Läänemere idaosa litoraali kalakoosluste varieeruvus ja selle põhjused

Väitekirja elektrooniline versioon ei sisalda publikatsiooneLitoraalialad on vee-elustikule oluliseks sigimis-, kasvu- ja toitumisalaks. Muutlike abiootiliste ja biootiliste keskkonnategurite koosmõjul varieerub litoraalialade kalakoosluste liigiline koosseis väga suurel määral nii ajas kui ka ruumis. Käesoleva töö eesmärkideks oli välja selgitada: 1) Läänemere litoraali asustavate kalaliikide ööpäevaringseid ja aastasiseseid käitumismustreid; 2) litoraali kalastiku sesoonse toitumisökoloogia eripärad meritindi näitel; 3) anadroomsete kalade (lõhe ja meriforell) noorjärkude alternatiivseid rändestrateegiaid jõgede ja Läänemere litoraalialade vahel. Selgus, et: 1) Läänemere litoraali asustavate kalaliikide ööpäevaringne käitumine on seni kirjeldatust oluliselt mitmetahulisem. Seega, mingi konkreetse litoraali piirkonna ööpäevas muutuva liigilise koosseisu täielikuks kirjeldamiseks on vajalik proovipüükide tegemine nii hommikul, keskpäeval, õhtul kui ka öösel; 2) Läänemere idaosa litoraaliala asustava meritindi toitumiskäitumine erineb avamere elupaikades kirjeldatust; 3) Läänemere riimveelised litoraalialad võivad olla seni arvatust olulisemaks kasvualaks alternatiivseid rändestrateegiaid kasutavatele lõhilaste noorjärkudele; 4) läbi riimvee vooluveekogu vahetavad noorkalad võivad osaliselt olla ka anadroomsete lõhilaste populatsioonides esinevate „eksijate“ varem kirjeldamata tekkemehhanismiks; 5) Läänemere litoraali asustavatel kalaliikidel võib esineda nii piirkonnaspetsiifilisi ööpäevaringseid toitumisrändeid (meritint) kui ka elukäigumustreid (lõhe, meriforell).The shallow littoral is an important reproduction, nursery, and foraging area to coastal marine biota. Due to variability in abiotic and biotic environmental parameters, near-shore fish communities of the Baltic Sea are highly variable. Thus, the occurrence and abundance of fish species may be spatially and temporally highly variable. The objectives of the present thesis were to: 1) assess diel variations in the composition of the fish assemblage in the surf-zone of the non-tidal Baltic Sea; 2) estimate the predatory role of European smelt in a littoral habitat by describing seasonal variation of prey composition; 3) investigate whether littoral zone of the Baltic Sea also function as a habitat for early out-migrating Atlantic salmon and anadromous brown trout (ABT) fry and parr. The main results and conclusions are the following: 1) fine-scale variations in littoral fish assemblages are more complex and may take place within shorter time frame than previously known; 2) European smelt inhabiting littoral areas of the Baltic Sea occupy different ecological niche than smelt in offshore areas; 3) alternative migrations of juvenile salmonids between freshwater and brackish environments indicate that the shallow littoral zone of the Baltic Sea may play a significant role as a permanent or provisional nursery area to these species; 4) the phenomenon of stream shifting through the marine environment may constitute at least one possible mechanism behind the straying behaviour documented during the spawning runs of Atlantic salmon and ABT in the Baltic Sea basin; 5) some coastal fish species inhabiting the Baltic Sea might show sub-basin specific behaviour in terms of their regular diel movements and alternative life history pattern

22.運動負荷時の血小板機能とヘモレオロジー(第636回千葉医学会例会・第3回千葉大学第三内科懇話会)

Additional file 2. Changes of residual nitrate concentration during the experiments

MIG-10 Functions with ABI-1 to Mediate the UNC-6 and SLT-1 Axon Guidance Signaling Pathways

<div><p>Extracellular guidance cues steer axons towards their targets by eliciting morphological changes in the growth cone. A key part of this process is the asymmetric recruitment of the cytoplasmic scaffolding protein MIG-10 (lamellipodin). MIG-10 is thought to asymmetrically promote outgrowth by inducing actin polymerization. However, the mechanism that links MIG-10 to actin polymerization is not known. We have identified the actin regulatory protein ABI-1 as a partner for MIG-10 that can mediate its outgrowth-promoting activity. The SH3 domain of ABI-1 binds to MIG-10, and loss of function of either of these proteins causes similar axon guidance defects. Like MIG-10, ABI-1 functions in both the attractive UNC-6 (netrin) pathway and the repulsive SLT-1 (slit) pathway. Dosage sensitive genetic interactions indicate that MIG-10 functions with ABI-1 and WVE-1 to mediate axon guidance. Epistasis analysis reveals that ABI-1 and WVE-1 function downstream of MIG-10 to mediate its outgrowth-promoting activity. Moreover, experiments with cultured mammalian cells suggest that the interaction between MIG-10 and ABI-1 mediates a conserved mechanism that promotes formation of lamellipodia. Together, these observations suggest that MIG-10 interacts with ABI-1 and WVE-1 to mediate the UNC-6 and SLT-1 guidance pathways.</p> </div

MIG-10 interacts physically with ABI-1.

<p>(A) Diagram of the RNAi screening strategy used to identify ABI-1. A sublibrary of RNAi clones encoding proline-binding domains (SH3, WW, EVH1) was created. Each clone was screened for the ability to phenocopy the HSN ventral guidance defect observed in <i>mig-10</i> loss of function mutants. This strategy led to the identification of ABI-1 as a potential interaction partner for MIG-10. In this study we have utilized the <i>abi-1(tm494)</i> allele, which is predicted to truncate the ABI-1 protein as indicated by the bracket. (B) Example of HSN axon in wild-type animals. The axon makes a direct ventral migration. (C) Example of HSN ventral guidance defect observed in <i>mig-10(RNAi)</i> animals. The axon migrates laterally prior to turning ventrally. (D) Example of HSN ventral guidance defect observed in <i>abi-1(RNAi)</i> animals. The HSN axon was observed with an <i>unc-86::myrGFP</i> transgene. Arrowheads mark approximate position of the vulva. Note that the migration of the HSN cell body was also affected by <i>mig-10(RNAi)</i> and <i>abi-1(RNAi)</i>. However, previous analysis has indicated that HSN axon guidance defects are not secondary consequences of defects in cell body migration <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003054#pgen.1003054-Quinn2" target="_blank">[18]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003054#pgen.1003054-Alexander1" target="_blank">[27]</a>. Scale bars represent 5 µm. (E) MIG-10 binds to the SH3 domain of ABI-1. MIG-10::GFP was incubated with the SH3 domain of ABI-1 fused to GST (GST::ABI-1-SH3) or GST as a control. Bound material was detected by western blotting with an antibody to GFP. For reference, an amount equivalent to 5% of the MIG-10::GFP starting material was run on a gel (5% SM).</p

ABI-1 and WVE-1 mediate outgrowth-promoting activity downstream of MIG-10.

<p>(A) Example of normal ALM neuron with a single anterior axon. (B) Example of ALM multipolar defect caused by transgenic expression of MIG-10A by the <i>mec-4::mig-10a</i> transgene. (C) Loss of function mutations <i>abi-1(tm494)</i> and <i>wve-1(ok3308)</i> suppress MIG-10 transgenic expression phenotype. The <i>max-2(nv162)</i> mutation, a likely null, does not suppress the MIG-10 transgenic expression phenotype. The <i>wve-1(ok3308)</i> mutants were maternally rescued. The AVM axon was visualized with a <i>zdIs5</i> transgene (<i>mec-4::gfp</i>). (D) The <i>abi-1(tm494)</i> loss of function mutation suppresses the AVM multipolar phenotype that results from transgenic expression of MIG-10 in the <i>unc-6; slt-1</i> double null mutant background. *Statistically significant difference compared to wild-type or <i>unc-6; slt-1</i> double mutant, z-test for proportions (p<0.005).</p

ABI-1 mediates the lamellipodia-forming activity of MIG-10 in cultured HEK293 cells.

<p>(A) Example of cell transfected with GFP and control shRNA. (B) Example of cell transfected with MIG-10::GFP and control shRNA. (C) Example of cell transfected with MIG-10::GFP and Abi1 shRNA. (D) Knockdown of Abi1 suppresses the lamellipodia-forming activity of MIG-10. Graph shows the average cell perimeter with lamellipodia. “Ctr.” means cells transfected with scrambled control shRNA. “−” means cells were not transfected with any shRNA. “Abi1” means cells were transfected with the PAV197 shRNA against Abi1. Error bars represent the standard error of the mean. *Bracket indicates statistically significant difference, t-test (p<0.0001). Scale bars are 5 µm.</p

iSulf-Cys: Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids

<div><p>Cysteine S-sulfenylation is an important post-translational modification (PTM) in proteins, and provides redox regulation of protein functions. Bioinformatics and structural analyses indicated that S-sulfenylation could impact many biological and functional categories and had distinct structural features. However, major limitations for identifying cysteine S-sulfenylation were expensive and low-throughout. In view of this situation, the establishment of a useful computational method and the development of an efficient predictor are highly desired. In this study, a predictor iSulf-Cys which incorporated 14 kinds of physicochemical properties of amino acids was proposed. With the 10-fold cross-validation, the value of area under the curve (AUC) was 0.7155 ± 0.0085, MCC 0.3122 ± 0.0144 on the training dataset for 20 times. iSulf-Cys also showed satisfying performance in the independent testing dataset with AUC 0.7343 and MCC 0.3315. Features which were constructed from physicochemical properties and position were carefully analyzed. Meanwhile, a user-friendly web-server for iSulf-Cys is accessible at <a href="http://app.aporc.org/iSulf-Cys/" target="_blank">http://app.aporc.org/iSulf-Cys/</a>.</p></div

Biodegradation of Ethyl Carbamate and Urea with <i>Lysinibacillus sphaericus</i> MT33 in Chinese Liquor Fermentation

It is important to reduce the concentration of ethyl carbamate (EC) in fermented foods. However, controlling the formation of EC and its precursor urea is difficult in spontaneous food fermentation because urea is a natural product of nitrogen metabolism. Biodegradation is a better solution to reduce the concentration of EC. This study aimed to reduce the concentration of EC in Chinese liquor via an indigenous strain <i>Lysinibacillus sphaericus</i> MT33. This strain produced urethanase (940 U/L) and urease (1580 U/L) and degraded 76.52% of EC and 56.48% of urea. After inoculation in liquor fermentation, the maximal relative abundance of <i>Lysinibacillus</i> increased from 0.02% to 8.46%, the final EC and urea contents decreased by 41.77% and 28.15%. Moreover, the concentration of EC decreased by 63.32% in liquor. The negative correlation between abundance of <i>Lysinibacillus</i> and contents of EC and urea indicated the effect of <i>L. sphaericus</i> on EC and urea degradation

A Chemistry-Based Method To Detect Individual Telomere Length at a Single Chromosome Terminus

The understanding of telomeres is expected to provide major insights into genome stability, cancer, and telomere-related diseases. In recent years, there have been considerable improvements in the technologies available to determine the length of telomeres of human chromosomes; however, the present methods for measuring telomere length are fraught with shortcomings that have limited their use. Here we describe a method for detection of individual telomere lengths (DITL) that uses a chemistry-based approach that accurately measures the telomere lengths from individual chromosomes. The method was successfully used to determine telomere DNA by breaking in the target sequence and producing a “real telomere fragment.” The DITL approach involves cleavage of the sequence adjacent to the telomere followed by resolution of the telomere length at the nucleotide level of a single chromosome. Comparison of the DITL method and the traditional terminal restriction fragment (TRF) analysis indicates that the DITL approach appears to be promising for the quantification of telomere repeats in each chromosome and the detection of accurate telomere lengths that can be missed using TRF analysis

Additional file 1: Table S1. of Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multi-carbon co-utilization

Statistics of the SNPs and Indels among the MT1 Chromosomes. Table S2. Annotation of SNPs. Table S3. Annotation of Indels. Table S4. Copy Number Variations (CNVs) between MT1 and S288c. Table S5. Functions of the missed genes. Figure S1. Statistical analysis on the number of contigs with identity <95 % in the amino acid levels. Figure S2. Analysis of two BIO genes present in the LI genome, but not in the S288c genome. A: Schematic organization of two relevant segments from MT1-contig40, S288c-Chr.IX and K7-Chr.IX; B: Dot Matrix Comparison maps of the DNA sequences between BIO1-MT1/BIO6-MT1 and BIO1-Ref/BIO6-Ref; C: Dot Matrix Comparison maps of the protein sequences between BIO1-MT1/BIO6-MT1 and BIO1-Ref/BIO6-Ref. Figure S3. A: Colinearity analysis of Chr. I. The same Locally Collinear Block is represented by same color and vertical lines represent the same LCB; The height of internal vertical lines in LCB on behalf of the level of sequence consistency; Blank in one strain stands for the region does not exist in the other. B: PCR profiles of the 25Kb fragment specific to S288c which was divided into 4 small segments (S1, S2, S3, S4). In addition, 26S rDNA gene was detected as the positive control. M: DNA maker of 5000 bp. (DOC 849 kb