The Effects of Larval Cryopreservation on the Epigenetics of the Pacific Oyster Crassostrea gigas.

High mortalities and highly variable results during the subsequent development of post-thaw larvae have been widely considered as key issues restricting the application of cryopreservation techniques to support genetic improvement programs and hatchery production in farmed marine bivalve species. To date, few studies have been undertaken to investigate the effects of cryodamage at the molecular level in bivalves. This study is the first to evaluate the effect of larval cryopreservation on the epigenetics of the resultant progenies of the Pacific oyster Crassostrea gigas. The results show that the level of DNA methylation was significantly (p < 0.05) higher and lower than that of the control when the trochophore larvae were revived and when they developed to D-stage larvae (day 1 post-fertilization), respectively, but the level returned to the control level from day 8 post-fertilization onwards. The expression of the epigenetic regulator genes DNMT3b, MeCP2, JmjCA, KDM2 and OSA changed significantly (p < 0.05) when the trochophore larvae were thawed, and then they reverted to the control levels at the D- and later larval developmental stages. However, the expression of other epigenetic regulator genes, namely, MBD2, DNMT1, CXXC1 and JmjD6, did not change at any post-thaw larval developmental stage. For the newly thawed trochophore larvae, the amount of methylated H3K4Me1 and H3K27Me1 significantly changed, and the expression of all Jumonji orthologs, except that of Jumonji5, significantly (p < 0.05) decreased. These epigenetic results agree with the data collected on larval performances (e.g., survival rate), suggesting that the effect period of the published cryopreservation technique on post-thaw larvae is short in C. gigas.

Comparison of the gut microbiota and untargeted gut tissue metabolome of Chinese mitten crabs (Eriocheir sinensis) with different shell colors.

Introduction: The Chinese mitten crab (Eriocheir sinensis) is a highly valued freshwater crustacean in China. While the natural shell color of E. sinensis is greenish brown (GH), we found a variety with a brownish-orange shell color (RH). Although RH is more expensive, it exhibits a lower molting frequency and growth rate compared with GH, which significantly reduces its yield and hinders large-scale farming. The growth and development of animals are closely related to their gut microbiota and gut tissue metabolic profiles. Methods: In this study, we compared the gut microbiome communities and metabolic profiles of juvenile RH and GH crabs using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Results: Our findings indicated that the intestinal microbial composition and metabolic characteristics of E. sinensis differed significantly between RH and GH. At the operational taxonomic unit (OTU) level, the α-diversity of the gut microbiota did not differ significantly between RH and GH, while the ß-diversity of the RH gut microbiota was higher than that of the GH gut microbiota. At the species level, the richness of unclassified_c_Alphaproteobacteria was significantly higher in the GH group, while the RH group had a significantly higher richness of three low-abundance species, Flavobacteria bacterium BAL38, Paraburkholderia ferrariae, and uncultured_bacterium_g__Legionella. In the current study, 598 gut tissue metabolites were identified, and 159 metabolites were significantly different between GH and RH. The metabolite profile of RH was characteristic of a low level of most amino acids and lipid metabolites and a high level of several pigments compared with that of GH. These metabolites were enriched in 102 KEGG pathways. Four pathways, including (1) Central carbon metabolism in cancer, (2) protein digestion and absorption, (3) alanine, aspartate and glutamate metabolism, and (4) aminoacyl-tRNA biosynthesis, were significantly enriched. The correlation analysis between metabolites and microbiotas indicated that most key differential metabolites were positively correlated with the abundance of Shewanella_sp_MR-7. Discussion: This research provided a greater understanding of the physiological conditions of E. sinensis varieties with different shell colors by comparing the gut microbiota and gut tissue metabolome.

New insights into inflammatory memory of epidermal stem cells.

Inflammatory memory, as one form of innate immune memory, has a wide range of manifestations, and its occurrence is related to cell epigenetic modification or metabolic transformation. When re-encountering similar stimuli, executing cells with inflammatory memory function show enhanced or tolerated inflammatory response. Studies have identified that not only hematopoietic stem cells and fibroblasts have immune memory effects, but also stem cells from various barrier epithelial tissues generate and maintain inflammatory memory. Epidermal stem cells, especially hair follicle stem cells, play an essential role in wound healing, immune-related skin diseases, and skin cancer development. In recent years, it has been found that epidermal stem cells from hair follicle can remember the inflammatory response and implement a more rapid response to subsequent stimuli. This review updates the advances of inflammatory memory and focuses on its mechanisms in epidermal stem cells. We are finally looking forward to further research on inflammatory memory, which will allow for the development of precise strategies to manipulate host responses to infection, injury, and inflammatory skin disease.

The Complete Mitochondrial Genome of Torix tukubana (Annelida: Hirudinea: Glossiphoniidae).

Torix tukubana is a poorly understood proboscidate leech species, generally an ectoparasite on amphibian species. In this study, the complete mitochondrial genome (mitogenome) of T. tukubana was sequenced using next-generation sequencing (NGS), and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the T. tukubana mitogenome was 14,814 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (CR). The mitogenome composition presented a strong A + T bias (73.6%). All tRNAs had the typical clover structure except the trnS1 (TCT), whose dihydrouridine (DHU) arm was short, having only one complementary base pair. Additionally, 8 gene order patterns were identified among 25 known Hirudinea species, and T. tukubana was identical to the Hirudinea ground pattern. A phylogenetic analysis based on 13 PCGs indicated that all the studied species clustered into three main clades. The relationships among Hirudinea species were basically consistent with their gene arrangement results, but different from their morphological taxonomy. T. tukubana was in the monophyletic group of Glossiphoniidae, a finding consistent with previous research. Our results provided the essential characteristics of the T. tukubana mitogenome. As the first complete mitogenome of Torix, it could offer valuable information for a systematic understanding of the Hirudinea species.

Genetic Diversity of Four Populations of Silver Carp (Hypophthalmichthys molitrix) Based on Mitochondrial Sequences.

Three mitochondrial DNA sequences (COI, ATP 8&6, and D-loop) were employed to assess the genetic diversity of four populations of silver carp from three main drainages in China, including the Yangtze River, the Amur River, and the Pearl River. As a result, 98 haplotypes were identified in combined sequences of COI, ATP8&6, and D-loop. A total of 196 variable sites and 116 parsimony-informative sites were observed. AMOVA based on assembled sequences indicated that 12.12% of the variation was among populations, while 87.88% of the variation was within populations. Additionally, the phylogenetic relationships of populations were depicted in a phylogenetic tree based on assembled sequences. Mismatch distribution analysis and the negative significant Fu's Fs values supported population expansion in all populations. Despite the high level of genetic diversity, the establishment of a state-level original breeding farm in the Amur River basin and the Pearl River basin may be an effective conservation strategy for the protection of local unique haplotypes.

Neuroprotective investigation of tanshinone in the cerebral infarction model in the Keap1-Nrf2/ARE pathway.

It was to investigate the neuroprotective mechanism of tanshinone after cerebral infarction via the Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant reaction element (ARE) signaling pathway. Forty specific pathogen-free (SPF) Sprague Dawley (SD) rats were selected, all of which were male, approximately seven weeks old, weighing 250 ± 25 g. They were randomly divided into a model group, a non-model operation group, a positive control group, and an experimental group with ten SD rats in each group. The model of cerebral infarction in rats was established by the wire occlusion method. The model group and non-model operation group (control group) were injected with normal saline daily, the negative control group was injected with Keap1 gene inhibitor daily, and the experimental group was injected with tanshinone IIA (10 mg·kg-1·d-1) daily. Animal behavior analysis was performed on the 7th day after the operation, and pathology and the neuroprotective effects of tanshinone IIA on cells were assessed, including cell proliferation, autophagy, oxidative damage, and mitochondrial membrane permeability. The neuroprotective mechanism based on the Keap1-Nrf2/ARE pathway was explored and analyzed. Compared with the model group, the number of Keap1 proteins in the experimental group and the control group was substantially reduced (P < 0.05), and the experimental group was substantially different from the model group (P < 0.01). The protein expression of Nrf2, HO-1, and NQO1 increased substantially (P < 0.05), and the experimental group was substantially different from the model group (P < 0.01). In summary, tanshinone IIA promoted the proliferation of nerve cells, inhibited the production of cellular reactive oxygen species, inhibited the change in mitochondrial membrane potential, and activated the Keap1-Nrf2/ARE signaling pathway. It also induced and regulated the upregulation of downstream NQO1, HO-1, etc. and protected cells from cerebral infarction.

Concomitant Medication Use With Xiyanping Injection and the Risk of Suspected Allergic Reactions: A Nested Case-Control Study Based on China's National Medical Insurance Database.

Introduction: Xiyanping injection (XYP), a type of Traditional Chinese Medicine, is widely used and often applied in combination with other medications in treating bronchitis, tonsillitis, and bacillary dysentery in China. In recent years, an elevated risk of allergic reactions has been observed following XYP, but whether concomitant medication use contributes to this risk is still unknown. Objective: This study aims to investigate the association between the concomitant use of XYP and the 25 most frequently co-applied medications with suspected allergic reactions for China's patients receiving XYP. Methods: A nested case-control study was conducted using the sampling data from 2015 China's Urban Employees Basic Medical Insurance and Urban Residents Basic Medical Insurance database. Four anti-allergic marker drugs were used to evaluate suspected allergic reactions. Univariate analyses and multivariable conditional logistic regression were conducted, and results were reported as odds ratios (ORs) with a 95% confidence interval (CI). Sensitivity analyses were performed on the expanded sample by including those prescribed with anti-allergic marker drugs on the same day as XYP and then stopped XYP on the next day. Results: Out of 57,612 participants with XYP prescription, we obtained 949 matched case-control pairs. Multivariable conditional logistic regression revealed that seven concomitant medications including gentamicin [OR = 4.29; 95% CI (2.52, 7.30)], cefoperazone-sulbactam [OR = 4.26; 95% CI (1.40, 13.01)], lidocaine [OR = 2.76; 95% CI (1.79, 4.25)], aminophylline [OR = 1.73; 95% CI (1.05, 2.85)], ribavirin [OR = 1.54; 95% CI (1.13, 2.10)], potassium chloride [OR = 1.45; 95% CI (1.10, 1.91)], and vitamin C [OR = 1.32; 95% CI (1.03, 1.70)] were associated with increased risk, while cefathiamidine [OR = 0.29; 95% CI (0.16, 0.51)] was associated with reduced risk. Sensitivity analysis on 2,438 matched pairs revealed similar findings. Conclusion: Increased risks for suspected allergic reactions were found for the concomitant use of XYP with seven medications. Our data suggest that gentamicin, cefoperazone-sulbactam, lidocaine, and ribavirin should be applied with precautions for patients receiving XYP, and further studies on drug interactions and allergy mechanisms are warranted.

Talaromarins A-F: Six New Isocoumarins from Mangrove-Derived Fungus Talaromyces flavus TGGP35.

Six new isocoumarin derivative talaromarins A-F (1-6), along with 17 known analogues (7-23), were isolated from the mangrove-derived fungus Talaromyces flavus (Eurotiales: Trichocomaceae) TGGP35. Their structures were identified by detailed IR, UV, 1D/2D NMR and HR-ESI-MS spectra. The absolute configurations of new compounds were determined by the modified Mosher's method and a comparison of their CD spectra with dihydroisocoumarins described in the literature. The antioxidant, antibacterial, anti-phytopathogenic and inhibitory activity against α-glucosidase of all the isolated compounds were tested. Compounds 6-11, 17-19 and 21-22 showed similar or better antioxidant activity than the IC50 values ranging from 0.009 to 0.27 mM, compared with the positive control trolox (IC50 = 0.29 mM). Compounds 10, 18, 21 and 23 exhibited strong inhibitory activities against α-glucosidase with IC50 values ranging from 0.10 to 0.62 mM, while the positive control acarbose had an IC50 value of 0.5 mM. All compounds showed no antibacterial or anti-phytopathogenic activity at the concentrations of 50 µg/mL and 1 mg/mL, respectively. These results indicated that isocoumarins will be useful to developing antioxidants and as diabetes control agents.

Activation of GIPR Exerts Analgesic and Anxiolytic-Like Effects in the Anterior Cingulate Cortex of Mice.

Background: Chronic pain is defined as pain that persists typically for a period of over six months. Chronic pain is often accompanied by an anxiety disorder, and these two tend to exacerbate each other. This can make the treatment of these conditions more difficult. Glucose-dependent insulinotropic polypeptide (GIP) is a member of the incretin hormone family and plays a critical role in glucose metabolism. Previous research has demonstrated the multiple roles of GIP in both physiological and pathological processes. In the central nervous system (CNS), studies of GIP are mainly focused on neurodegenerative diseases; hence, little is known about the functions of GIP in chronic pain and pain-related anxiety disorders. Methods: The chronic inflammatory pain model was established by hind paw injection with complete Freund's adjuvant (CFA) in C57BL/6 mice. GIP receptor (GIPR) agonist (D-Ala2-GIP) and antagonist (Pro3-GIP) were given by intraperitoneal injection or anterior cingulate cortex (ACC) local microinjection. Von Frey filaments and radiant heat were employed to assess the mechanical and thermal hypersensitivity. Anxiety-like behaviors were detected by open field and elevated plus maze tests. The underlying mechanisms in the peripheral nervous system and CNS were explored by GIPR shRNA knockdown in the ACC, enzyme-linked immunosorbent assay, western blot analysis, whole-cell patch-clamp recording, immunofluorescence staining and quantitative real-time PCR. Results: In the present study, we found that hind paw injection with CFA induced pain sensitization and anxiety-like behaviors in mice. The expression of GIPR in the ACC was significantly higher in CFA-injected mice. D-Ala2-GIP administration by intraperitoneal or ACC local microinjection produced analgesic and anxiolytic effects; these were blocked by Pro3-GIP and GIPR shRNA knockdown in the ACC. Activation of GIPR inhibited neuroinflammation and activation of microglia, reversed the upregulation of NMDA and AMPA receptors, and suppressed the enhancement of excitatory neurotransmission in the ACC of model mice. Conclusions: GIPR activation was found to produce analgesic and anxiolytic effects, which were partially due to attenuation of neuroinflammation and inhibition of excitatory transmission in the ACC. GIPR may be a suitable target for treatment of chronic inflammatory pain and pain-related anxiety.

Visualising the Emerging Platform of Using Microalgae as a Sustainable Bio-Factory for Healthy Lipid Production through Biocompatible AIE Probes.

Nowadays, a particular focus is using microalgae to get high-valued health beneficiary lipids. The precise localisation of the lipid droplets (LDs) and biochemical changes are crucial to portray the lipid production strategy in algae, but it requires an in vivo tool to rapidly visualise LD distribution. As a novel strategy, this study focuses on detecting lipid bioaccumulation in a green microalga, Chlamydomonas reinhardtii using the aggregation-induced emission (AIE) based probe, 2-DPAN (C24H18N2O). As the messenger molecule and stress biomarker, hydrogen peroxide (H2O2) activity was detected in lipid synthesis with the AIE probe, TPE-BO (C38H42B2O4). Distinctive LDs labelled with 2-DPAN have elucidated the lipid inducing conditions, where more health beneficiary α-linolenic acid has been produced. TPE-BO labelled H2O2 have clarified the involvement of H2O2 during lipid biogenesis. The co-staining procedure with traditional green BODIPY dye and red chlorophyll indicates that 2-DPAN is suitable for multicolour LD imaging. Compared with BODIPY, 2-DPAN was an efficient sample preparation technique without the washing procedure. Thus, 2-DPAN could improve traditional fluorescent probes currently used for lipid imaging. In addition, the rapid, wash-free, multicolour AIE-based in vivo probe in the study of LDs with 2-DPAN could advance the research of lipid production in microalgae.

Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene.

BACKGROUND: Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding. METHODS: Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package. RESULTS: Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others. CONCLUSIONS: Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

Microalgae-Derived Health Supplements to Therapeutic Shifts: Redox-Based Study Opportunities with AIE-Based Technologies.

Reactive oxygen species (ROS) are highly reactive molecules, serve the normal signaling in different cell types. Targeting ROS as the chemical signals, different stress based strategies have been developed to synthesis different anti-inflammatory molecules in microalgae. These molecules could be utilized as health supplements in human. To provoke the ROS-mediated defence systems, their connotation with the associated conditions must be well understood, therefore, proper tools for studying ROS in natural state are essential. The in vivo detection of ROS with phosphorescent probes offers promising opportunities to study these molecules in a non-invasive manner. Most of the common problems in the traditional fluorescent probes are lower photostability, excitation intensity, slow responsiveness, and the microenvironment that challenge their performance. Some ROS-specific aggregationinduced emission luminogens (AIEgens) with pronounced spatial and temporal resolution have recently demonstrated high selectivity, rapid responsiveness, and efficacies to resolve the aggregation-caused quenching issues. The nanocomposites of some AIE-photosensitizers can also improve the ROS-mediated photodynamic therapy. These AIEgens could be used to induce bioactive components in microalgae through altering the ROS signaling, therefore are more auspicious for biomedical research. This study reviews the prospects of AIEgen-based technologies to understand the ROS mediated bio-physiological processes in microalgae for better healthcare benefits.

One new α,ß-unsaturated 7-ketone sterol from the mangrove-derived fungus Phomopsis sp.MGF222.

A new α,ß-unsaturated 7-ketone sterol, 5ß,6ß-epoxy-3ß, 15α-dihydroxy-(22E,24R)-ergosta-8(14),22-dien-7-one (1), along with five known sterone derivatives, 5ß,6ß-epoxy-3ß,7α-dihydroxy-(22E,24R)-ergosta-8(14),22-dien-15-one (2), 5ß,6ß-epoxy-3ß,7α,9α-trihydroxy-(22E,24R)-ergosta-8(14),22-dien-15-one (3), 3ß,9α,15α-trihydroxy-(22E,24R)-10(5→4)-abeo-ergosta-6,8(14),22-trien-5-one (4), 3,15-dihydroxyl-(22E,24R)-ergosta-5,8(14),22-trien-7-one (5) and (22E,24R)-ergosta-4,6,8(14),22-tetraen-3,15-dione (6) were isolated from the mangrove-derived fungus Phomopsis sp. MGF222. Their structures were established on the basis of extensive spectroscopic data and comparison with the data of literature. Compound 2 showed weak antibacterial activity against Micrococcus tenuis with the MIC value of 28.2 (±0.52) µM. Compound 5 exhibited moderate antibacterial activity against Staphylococcus aureus with the MIC value of 14.6 (±0.47) µM.

Antioxidant activities of Clerodendrum cyrtophyllum Turcz leaf extracts and their major components.

This study was designed to investigate the antioxidant properties of the extracts and subfractions of various polarities from Clerodendrum cyrtophyllum Turcz leaves and the related phenolic compound profiles. The ethyl acetate fraction (EAF) showed the most potent radical-scavenging activity for DPPH radicals, ABTS radicals, and superoxide anion (O2·-) radicals as well as the highest reducing power of the fractions tested; the n-butyl alcohol fraction (BAF) was the most effective in scavenging hydroxyl radical (OH·), and the dichloromethane fraction (DMF) exhibited the highest ferrous ion chelating activity. Twelve phenolic components were identified from the EAF of C. cyrtophyllum. Additionally, acteoside (1) was found to be a major component (0.803 g, 0.54%) and show DPPH and ABTS radical scavenging activities with IC50 values of 79.65±3.4 and 23.00±1.5 µg/ml, indicating it is principally responsible for the significant total antioxidant effect of C. cyrtophyllum. Our work offers a theoretical basis for further utilization of C. cyrtophyllum as a potential source of natural, green antioxidants derived from plants.

Pharmacogenetic association of bi- and triallelic polymorphisms of SLC6A4 with antidepressant response in major depressive disorder.

BACKGROUND: Antidepressants (ADs) are the main clinical therapy for depression, but approximately half of users do not get adequate response. The biallelic (5-HTTLPR) and triallelic (5-HTTLPR/rs25531) polymorphisms in SLC6A4 have been frequently investigated, but their associations with ADs response are in controversy. Here, we performed a meta-analysis to assess their modulation effect to ADs response in major depressive disorder (MDD). METHODS: We performed literature search in PubMed, Web of Science and EMBASE before June 2019. Pooled analysis of genetic associations with response and remission, meta-regression and sensitivity analysis were performed, and publication bias was assessed. RESULTS: Literature search yielded 49 eligible studies with 46 and 10 studies for biallelic and triallelic polymorphism, respectively. L allele of 5-HTTLPR was associated with both of response and remission rates. In the Caucasians using SSRIs only, carriers of LL/LS or LL genotype were more likely to be responders compared to SS carriers (LL/LS vs. SS: OR=1.55, 95%CI 1.20-2.00, p=0.001; LL vs. SS: OR=1.97, 95%CI 1.45-2.67, p<0.001). Similar associations were also found with remission rate. However, no effects on response or remission were found in the Asians or mixed/other antidepressant subgroups. Additionally, the 5-HTTLPR/rs25531 triallelic polymorphism may not associate with ADs response. Meta-regression showed that percent of female in participants, year of publication and treatment duration modulated the association in Caucasians. CONCLUSION: 5-HTTLPR, instead of 5-HTTLPR/rs25531 triallelic polymorphism, may exert as a marker for the prediction of response to SSRIs in Caucasians with MDD.

Discovery and SARs of 5-Chloro-N4-phenyl-N2-(pyridin-2-yl)pyrimidine-2,4-diamine Derivatives as Oral Available and Dual CDK 6 and 9 Inhibitors with Potent Antitumor Activity.

Cyclin-dependent kinases (CDKs) are promising therapeutic targets for cancer therapy. Herein, we describe our efforts toward the discovery of a series of 5-chloro-N4-phenyl-N2-(pyridin-2-yl)pyrimidine-2,4-diamine derivatives as dual CDK6 and 9 inhibitors. Intensive structural modifications lead to the identification of compound 66 as the most active dual CDK6/9 inhibitor with balancing potency against these two targets and good selectivity over CDK2. Further biological studies revealed that compound 66 was directly bound to CDK6/9, resulting in suppression of their downstream signaling pathway and inhibition of cell proliferation by blocking cell cycle progression and inducing cellular apoptosis. More importantly, compound 66 significantly inhibited tumor growth in a xenograft mouse model with no obvious toxicity, indicating the promising therapeutic potential of CDK6/9 dual inhibitors for cancer treatment. Therefore, the above results are of great importance in the development of dual CDK6/9 inhibitors for cancer therapy.

Comparative analysis of transcriptomes from different coloration of Chinese mitten crab Eriocheir sinensis.

Chinese mitten crab Eriocheir sinensis is probably the most important freshwater cultured crab in China. A tiny minority of brownish-orange individuals have been discovered in the long period of artificial breeding history of E. sinensiss. Those mutants are usually accompanied with slow growth rate, low molting frequency and poor survival rate, which may be the results of growth defects and immunodeficiency. To better understand the relationship between body color determination and the immune system as well as the related genes expression in E. sinensiss, we performed the whole-body transcriptome analysis in different color of first stage zoea (ZI) larvae using next-generation sequencing (NGS) technology. We randomly assembled 175.40 and 177.52million clean reads from the wild and mutant ZIs, respectively. Finally, we identified 7153 differentially expressed genes (DEGs) (p < 0.05), with 5194 up-regulated and 1959 down-regulated. A total of 13 KEGG pathways related to immune system were detected among 248 pathways. Except the first whole-body RNA sequencing of color-specific transcriptomes for E. sinensis, this study will offer a better understanding of the underlying molecular mechanisms of interaction between color determination and the immune system.

Group sequential comparison of positive predictive value curves for correlated biomarker data.

Clinical studies of predictive diagnostic tests consider the evaluation of a single test and comparison of two tests regarding their predictive accuracy of disease status. The positive predictive value (PPV) curve is used for assessing the probability of predicting the disease given a positive test result. The sequential property of one PPV curve had been studied. However, in later stages of diagnostic test development, it is more interesting to compare predictive accuracy of two tests. In this article, we propose a group sequential test for the comparison of PPV curves for paired designs when both diagnostic tests are applied to the same subject. We first derive asymptotic properties of the sequential differences of two correlated empirical PPV curves under the common case-control sampling. We then apply these results to develop a group sequential test procedure. The asymptotic results are also critical for deriving both the optimal sample size ratio and minimal required sample sizes for the proposed procedure. Our simulation studies show that the proposed sequential testing maintains the nominal type I error rate in finite samples. The proposed design is illustrated in a hypothetical lung cancer predictive trial and in a cancer diagnostic trial.

Insulin-like growth factor I of Yellow catfish (Pelteobagrus fulvidraco): cDNA characterization, tissue distribution, and expressions in response to starvation and refeeding.

The full-length cDNA coding IGF-I was cloned from the liver of Yellow catfish Pelteobagrus fulvidraco. The tissue distributions of IGF-I in adults were then analyzed by using real-time PCR. The effects of starvation (3 weeks) and subsequent refeeding (3 weeks) on the compensatory growth performance in juvenile fish weighing 3.80 ± 0.78 g and hepatic IGF-I mRNA expressions were also investigated. The cDNA obtained covered 884 bp with an open reading frame of 480 bp encoding 159 amino acids. It is composed of a signal peptide with 41 amino acids (AAs), a mature peptide comprising the B, C, A, and D domains (71 AAs) and E domain of 47 AAs. Sequence alignment and phylogenetic analysis revealed a high degree of conservation (71-87%) among the species of Siluriformes and some closely related species. In adults, the highest IGF-I expression was observed in the liver, followed by the brain, whereas relatively low expressions were detected in muscle and stomach. Both body weight and length increased significantly in fish fed to satiation continuously. Body weight, body length, condition factor, and hepatic IGF-I expressions were all decreased remarkably with increasing starvation times, but increased significantly after refeeding. The results showed that the expression of IGF-I was positively correlated with feed intakes and IGF-I may play a key regulatory role for somatic growth induced by compensatory growth in Yellow catfish.

Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species.

The mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T-. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.