We propose that ligand-independent UNC-40 clustering provides a robust and adaptable mechanism to polarize toward netrin.

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.

Regulation of DLK-1 kinase activity by calcium-mediated dissociation from an inhibitory isoform.

MAPKKK dual leucine zipper-bearing kinases (DLKs) are regulators of synaptic development and axon regeneration. The mechanisms underlying their activation are not fully understood. Here, we show that C. elegans DLK-1 is activated by a Ca(2+)-dependent switch from inactive heteromeric to active homomeric protein complexes. We identify a DLK-1 isoform, DLK-1S, that shares identical kinase and leucine zipper domains with the previously described long isoform DLK-1L but acts to inhibit DLK-1 function by binding to DLK-1L. The switch between homo- or heteromeric DLK-1 complexes is influenced by Ca(2+) concentration. A conserved hexapeptide in the DLK-1L C terminus is essential for DLK-1 activity and is required for Ca(2+) regulation. The mammalian DLK-1 homolog MAP3K13 contains an identical C-terminal hexapeptide and can functionally complement dlk-1 mutants, suggesting that the DLK activation mechanism is conserved. The DLK activation mechanism is ideally suited for rapid and spatially controlled signal transduction in response to axonal injury and synaptic activity.

To plasticity and back again.

Both the gain and the loss of flexibility in the development of phenotypes have led to an increased diversity of physical forms in nematode worms.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010

This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp. Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus. © 2010 Blackwell Publishing Ltd.

Notes and memoranda

Callionymus maculatus. Phrynorhombus unimaculatus. Motella cimbria. Sepia elegans. Mysis longicornis. Mysidopsis angusta. Malformation of the mouth in the common sea-bream.

Marine snow studies in the Northeast Atlantic Ocean: distribution, composition and role as a food source for migrating plankton

During a 25 d Lagrangian study in May and June 1990 in the Northeast Atlantic Ocean, marine snow aggregates were collected using a novel water bottle, and the composition was determined microscopically. The aggregates contained a characteristic signature of a matrix of bacteria, cyanobacteria and autotrophic picoplankton with inter alia inclusions of the tintiniid Dictyocysta elegans and large pennate diatoms. The concentration of bacteria and cyanobacteria was much greater on the aggregates than when free-living by factors of 100 to 6000 and 3000 to 2 500 000, respectively, depending on depth. Various species of crustacean plankton and micronekton were collected, and the faecal pellets produced after capture were examined. These often contained the marine snow signature, indicating that these organisms had been consuming marine snow. In some cases, marine snow material appeared to dominate the diet. This implies a food-chain short cut wherby material, normally too small to be consumed by the mesozooplankton, and considered to constitute the diet of the microplankton can become part of the diet of organisms higher in the food-chain. The micronekton was dominated by the amphipod Themisto compressa, whose pellets also contained the marine snow signature. Shipboard incubation experiments with this species indicated that (1) it does consume marine snow, and (2) its gut-passage time is sufficiently long for material it has eaten in the upper water to be defecated at its day-time depth of several hundred meters. Plankton and micronekton were collected with nets to examine their vertical distribution and diel migration and to put into context the significance of the flux of material in the guts of migrants. “Gut flux” for the T. compressa population was calculated to be up to 2% of the flux measured simultaneously by drifting sediment traps and <5% when all migrants are considered. The in situ abundance and distribution of marine snow aggregates (>0.6 mm) was examined photographically. A sharp concentration peak was usually encountered in the depth range 40 to 80 m which was not associated with peaks of in situ fluorescence or attenuation but was just below or at the base of the upper mixed layer. The feeding behaviour of zooplankton and nekton may influence these concentration gradients to a considerable extent, and hence affect the flux due to passive settling of marine snow aggregates.

Historical data reveal power-law dispersal patterns of invasive aquatic species.

Understanding how invasive species spread is of particular concern in the current era of globalisation and rapid environmental change. The occurrence of super-diffusive movements within the context of Lévy flights has been discussed with respect to particle physics, human movements, microzooplankton, disease spread in global epidemiology and animal foraging behaviour. Super-diffusive movements provide a theoretical explanation for the rapid spread of organisms and disease, but their applicability to empirical data on the historic spread of organisms has rarely been tested. This study focuses on the role of long-distance dispersal in the invasion dynamics of aquatic invasive species across three contrasting areas and spatial scales: open ocean (north-east Atlantic), enclosed sea (Mediterranean) and an island environment (Ireland). Study species included five freshwater plant species, Azolla filiculoides, Elodea canadensis, Lagarosiphon major, Elodea nuttallii and Lemna minuta; and ten species of marine algae, Asparagopsis armata, Antithamnionella elegans, Antithamnionella ternifolia, Codium fragile, Colpomenia peregrina, Caulerpa taxifolia, Dasysiphonia sp., Sargassum muticum, Undaria pinnatifida and Womersleyella setacea. A simulation model is constructed to show the validity of using historical data to reconstruct dispersal kernels. Lévy movement patterns similar to those previously observed in humans and wild animals are evident in the re-constructed dispersal pattern of invasive aquatic species. Such patterns may be widespread among invasive species and could be exacerbated by further development of trade networks, human travel and environmental change. These findings have implications for our ability to predict and manage future invasions, and improve our understanding of the potential for spread of organisms including infectious diseases, plant pests and genetically modified organisms.