Proteomics-Based Investigation of Different Live Prey Administered to Freshwater Dark Sleeper (Odontobutis potamophila): Examining the Effects on Glycolipids and Energy Metabolism.

Live prey is characterized by balanced rich nutrients and high palatability and is widely used for the seedling cultivation of freshwater dark sleeper (Odontobutis potamophila) larvae. In this study, we evaluated the effects of four groups of paired feeding regimens (group C (Daphnia magna), group L (Limnodrilus hoffmeisteri), group H (Hypophthalmichthys molitrix fry), and group M (mixed groups C, L, and H)) on glycolipid and energy metabolism in O. potamophila larvae. We observed that fatty acid synthase (FAS) and sterol-regulatory-element-binding protein-1 (SREBP-1) mRNA levels were significantly lower in group H when compared to mRNA levels in the other three groups (p < 0.05) and that carnitine palmitoyltransferase 1α (CPT1-α) mRNA levels were significantly lower in group L when compared to group M (p < 0.05). Relative glucokinase (GK) expression levels were significantly lower in group M when compared to the other three groups (p < 0.05). Using proteomics, we analyzed and compared groups H and L and identified 457 differentially expressed proteins (DEPs), of which 151 were significantly up-regulated and 306 were significantly down-regulated. In the comparison of group M with groups C, L, and H, we found significant enrichment in glycolytic processes, the endoplasmic reticulum lumen, NAD binding, intermediate filaments, and nutrient reservoir activity. Our results provide a theoretical guidance for bait selection during larvae cultivation stages in carnivorous fish.

Transcriptome analysis of immune response against Siniperca chuatsi rhabdovirus infection in mandarin fish Siniperca chuatsi.

As one of the piscine rhabdoviruses, Siniperca chuatsi rhabdovirus (SCRV) has caused considerable losses to mandarin fish aquaculture industry. RNA-seq, as efficient transcriptome research method, has been widely used to study the immune response of fish to pathogens. This study reported the effect of SCRV infection at 0, 24 and 60 hr on S. chuatsi at the transcriptome level. A total of 61,527 unigenes with high quality were obtained, and 3,095, 1,854 and 227 differentially expressed genes (DEGs) were labelled between the Sc24 and Sc0 groups, the Sc60 and Sc0 groups and the Sc60 and Sc24 groups, respectively. Genes involved in innate and adaptive immunity were highlighted. In Gene Ontology analysis, the DEGs that participated in immune response, innate immune response and the regulation of apoptotic process were identified as enriched classes. Kyoto Encyclopedia of Genes and Genomes pathway results indicated that most DEGs caused by SCRV infection were identified in the immune system (retinoic acid-inducible gene-I-like receptor/Toll-like receptor/nucleotide-binding oligomerization domain-like receptor/C-type lectin receptor signalling pathway), cellular processes, cell growth and death (p53 signalling pathway, cellular senescence, apoptosis and phagosome), and metabolism. Quantitative real-time PCR was used to further verify the expression levels of 15 immune-related DEGs. The transcriptome database obtained in this study provided further in-depth insight into the immune response of S. chuatsi against SCRV.

A Gram-Negative Bacterial Secreted Protein Types Prediction Method Based on PSI-BLAST Profile.

Prediction of secreted protein types based solely on sequence data remains to be a challenging problem. In this study, we extract the long-range correlation information and linear correlation information from position-specific score matrix (PSSM). A total of 6800 features are extracted at 17 different gaps; then, 309 features are selected by a filter feature selection method based on the training set. To verify the performance of our method, jackknife and independent dataset tests are performed on the test set and the reported overall accuracies are 93.60% and 100%, respectively. Comparison of our results with the existing method shows that our method provides the favorable performance for secreted protein type prediction.

Endoplasmic Reticulum Stress May Play a Pivotal Role in Lipid Metabolic Disorders in a Novel Mouse Model of Subclinical Hypothyroidism.

Subclinical hypothyroidism (SCH) is becoming a global health problem due to its increasing prevalence and potential deleterious effects. However, the molecular mechanisms underlying the lipid metabolic disorders in SCH have not been fully clarified. Additionally, progress in elucidating the exact pathogenesis of SCH has been hampered by the lack of optimized mouse models. Methimazole (MMI) was applied to construct a noninvasive SCH mouse model. Eight-week-old C57BL/6 mice were administrated MMI through the drinking water. After 12 weeks, the MMI-treated mice showed the diagnostic criteria for SCH: increased serum thyrotropin (TSH) levels with constant thyroid hormone levels that persisted for approximately 8 weeks. Notably, SCH mice presented evident lipid metabolic disturbances, including dyslipidemia and hepatic lipid accumulation. Further analysis showed that hepatic endoplasmic reticulum stress (ER stress) was induced in the SCH mice or by the elevation of TSH in vitro, likely via the IRE1α/XBP-1 pathway. Interestingly, when we used 4-phenyl butyric acid to repress ER stress in SCH mice for 4 weeks, dyslipidemia and hepatic lipid accumulation were both significantly alleviated. Our findings indicate that an optimized SCH mouse model could be established using MMI, and ER stress may play a pivotal role in the lipid metabolic abnormalities in SCH.

A protein structural classes prediction method based on PSI-BLAST profile.

Knowledge of protein structural classes plays an important role in understanding protein folding patterns. Prediction of protein structural class based solely on sequence data remains to be a challenging problem. In this study, we extract the long-range correlation information and linear correlation information from position-specific score matrix (PSSM). A total of 3600 features are extracted, then, 278 features are selected by a filter feature selection method based on 1189 dataset. To verify the performance of our method (named by LCC-PSSM), jackknife tests are performed on three widely used low similarity benchmark datasets. Comparison of our results with the existing methods shows that our method provides the favorable performance for protein structural class prediction. Stand-alone version of the proposed method (LCC-PSSM) is written in MATLAB language and it can be downloaded from http://bioinfo.zstu.edu.cn/LCC-PSSM/.

A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile.

Knowledge of protein secondary structural classes plays an important role in understanding protein folding patterns. In this paper, 25 features based on position-specific scoring matrices are selected to reflect evolutionary information. In combination with other 11 rational features based on predicted protein secondary structure sequences proposed by the previous researchers, a 36-dimensional representation feature vector is presented to predict protein secondary structural classes for low-similarity sequences. ASTRALtraining dataset is used to train and design our method, other three low-similarity datasets ASTRALtest, 25PDB and 1189 are used to test the proposed method. Comparisons with other methods show that our method is effective to predict protein secondary structural classes. Stand alone version of the proposed method (PSSS-PSSM) is written in MATLAB language and it can be downloaded from http://letsgob.com/bioinfo_PSSS_PSSM/.

A simple k-word interval method for phylogenetic analysis of DNA sequences.

In this study, the normalized k-word average interval distance is proposed to extract phylogenetic information from DNA sequences. The phylogenetic trees of 30 mammalian species based on Euclidean distance measure are reconstructed with k ranging from 2 to 9. Comparison of our results with other methods shows that our method is efficient and powerful for phylogenetic analysis. In addition, for a fixed k, 4(k) distinct k-words are divided into n classes based on a new proposed indicator, where n is the number of DNA sequences. The effect of each k-word class on phylogeny is discussed.

A novel protein structural classes prediction method based on predicted secondary structure.

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E-H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between α/ß class and α + ß class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate α/ß and α + ß classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from http://web.xidian.edu.cn/slzhang/paper.html.

Comparative study on the toxicity of pyrethroids, α-cypermethrin and deltamethrin to Ceriodaphnia dubia.

Two synthetic pyrethroid pesticides, α-cypermethrin and deltamethrin were investigated as potential toxic contaminants. The acute and chronic bioassays were conducted using Ceriodaphnia dubia. The toxicity of α-cypermethrin and deltamethrin to C. dubia increased with increasing concentrations and exposure time. C. dubia was three times more sensitive to deltamethrin than to α-cypermethrin with 48-h EC(50) of 0.06 µg/L and 0.23 µg/L, respectively. The chronic EC(50) values for α-cypermethrin and deltamethrin were 97.8 and 34.7 ng/L, respectively. Eight-day growth of Ceriodaphnia neonates during chronic exposures was the most sensitive endpoint measured in comparison to the endpoints of survival and number of neonates produced. To gain a better understanding of the link between acute and chronic toxicity, the acute-to chronic ratios (ACRs) were also calculated for survival, growth and reproduction endpoints. ACRs varied between 11 and 224 for the two pyrethroids. These results suggest that at environmentally relevant low concentrations, α-cypermethrin and deltamethrin could have significant adverse effects on the survival, reproduction and growth of C. dubia.

High-accuracy prediction of protein structural class for low-similarity sequences based on predicted secondary structure.

Information on the structural classes of proteins has been proven to be important in many fields of bioinformatics. Prediction of protein structural class for low-similarity sequences is a challenge problem. In this study, 11 features (including 8 re-used features and 3 newly-designed features) are rationally utilized to reflect the general contents and spatial arrangements of the secondary structural elements of a given protein sequence. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark datasets, 1189 and 25PDB with sequence similarity lower than 40% and 25%, respectively. Comparison of our results with other methods shows that our proposed method is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity datasets.

A simple feature representation vector for phylogenetic analysis of DNA sequences.

In this study, a simple 4k-dimension feature representation vector is proposed to reconstruct phylogenetic trees, where k is the length of a word. The vector is composed of elements which characterize the relative difference of biological sequence from sequence generated by an independent random process. In addition, the variance of a vector which is obtained by averaging every column of feature representation matrix is employed to determine appropriate word length. In our experiments, reliable results can always be generated when word length is < 7 which appears to be of lower computational complexity. Phylogenetic trees of 24 transferrins and 48 Hepatitis E viruses reconstructed at word length 6 are in good agreements with previous study, it shows that our method is efficient and powerful.

Risk to humans of consuming metals in anchovy (Coilia sp.) from the Yangtze River Delta.

Concentrations of metals were determined in four species of anchovy (Coilia sp.) from the Yangtze River, Taihu Lake, and Hongze Lake in Jiangsu Province, China. Concentrations of Cr in anchovy fish muscle ranged from 2.6 × 10(-2) to 5.0 mg/kg ww, and Coilia nasus taihuensis in Jiaoshan, Taihu Lake contained the highest concentrations of Cr, which was almost 111-fold higher than the mean value at other locations. Concentrations of Pb ranged from 1.5 × 10(-2) to 1.3 × 10(-1) mg/kg ww. Comparisons of concentrations of lead (Pb) among the four species indicated that anadromous species contained higher concentrations of Pb than did freshwater species. However, concentrations of Pb in C. nasus from the Nanjing and Haimen locations in the Yangtze River were not significant higher than those of two freshwater species: C. nasus taihuensis from Taihu Lake and C. brachygnathus from Hongze Lake (Duncan's test, α = 0.05). While concentrations of Cd and Zn ranged from 7.0 × 10(-4) to 3.6 × 10(-3) mg/kg ww and 3.4 to 4.8 mg/kg ww, respectively, there were no significant differences in concentrations among the eight locations. The only concentration of the metals studied that exceeded the Chinese National Standard was Cr in Coilia from Jiaoshan, Taihu Lake, which was 2.5-fold higher than the standard. These results indicate that people who consume the genus Coilia are not at risk due to concentrations of metals, except Cr in C. nasus taihuensis from Jiaoshan in Taihu Lake. Concentrations of all of the metals studied except for Cr were similar to or less than those of metals in most other areas in the world.

RETARDED PALEA1 controls palea development and floral zygomorphy in rice.

Poaceae, one of the largest flowering plant families in angiosperms, evolved distinct inflorescence and flower morphology diverging from eudicots and other monocots. However, the mechanism underlying the specification of flower morphology in grasses remains unclear. Here we show that floral zygomorphy along the lemma-palea axis in rice (Oryza sativa) is partially or indirectly determined by the CYCLOIDEA (CYC)-like homolog RETARDED PALEA1 (REP1), which regulates palea identity and development. The REP1 gene is only expressed in palea primordium during early flower development, but during later floral stages is radially dispersed in stamens and the vascular bundles of the lemma and palea. The development of palea is significantly retarded in the rep1 mutant and its palea has five vascular bundles, which is similar to the vascular pattern of the wild-type lemma. Furthermore, ectopic expression of REP1 caused the asymmetrical overdifferentiation of the palea cells, altering their floral asymmetry. This work therefore extends the function of the TCP gene family members in defining the diversification of floral morphology in grasses and suggests that a common conserved mechanism controlling floral zygomorphy by CYC-like genes exists in both eudicots and the grasses.

Long-term cryopreservation of sperm from Mandarin fish Siniperca chuatsi.

In order to develop cryopreservation techniques for long-term preserving the sperm of Mandarin fish Siniperca chuatsi, we examined the effects of various extender and cryopreservation on post-thaw motility. We found the optimal freezing procedures for the Mandarin fish sperm is diluting the semen in D-15 extender, chilling it to 4 degrees C, adding ME2SO to a final concentration of 10% (v/v), then transferring the semen in cryotubes, holding the cryotubes for 10 min at 6 cm (about -180 degrees C) above the surface of liquid nitrogen, for 5 min on the surface of liquid nitrogen, and finally plunged into liquid nitrogen. After thawed at 37 degrees C for 60s, the sperm had the highest post-thaw motility (96.00+/-1.73%). The optimal fertilization procedures for the frozen sperm is mixing the eggs with sperm, then adding 1 ml of swimming medium (SM=45 mM NaCl+5 mM KCl+20mM Tris-HCl, pH 8.0) immediately. At the sperm/egg ratio of 100,000:1, the fertilization rate and the hatching rate of the frozen sperm cryopreserved for 1 week or 1 year in liquid nitrogen (66.01+/-5.14% and 54.76+/-4.40% & 62.97+/-14.28% and 52.58+/-11.17%) were similar to that of fresh sperm (69.42+/-8.11% and 59.82+/-5.27%) (p>0.05). This is the first report that the Mandarin fish (S. chuatsi) sperm can successfully fertilized eggs after long-term cryopreservation.

[Genetic analysis and mapping of the rice leafy-hull mutant Oslh].

Oslh (lh=leafy hull), in the japonica cultivar 9522 background, a mutant of Oryza sativa L. spp. japonica cv. 9522 identified from an M(2) population, was mutagenized by irradiation with (60)Co gamma-ray. The Oslh mutant plants flowered about 15 days later than the wild-type plants (Fig.1e). The paleas, lemmas and lodicules of the flowers of Oslh mutant were transformed into leaf-like structures (Fig.1b, d). Genetic analysis of the F(2) progeny from a cross between the Oslh mutant and wild-type japonica cv. 9522 revealed that the Oslh mutant arouse from a single recessive nuclear gene mutation of the cv. 9522. To map the Oslh locus, an F(2) population generated by crossing between Oslh (japonica) mutant and Guangluai4 (indica) was analyzed. The Oslh locus was mapped to the long arm of rice chromosome 3, between a SSR marker RM5475 and an InDel marker GY305, 2.9 and 1.5 cM away from these two markers respectively (Fig.4). These results are useful for further cloning and functional analysis of the OsLH gene.