A single-nucleus transcriptomic atlas characterizes cell types and their molecular features in the ovary of adult Nile tilapia.

In fish species, there is limited analysis of signature transcriptome profiles at the single-cell level in gonadal cells. Here, the molecular signatures of distinct ovarian cell categories in adult Nile tilapia (Oreochromis niloticus) were analysed using single-nucleus RNA sequencing (snRNA-seq). We identified four cell types (oogonia, oocytes, granulosa cell, and thecal cell) based on their specifically expressed genes and biological functions. Similarly, we found some key pathways involved in ovarian development that may affect germline-somatic interactions. A cell-to-cell communication network between the distinct cell types was constructed. We found that the bidirectional communication is mandatory for the development of germ cells and somatic cells in fish ovaries, and the granulosa cells and thecal cells play a central regulating role in the cell network in fish ovary. Additionally, we identified some novel candidate marker genes for various types of ovarian cells and also validated them using in situ hybridization. Our work reveals an ovarian atlas at the cellular and molecular levels and contributes to providing insights into oogenesis and gonad development in fish.

Transcriptome analysis in the spleen of Northern Snakehead (Channa argus) challenged with Nocardia seriolae.

Northern snakehead (Channa argus) is an indigenous fish species and is one of popularly cultured snakeheads in China and other Asian countries. Unfortunately, Nocardia seriolae infections have caused considerable losses in the snakehead aquaculture industry. However, the infectivity and the immune response induced by N. seriolae in snakehead are unclear. In order to better understand the immune response of Northern snakehead in a series of time points after N. seriolae challenge, we conducted the transcriptomic comparison in snakehead spleen at 48, 96, and 144 h after the challenge of N. seriola against their control counterparts. Gene annotation and pathway analysis of differentially expressed genes (DEGs) were carried out to understand the functions of the DEGs. Additionally, protein-protein interaction networks were conducted to obtain the interaction relationships of immune-related DEGs. These results revealed the expression changes of multiple DEGs and signaling pathways involved in immunity during N. seriolae infection, which will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection in the northern snakehead.

Global expression response of genes in sex-undifferentiated Nile tilapia gonads after exposure to trace letrozole.

The aromatase inhibitor letrozole can be found in rivers, effluents, and even drinking water. Studies have demonstrated that letrozole affects various metabolic pathways and may cause reproductive toxicity, especially in fish exposed during development. However, studies on the effect of a low concentration of letrozole at the whole-gonad transcriptomic level in the early stage of fish sexual development have not been investigated. The aim of our study was to explore the potential effects of a low concentration of letrozole on the gonad transcriptome of Nile tilapia at an early stage of sexual development. In this study, 9 dpf (days postfertilization) Nile tilapia were exposed to trace letrozole for 12 days. Letrozole exposure from 9 dpf to 21 dpf persistently altered phenotypic sex development and induced the male-biased sex ratio. The transcriptome results showed that 1173 differentially expressed genes (DEGs) were present in the female control vs 1.5 µg/L letrozole-treated female comparison group and that 1576 DEGs were present in the 1.5 µg/L letrozole-treated female vs male control comparison group. Differentially expressed gene enrichment analysis revealed several crucial pathways, including the drug metabolism-cytochrome P450 pathway, the ErbB-PI3K/Akt/mTOR pathway, and the calcium signalling pathway. Further analysis of these identified DEGs indicated that some key genes correlated with metabolism and epigenetic regulation were significantly affected by letrozole, such as UDP-glucuronosyltransferase (Ugt), glutathione S-transferase omega-1 (Gsto1), lysine-specific demethylase 6bb (Kdm6bb, original name is Kdm6a), jumonji and AT-rich interaction domain containing 2 (Jarid2b, original name is Jarid2), growth arrest and DNA damage inducible gamma (Gadd45g), and chromobox protein 7 (Cbx7). The qRT-PCR validation results for twelve DEGs showed that the Pearson's correlation of the log10fold change values between the qPCR and RNA-Seq results was 0.90, indicating the accuracy and reliability of the RNA-Seq results. Our study is the first to report the effect of letrozole on the transcriptome of gonads from fish during early-stage sexual development. These findings will be useful for understanding the toxic effects and molecular mechanisms of letrozole exposure at the early stage of gonad development on the sexual development of aquatic organisms.

Profiling expression changes of genes associated with temperature and sex during high temperature-induced masculinization in the Nile tilapia brain.

Fish sex-determining mechanisms can be classified as genotypic (GSD), temperature (TSD), or genotypic plus temperature effects (GSD+TE). Previous studies have shown that culturing water temperature during thermosensitive periods (TSP) could affect the expression of many genes in the gonad in some fish. However, few studies have focused on gene expression changes in the brain after temperature treatment during TSP in fish species. In this study, three families were developed by crossing XX neomales with XX females and one of them was used for transcriptome analysis. The results showed that a total of 105, 3164 and 4666 DEGs were respectively obtained in FC (female control) vs. FT (high temperature-treated females at TSP), FC vs. MC (male control), and MC vs. FT comparison groups. By profiling analysis, we show that the mRNA expression levels of 16 differentially expressed genes (DEGs) exhibited significant downregulation or upregulation after high temperature treatment and reached a similar level as that in MC. Among the 16 DEGs, LOC100699848 (lysine specific demethylase 6A) and Jarid2 contained JmjC domain, showing the possible important role of JmjC domain in response to temperature treatment in Nile tilapia. Kdm6b (lysine demethylase 6B) and Jarid2 have been shown to play important roles in reptile TSD, showing the relative conservation of underlying regulation mechanisms between TSD in reptile and TSD or GSD+TE in fish species. Finally, the transcriptome profiling was validated by quantitative real-time PCR in nine selected genes. These results provide a direction for investigating the GSD+TE molecular mechanism in fish species.

[Effects of PINK1 gene on cell apoptosis and cell autophagy in neonatal mice with hypoxic-ischemic brain damage].

OBJECTIVE: To study the effect of PINK1 (phosphatase and tensin homolog deleted on chromosome ten induced putative kinase 1) gene on cell apoptosis and cell autophagy in neonatal mice with hypoxic-ischemic brain damage (HIBD). METHODS: Seventy-two wild-type C57BL/6 mice and 72 PINK1 gene knockout neonatal C57BL/6 mice were randomly divided into four groups: sham-operated wild-type (SWT), HIBD model wild-type (MWT), sham-operated knockout (SKO) and HIBD model knockout (MKO). HIBD model was prepared by low oxygen exposure for 2.5 hours after right carotid artery ligation. After 24 hours of hypoxia-ischemia treatment, TTC (2,3,5-triphenyl four azole nitrogen chloride) staining was used to measure brain infarct volume. The immunohistochemical staining was used to measure the expression of cell apoptosis protein cleaved-caspase-3 (CC3) in brain tissues. The TUNEL method was used to measure cell apoptosis. The immunofluorescence staining and Western blot were used to measure the expression of cell autophagy protein LC3. RESULTS: Compared with the MWT group, the infarct volume of brain tissues was markedly reduced in the MKO group (P<0.05), the number of apoptotic cells and the cell apoptosis index were markedly decreased in the MKO group (P<0.05), the expression of apoptosis protein CC3 was significantly reduced in the MKO group (P<0.05), the expression of cell autophagy protein LC3 was significantly decreased in the MKO group, and the autophagy indicator LC3II/LC3I was also markedly reduced in the MKO group (P<0.05). CONCLUSIONS: PINK1 gene knockout can protect neonatal mice from HIBD.

[Instrumentation and Application of a Portable Pretreating System for a Speedy Plasmon-Enhanced Raman Spectroscopy Detection Towards Food Safety].

The present paper developed a portable and fast sample pretreatment apparatus. It has many virtues like being portable, low power consumption and convenient operation, short extraction time and sound repeatability. Therefore, it can meet the requirements of on-site rapid detection pretreatment. The apparatus consists of four functional modules: ultrasonic extraction unit, heating unit, exhaust gas evaporation and absorption unit and control system. In addition, LED control panel and alarm device were designed. The whole treatment process needs three steps: ultrasonic extraction, liquid-liquid extraction and solvent evaporation by heating and pumping. For test of this apparatus performance, three real samples (pepper powder, pepper oil, bean sauce) containing banned additive Rhodamine B were taken as experiment objects. Compared with conventional laboratory pretreatment method, the PERS spectra achieved by two methods were little changed, but the experiment time was halved. In addition, the test results showed relative standard deviation less than ±5%.

[The Involvement of CRMP-2 on Axonal and Dendrictic Injury after Hypoxic-Ischemic Brain Injury in Neonatal Rat].

OBJECTIVE: To investigate the activity of collapsin response mediator protein 2 (CRMP-2) and its possible regulation for axonal and dendrictic injury under hypoxia-ischemia (HI). METHODS: Postnatal day 10 SD rats were suffered the right common carotid artery ligation and 8% mixture of oxygen and nitrogen hypoxia 2.5 h to produce HI model. The expression of total and phosphorylated CRMP-2 and amyloid precursor protein (APP) were detected by Western blot after HI. After pretreatment of protein kinase B (Akt) inhibitor, wortmannin or LY294002, western blot and immunohistochemistry were applied to detect the expression of total and phosphorylated of CRMP-2 at 4 h and 24 h after HI. At 72 h after HI, APP was detected by Western blot and immunohistochemistry, axonal and dendrictic injury was determined by electron microscope. RESULTS: Total CRMP-2 was not obviously changed after HI, compared with that of sham controls. However, the phosphorylated CRMP-2 (p-CRMP-2) protein transiently increased at 0.5 h, started to decrease at 2 h, remained at a low level at the rest of the time points, compared with that of sham controls. APP protein started to increase at 2 h, remained at a high level at 4, 8, 24 h, and then progressively increased at 48 and 72 h. In wortmannin and LY294002 group, CRMP-2 protein was not obviously changed at 4 h and 24 h after HI. However, p-CRMP-2 increased at 4 h and 24 h. At 72 h, wortmannin pretreatment increased APP expression, leading to more severe ultrastructure failure of axon and dendrite. CONCLUSION: As a downstream effector of Akt pathway, CRMP-2 is involved in axonal and dendritic injury regulation after HI in neonatal rat.

[SERS spectrum recognition for Malachite Green real-time detection in aquaculture used seawater].

Surface enhanced Raman spectroscopy (SERS) is a useful chemical analysis technique for its high sensitivity, which was used for Malachite Green qualitative analysis in real cases in the present article. Automatic recognition algorithms were put forward, which is a combination of three modules, including a robust Fourier transform for background rejection, a principal component analysis based character extraction method and artificial neural networks for classifying. Low-frequency background was rejected by iterative Fourier transform in order to eliminate the effect of variable background. The best principal component combination was obtained according to the Euclidean distances between-class and within-class in the sample space. And a three-layer back-propagating neural network was constructed for classifying. As it was shown, it would both minimize the network and reduce the classifying mistakes from variable baseline and Raman characters of other substances in seawater with best principal component combination. Malachite Green real-time detection in aquaculture used seawater was realized with a lower density limit of 0. 1 microg L-1. Moreover, the method proposed in this article could be extended for other sol analysis based on SERS technique.

[The regulation of Akt signaling on axonal density after hypoxic-ischemic brain injury in neonatal rat].

OBJECTIVE: To investigate the activity of protein kinase B (Akt) and its downstream protein, glycogen synthase kinase-3beta (GSK-3beta) under hypoxia-ischemia (HI), and the possible regulation for axonal density. METHODS: Postnatal day 10 SD rats were suffered the right common carotid artery ligation and 8% mixture of oxygen and nitrogen hypoxia 2.5 h to produce HI model. The expression of total and phosphorylated Akt and GSK-3beta was detected by western blot after HI. After pretreatment of Akt inhibitor, wortmannin or LY294002, Western blot detect the expression of total and phosphorylated of Akt, GSK-3beta at 4 h and 24 h after HI. After pretreatment of wortmannin, axonal density was determined by Bielschowsky silver impregnation, and histological injury was evaluated by hematoxylin and eosin (HE) staining. RESULTS: The expression of total Akt and GSK-3beta remained unchanged after HI. p-Akt protein significantly decreased at 0.5 h, increased at 2 h and reached the highest at 4 h, returned to baseline at 8 h, declined at 24 and 48 h after HI, and finally returned to baseline again at 72 h compared with that of sham controls, p-GSK-3beta protein decreased at 0. 5 h, increased at 2 h, reached the highest at 4 h, returned to baseline at 8 and decreased at 24 h, reached the lowest at 48 h, and returned to baseline at 72 h. Wortmannin or LY294002 intervention didn't change the expression of total Akt and GSK-3beta, while decrease the p-Akt and p-GSK-3beta expression. HI cause decreased axonal density, and the histological injury of brain. Wortmannin pretreatment could aggravate the histological injury and decrease axonal density after HI. CONCLUSION: The Akt pathway is involved in axonal density and histological brain injury after HI in neonatal rat.

CXCL8 Promotes Endothelial-to-Mesenchymal Transition of Endothelial Cells and Protects Cells from Erastin-Induced Ferroptosis via CXCR2-Mediated Activation of the NF-κB Signaling Pathway.

CXCL8-CXCR1/CXCR2 signaling pathways might form complex crosstalk among different cell types within the ovarian tumor microenvironment, thereby modulating the behaviors of different cells. This study aimed to investigate the expression pattern of CXCL8 in the ovarian tumor microenvironment and its impact on both endothelial-to-mesenchymal transition (EndMT) and ferroptosis of endothelial cells. The human monocytic cell line THP-1 and the human umbilical vein endothelial cell line PUMC-HUVEC-T1 were used to conduct in vitro studies. Erastin was used to induce ferroptosis. Results showed that tumor-associated macrophages are the major source of CXCL8 in the tumor microenvironment. CXCL8 treatment promoted the nucleus entrance of NF-κB p65 and p65 phosphorylation via CXCR2 in endothelial cells, suggesting activated NF-κB signaling. Via the NF-κB signaling pathway, CXCL8 enhanced TGF-ß1-induced EndMT of PUMC-HUVEC-T1 cells and elevated their expression of SLC7A11 and GPX4. These trends were drastically weakened in groups with CXCR2 knockdown or SB225002 treatment. TPCA-1 reversed CXCL8-induced upregulation of SLC7A11 and GPX4. CXCL8 protected endothelial cells from erastin-induced ferroptosis. However, these protective effects were largely canceled when CXCR2 was knocked down. In summary, CXCL8 can activate the NF-κB signaling pathway in endothelial cells in a CXCR2-dependent manner. The CXCL8-CXCR2/NF-κB axis can enhance EndMT and activate SLC7A11 and GPX4 expression, protecting endothelial cells from ferroptosis.

Expression changes of non-specific cytotoxic cell receptor (NCCRP1) and proliferation and migration of NCCs post-Nocardia seriolae infection in Northern Snakehead.

Non-specific cytotoxic cells (NCCs) are essential to the cytotoxic cell-mediated immune response in teleost. The fish non-specific cytotoxic cell receptor protein 1 (NCCRP1) plays an important role as a membrane protein in the recognition of target cells and the activation of NCC. However, the roles of fish NCCs during pathogen infection require comprehensive studies. In this study, the coding sequence of northern snakehead (Channa argus) nccrp1 (Canccrp1) was cloned. Canccrp1 contains an open reading frame of 690 bp, encoding a peptide of 229 amino acids with a conserved F-box-associated domain (FBA) and proline-rich motifs (PRMs). Transcriptional expression analysis revealed that the constitutive expression of Canccrp1 was higher in the immune-related organs, such as liver, kidneys, and spleen. Moreover, mRNA and protein expression of Canccrp1 gradually increased in the spleen at 1-6 days post infection (dpi) with Nocardia seriolae, in addition to reaching peak expression in both the kidneys and liver at 2 dpi. A polyclonal antibody prepared against recombinant CaNCCRP1 effectively labeled NCCs in peripheral blood and different tissues. Then, immunofluorescence (IF) staining showed that the number of NCCs was significantly increased and showed a scattered distribution in the early stages of N. seriolae infection (2 and 4 dpi) before the forming of granulomas. At the late stages of N. seriolae infection (6 dpi), more NCCs migrated to preexisting granulomas, showing significant coaccumulation with N. seriolae. All these results clearly indicate the expression changes of CaNCCRP1, and the number and localization changes of NCCs post-N. seriolae infection, implying potential roles for fish NCCs in the antimicrobial infection process in fish.

Alternative splicing of histone demethylase Kdm6bb mediates temperature-induced sex reversal in the Nile tilapia.

Sex determination in many fish species is remarkably plastic and temperature sensitive. Nile tilapia display a genetic sex-determination system (XX/XY). However, high-temperature treatment during critical thermosensitive periods can induce XX females into XXm pseudo-males, and this phenomenon is termed temperature-induced sex reversal (TISR). To investigate the molecular mechanism of TISR in Nile tilapia, we performed Iso-seq analysis and found a dramatic effect of high temperature on gene alternative splicing (AS). Kdm6bb histone demethylase showed a novel AS at intron 5 that generates Kdm6bb_tv1 transcripts without intron 5 and Kdm6bb_tv2 with intron 5. Kdm6bb_tv1 encodes a full-length protein while Kdm6bb_tv2 encodes a truncated protein. Expression analysis revealed that intron 5 splicing of Kdm6bb is male and gonad biased at larval stage, and only gonad biased at adult stage. High-temperature treatment induced intron 5 splicing in the gonads of XX and XY fish, resulting in increased Kdm6bb_tv1 expression. To directly test the role of Kdm6bb_tv1 in Nile tilapia TISR, we knocked out expression of Kdm6bb_tv1. However, Kdm6bb_tv1-/- homozygous mutants showed embryonic lethality. Overexpression of Kdm6bb_tv1, but not Kdm6bb_tv2, induced sex reversal of XX females into pseudo-males. Overexpression of Kdm6bb_tv1, as with high-temperature treatment, modified the promotor region of Gsdf and Dmrt1 by demethylating the trimethylated lysine 27 of histone 3 (H3K27me3), thereby increasing expression. Collectively, these studies demonstrate that AS of Kdm6bb intron 5 increases the expression of Kdm6bb_tv1, which acts as a direct link between high temperature and activation of Gsdf and Dmrt1 expression, leading to male sex determination.

Rapid visual detection of aluminium ion using citrate capped gold nanoparticles.

We report the visual detection of Al(3+) using unlabeled gold nanoparticles (AuNPs) based on the complexation of Al(3+) with citric acid, resulting in the aggregation of AuNPs. The distinction of color change can be observed by the naked eye at concentrations down to 1.0 µM which is lower than the permissable level (7.4 µM) for drinking water as defined by the World Health Organization.

Telomerase reverse transcriptase (TERT) promotes neurogenesis after hypoxic-ischemic brain damage in neonatal rats.

OBJECTIVE: Neonatal hypoxic-ischemic encephalopathy (HIE) endangers quality of life in children, and curative attempts are rarely effective. Neurogenesis plays an important role in neural repair following brain damage. This study aimed to investigate the role of telomerase reverse transcriptase (TERT) in neurogenesis after neonatal hypoxic-ischemic brain damage (HIBD). METHODS: Neonatal HIBD models were established in vivo (Sprague-Dawley rats, 7 days old) and in vitro (cultured neural stem cells, NSCs). Lentivirus and adenovirus transfection was used to induce TERT overexpression. Expression of TERT was detected by quantitative real-time PCR and immunofluorescence staining. NSCs apoptosis and proliferation were measured by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining and cell counting assays, respectively. Migration and differentiation of NSCs were assessed by western blotting and immunofluorescence staining. Morris water maze test and modified neurological severity scores were conducted to evaluate the neurological function of rats. RESULTS: Overexpression of TERT attenuated apoptosis of NSCs; promoted proliferation, migration, and differentiation of NSCs; and induced myelination in the brains of neonatal rats after HIBD. Moreover, it reduced the impairment of learning, memory, and neurological function after HIBD in neonatal rats. In vitro findings indicated that the expression of Gli1 was increased after OGD, and overexpression of TERT further increased the expression of Gli1 in NSCs after OGD. DISCUSSION: TERT promotes neurogenesis and decreases neurological function injury after HIBD in neonatal rats. This neuroprotective pathway may provide a basis for developing therapeutic strategies for neonatal HIE. Furthermore, TERT may represent a target during neural injury and repair in patients with various diseases affecting the nervous system.

Effectiveness of azithromycin mass drug administration on trachoma: a systematic review.

BACKGROUNDS: Azithromycin mass drug administration (MDA) is a key part of the strategy for controlling trachoma. This systematic review aimed to comprehensively summarize the present studies of azithromycin MDA on trachoma; provide an overview of the impact of azithromycin MDA on trachoma in different districts; and explore the possible methods to enhance the effectiveness of azithromycin MDA in hyperendemic districts. METHODS: PubMed, Embase, the Cochrane Central Register of Controlled Trials, Web of Science, and ClinicalTrials.gov were searched up to February 2021 with no language restriction. Studies reporting the effect of azithromycin MDA on trachoma were included. Mathematical modeling studies, animal studies, case reports, and reviews were excluded. The trachomatous inflammation-follicular (TF) <5.0% was used to judge the effect of azithromycin MDA on eliminating trachoma as a public health problem. Two researchers independently conducted the selection process and risk of bias assessment. RESULTS: A total of 1543 studies were screened, of which 67 studies including 13 cluster-randomized controlled trials and 54 non-randomized studies were included. The effect of azithromycin MDA on trachoma was closely related to the baseline prevalence in districts. For the districts with baseline prevalence between 5.0% and 9.9%, a single round of MDA achieved a TF <5.0%. For the districts with baseline between 10.0% and 29.9%, annual MDA for 3 to 5 years reduced TF <5.0%. However, for the districts with high level of baseline prevalence (TF >30.0%), especially with baseline TF >50.0%, annual MDA was unable to achieve the TF <5.0% even after 5 to 7 years of treatment. Quarterly MDA is more effective in controlling trachoma in these hyperendemic districts. CONCLUSIONS: Azithromycin MDA for controlling trachoma depends on the baseline prevalence. The recommendation by the World Health Organization that annual MDA for 3 to 5 years in the districts with TF baseline >10.0% is not appropriate for all eligible districts.

Transcriptome Profiling and Analysis of Genes Associated with High Temperature-Induced Masculinization in Sex-Undifferentiated Nile Tilapia Gonad.

Artificially high temperatures during critical thermosensitive periods (TSPs) can induce the sex reversal of Nile tilapia (Oreochromis niloticus) females into pseudomales; Nile tilapia is a GSD + TE (genotypic plus temperature effects) fish species. Previous studies have shown that water temperature affects the expression levels of many genes in the gonad or brain in various teleost species. However, few studies on the effect of temperature at the whole-gonad transcriptomic level in the early stage of sex differentiation have been reported in fish species exhibiting GSD + TE. In this study, RNA-Seq was performed to characterize the transcriptomic profile and identify genes exhibiting temperature- and sex-biased expressions in the Nile tilapia gonad at 21 dpf. A total of 42 genes were found to be associated with both high-temperature treatment and sex development, as the expression levels of these genes differed in both FC (female control) vs MC (male control) and FC vs FT (high temperature-treated females in the TSP). Among these genes, the transcriptional alterations of many male sex determination and differentiation genes, such as Dmrt1, Gsdf, and the DNA damage-inducible protein GADD45 alpha, suggested that the male pathway is initiated after high-temperature treatment and that its initiation may play a role in high temperature-induced masculinization in Nile tilapia. The qRT-PCR validation results for thirteen differentially expressed genes showed that the Pearson's correlation of the log10 fold change values between the qPCR and RNA-Seq results was 0.70 (p < 0.001), indicating the accuracy and reliability of the RNA-Seq results. Our study provides insights into how high-temperature treatment induces the sex reversal of Nile tilapia females.

Differential expression analysis of genes involved in high-temperature induced sex differentiation in Nile tilapia.

Nowadays, high temperature effects on the molecular pathways during sex differentiation in teleosts need to be deciphered. In this study, a systematic differential expression analysis of genes involved in high temperature-induced sex differentiation was done in the Nile tilapia gonad and brain. Our results showed that high temperature caused significant down-regulation of CYP19A1A in the gonad of both sexes in induction group, and FOXL2 in the ovary of the induction group. The expressions of GTHα, LHß and ERα were also significantly down-regulated in the brain of both sexes in the induction and recovery groups. On the contrary, the expression of CYP11B2 was significantly up-regulated in the ovary, but not in the testis in both groups. Spearman rank correlation analysis showed that there are significant correlations between the expressions of CYP19A1A, FOXL2, or DMRT1 in the gonads and the expression of some genes in the brain. Another result in this study showed that high temperature up-regulated the expression level of DNMT1 in the testis of the induction group, and DNMT1 and DNMT3A in the female brain of both groups. The expression and correlation analysis of HSPs showed that high temperature action on tilapia HSPs might indirectly induce the expression changes of sex differentiation genes in the gonads. These findings provide new insights on TSD and suggest that sex differentiation related genes, heat shock proteins, and DNA methylation genes are new candidates for studying TSD in fish species.

[A bird's eye view of the algorithms and software packages for reconstructing phylogenetic trees].

The prototype phylogenetic tree, i.e., evolutionary "tree" or "tree of life", was first conceived by Charles Darwin in his seminal book "The Origin of Species", and its reconstructions have been approached by generations of biologists ever since. In this article, we briefly reviewed the major algorithms and software packages for reconstructing phylogenetic trees. Specifically we discuss four categories of phylogeny algorithms including distance-matrix, maximum parsimony, maximum likelihood, and Bayesian framework, as well as software packages (PHYLIP, MEGA, MrBayes) based on them.

[A review on the bioinformatics pipelines for metagenomic research].

Metagenome, a term first dubbed by Handelsman in 1998 as "the genomes of the total microbiota found in nature", refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.