Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp (Oratosquilla oratoria) under Thermal Stress

Simple Summary

Rising ocean temperature would change the seawater chemistry and affect the external and internal physiology of crustaceans due to their lack of certain efficient temperature regulators. In addition, the infraspecific populations of crustaceans might also have different response strategies to the rising of temperature. Therefore, we identified the transcriptomic variations to the same thermal stress between ecologically divergent populations of Oratosquilla oratoria. The aim of this study was to investigate the population-specific function genes and relevant pathways in response to thermal stress in O. oratoria. The results showed that gene-expressed variation was in a population-specific pattern, which indicated that the local environment could lead to the evolvement of changes in gene regulation, ultimately leading to adaptive divergences. Additionally, we found several genes with large pleiotropic effects in the Zhoushan population, which might indicate that the regulation mechanisms of the Zhoushan population were more efficient than those of the Qingdao population under same thermal stress. The results provided some novel insights into the local adaptive differences of the infraspecific populations of O. oratoria and other crustaceans.

Abstract

Crustaceans are generally considered more sensitive to ocean warming due to their lack of certain efficient regulators. However, the alterations in the physiology and behavior of crustaceans in response to thermal stress differ vastly even among the infraspecific populations of heterogeneous landscapes. Consequently, understanding the impact of temperature fluctuation on crustacean infraspecific populations might be essential for maintaining a sustainable persistence of populations at existing locations. In the present study, we chose the Japanese mantis shrimp (Oratosquilla oratoria) as the representative crustacean population, and conducted transcriptome analyses in two divergent O. oratoria populations (the Zhoushan and Qingdao populations) under same thermal stress (20–28 °C) to identify the population-specific expression response to thermal stress. The results showed significant differences in gene expressions, GO terms and metabolic pathways between the two populations. We hypothesized that intraspecific mutations in the same or different genes might lead to thermal adaptive divergences. Temperature increases from 20–28 °C produced significant enrichment in GO terms and altered the metabolic pathways in the Zhoushan population despite the lack of differentially expressed unigenes. Therefore, several functional genes with large pleiotropic effects may underlie the response to thermal stress in the Zhoushan population. Furthermore, the most significantly enriched biological processes of the Qingdao population were associated with the state or activity of cells and its significant enriched pathways with genetic information processing as well as immune and environmental information processing. In contrast, the differentially regulated unigenes of the Zhoushan population were primarily involved in the regulatory cellular and transcription processes and the most significant pathways found were metabolic and digestive. Consequently, the regulatory mechanisms of the Zhoushan population are probably more efficient than those of the Qingdao population under the same thermal stress.

Single-molecule characterization of extrinsic transcription termination by Sen1 helicase

Extrinsic transcription termination typically involves remodeling of RNA polymerase by an accessory helicase. In yeast this is accomplished by the Sen1 helicase homologous to human senataxin (SETX). To gain insight into these processes we develop a DNA scaffold construct compatible with magnetic-trapping assays and from which S. cerevisiae RNA polymerase II (Pol II), as well as E. coli RNA polymerase (ecRNAP), can efficiently initiate transcription without transcription factors, elongate, and undergo extrinsic termination. By stalling Pol II TECs on the construct we can monitor Sen1-induced termination in real-time, revealing the formation of an intermediate in which the Pol II transcription bubble appears half-rewound. This intermediate requires ~40 sec to form and lasts ~20 sec prior to final dissociation of the stalled Pol II. The experiments enabled by the scaffold construct permit detailed statistical and kinetic analysis of Pol II interactions with a range of cofactors in a multi-round, high-throughput fashion.

Yeast’s Sen1 helicase is involved in the suppression of antisense transcription from bidirectional eukaryotic promoters. Here authors develop and utilize a quantitative single-molecule assay reporting on the kinetics of extrinsic eukaryotic transcription termination by the Sen1 helicase and a reaction intermediate in which the Pol II transcription bubble appears half-rewound.

Key factors determining variations in RNA interference efficacy mediated by different double-stranded RNA lengths in Tribolium castaneum

Double-stranded RNA (dsRNA) length may affect RNA interference (RNAi) efficacy. Herein, variation in RNAi efficacy associated with dsRNA molecular length was confirmed via comparison of knockdown results following dsRNA injection into Tribolium castaneum. Through in vitro experiments with T. castaneum midgut, dsRNA accumulation in the midgut, degradation by midgut homogenates and persistence in haemolymph after injection were tested to determine the causes of RNAi efficacy variation. The comparative efficacies of dsRNAs were 480 bp ≈ 240 bp > 120 bp > 60 bp >> 21 bp. The combined midgut dsRNA accumulation and midgut homogenate-induced degradation analyses suggested cellular uptake to be the key barrier for 21 bp dsRNA functioning, but was likely not the main determinant of the variation in longer dsRNAs' (≥60 bp) bioactivity. In vitro RNAi experiment with T. castaneum midgut showed that long dsRNAs all significantly depleted the expression of corresponding genes, suggesting little variation in intracellular RNAi machinery's affinity for different dsRNA lengths. In vivo haemolymph content dynamics of different dsRNAs following injection indicated higher persistence of longer dsRNAs. In addition, comparison of the in vivo and in vitro RNAi efficacy also indicated the importance of haemolymph degradation. Thus, the varied efficacy of long dsRNAs resulted from their degradation by nucleases, which varied with dsRNA length.

Accumulation, temporal variation, source apportionment and risk assessment of heavy metals in agricultural soils from the middle reaches of Fenhe River basin, North China

The Fenhe River basin is the main agricultural and industrial developed area in Shanxi province, China. In recent years, agricultural non-point source pollution in the Fenhe River basin intensified, threatening soil quality and safety in the area. Accumulation of eight heavy metals (HMs) including chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd), lead (Pb) and mercury (Hg) has been detected in soil samples from 50 agricultural sites (0–20 cm) from the middle reaches of the Fenhe River basin. The ecological and human health risk and potential sources of the eight HMs were investigated. In addition, the human health and ecological risks imposed by the possible sources of the eight HMs were quantitatively apportioned. The enrichment factor (EF) values of Cr, Ni, Cu, Pb and Zn were lower than 2, indicating minimal enrichment, while values for As, Cd and Hg were between 2 and 5, exhibiting moderate enrichment. Temporal variation analysis suggested that most HMs in the study area exhibited low concentrations after 2015, except As. The potential ecological risk index was 174.09, indicating low ecological risk. The total hazard index and cancer risk values were 0.395 and 5.35 × 10⁻⁴ for adults and 2.75 and 3.63 × 10⁻⁴ for children, indicating the accepted standard levels were exceeded for non-carcinogenic risk for children and carcinogenic risks for both adults and children. Four potential sources were identified: (1) natural sources, (2) farming activities, (3) coal combustion, and (4) exhaust emissions. Natural sources represented the largest contributor to ecological risk, accounting for 57.42% of the total. Coal combustion was the major contributor to human health risks, accounting for 43.27% and 43.73% of the total non-carcinogenic risk and carcinogenic risk for adults, respectively, and 42.72% and 43.88% for children, respectively.

The Fenhe River basin is the main agricultural and industrial developed area in Shanxi province, China.

Assessing the Speciation of a Cold Water Species, Japanese Sand Lance Ammodytes personatus, in the Northwestern Pacific by AFLP Markers

The use of molecular techniques in biodiversity research increasingly results in the recognition of multiple divergent mitochondrial DNA (mtDNA) lineages below the morphospecies level. However, the overlapping distribution of multiple divergent lineages raises the question of whether some of these lineages are in fact cryptic species. Assessing the status of these divergent lineages, delimiting evolutionarily significant units (ESUs), and identifying the dominant evolutionary and ecological drivers are critical components of successful wildlife conservation and management strategies. Amplified fragment length polymorphism (AFLP) markers were applied to characterize the phylogeography pattern of a cold water species, the Japanese sand lance Ammodytes personatus, in warm and cold ocean currents. A total of 211 individuals sampled from 12 populations through the species' range, including samples from Kuroshio Current, Oyashio Current, Tsushima Current, and Yellow Sea, were analyzed. The Bayesian assignment probability test and Neighbor joining (NJ) analysis divided these populations into two genetically and geographically distinct clades (northern and southern clades) characterized by different sea surface temperatures. The incongruence between nuclear clades and previous mitochondrial lineages suggested that A. personatus is indeed composed of at least two genetically divergent cryptic species. Pleistocene glaciation isolation after secondary contact, local thermal adaptation, and isolation by distance may explain the observed geographic pattern of two cryptic species and genetic structure within clades.

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition

AIMS

To select apple rootstocks that are tolerant to low nitrogen and reveal the relationship between the rhizosphere bacterial communities and the low nitrogen tolerance of the apple rootstock.

METHODS AND RESULTS

In total, 235 lines of hybrids of Malus robusta Rehd. × M.9 with low nitrogen stress were cultivated in pots in a greenhouse equipped with a drip irrigation system, and growth characteristics, photosynthesis traits and mineral elements were monitored. The bacterial community structure of the rhizosphere from different rootstocks was determined via Illumina MiSeq sequencing. This study selected three low nitrogen-tolerant (NT) lines that had higher nitrogen concentration, and higher photosynthesis rate than the three low nitrogen-sensitive (NS) lines. The bacterial community structure significantly differed (P ≤ 0·001) among the rootstocks. The bacterial phyla Proteobacteria and Actinobacteria were the dominant groups in the rhizosphere and presented higher abundance in the NT rhizosphere. The N concentration in the apple rootstocks exhibited highly positive Pearson correlations with the bacterial genera Sphingomonas, Pseudoxanthomonas, Bacillus and Acinetobacter, and negative correlations with the bacterial genera Pseudarthrobacter and Bradyrhizobium.

CONCLUSIONS

This study showed that investigated rootstocks achieved increased nitrogen concentration by enhancing their photosynthetic production capacity and shaping their rhizobacteria community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings provide a basis for studying the mechanisms of resistance to low nitrogen stress in apple rootstocks. Based on these beneficial bacteria, microbial inoculants can be developed for use in sustainable agricultural and horticultural production.

Supplementation with CTGF, SDF1, NGF, and HGF promotes ovine in vitro oocyte maturation and early embryo development

The strategies for improving the in vitro maturation (IVM) of domestic animal oocytes focus on promoting nuclear and cytoplasmic maturation. The identification of paracrine factors and their supplementation in the culture medium represent effective approaches for oocyte maturation and embryo development. This study investigated the effects of paracrine factor supplementation including connective tissue growth factor (CTGF), nerve growth factor (NGF), hepatocyte growth factor (HGF), and stromal derived factor 1 (SDF1) on ovine oocytes and early parthenogenetic embryos using an in vitro culture system. First, we identified the optimal concentrations of CTGF (30 ng/mL), SDF1 (10 ng/mL), NGF (3 ng/mL), and HGF (100 ng/mL) for promoting oocyte maturation, which combined, induced nuclear maturation in 94.19% of oocytes. This combination also promoted cumulus cell expansion and inhibited oocyte/cumulus apoptosis, while enabling a larger proportion (33.04%) of embryos to develop into blastocysts than in the controls and prevented embryo apoptosis. These novel findings demonstrate that the paracrine factors CTGF, SDF1, NGF, and HGF facilitate ovine oocyte and early parthenogenetic embryo development in vitro. Thus, supplementation with these factors may help optimize the IVM of ovine oocytes and early parthenogenetic embryo development strategies.

Genetic structure analysis of mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region sequence

The genetic relationships of mantis shrimp Oratosquilla oratoria between the coastal waters of China and Japan were not well studied. To reveal the genetic differentiation and genetic structure among populations, we collected populations of mantis shrimp O. oratoria from the coastal waters of China and Japan to analyze the mtDNA control region variation. A total of 309 individuals of O. oratoria were collected from 13 localities (11 from China and 2 from Japan) and a segment of mitochondrial DNA control region was sequenced. Three hundred nine haplotypes were defined, yielding a very high haplotype diversity and nucleotide diversity. Two lineages of O. oratoria were revealed and displayed strong differences in the geographical distribution. In the coastal waters of China, the geographic distribution of the two lineages was completely separated by the Yangtze River estuary; however, the lineages showed geographic sympatry in two populations from Japan. Based on the lineage distribution, three groups were defined. There was no significant genetic differentiation among the populations within the three groups, indicating high gene flow within each group. Significant and negative values for Tajima D and Fu's Fs tests, and mismatch distributions for two lineages indicated population expansion. The present result confirmed that the freshwater outflow from the Yangtze River formed a physical barrier and affected gene exchange. The different distribution patterns of the two lineages in coastal waters of China and Japan indicated that the larvae of O. oratoria were transferred from China to the coastal waters of Japan with a one-way gene flow.

Transcriptome analysis for identification of candidate genes related to sex determination and growth in Charybdis japonica

Charybdis japonica is an important cultured crab in China and it exhibits sex differences in their growth. Growth is an important economic trait that is controlled by many genes. In order to discover the growth-related regulatory mechanisms, whole-body transcriptomic sequencing and comparative analyses in different genders of C. japonica were conducted based on Illumina RNA-seq technology. In the present study, we obtained 62,879,204 and 60,226,334 clean reads in female and male libraries, respectively. 25,000,000 clean reads of every library were randomly selected and compared with Nt database to examine the possible contamination. Results showed that all clean reads were distributed among C. japonica or other species that were closely relative to this species, indicating no-pollution. De novo assembly was performed and a total of 32,543 and 44,174 unigenes were produced in female and male of C. japonica, respectively. Among all the unigenes, 12,591 and 14,455 unigenes of female and male crabs were annotated based on protein databases. Moreover, a total of 33,926 unigenes were found to contain ORFs and 52,839 SSRs were detected. The contrast between male and female C. japonica identifying 1939 unigenes were significantly differentially expressed. In addition, we specifically discussed some gene functions and pathways potentially associated with sex determination and growth. This is the first systematic report of whole transcriptome in C. japonica. The transcriptome information provides a basic resource for further studies on understanding the molecular basis of biological processes in C. japonica and other crustaceans.

Risk factors of haemoglobinuria after microwave ablation of liver tumours

AIM

To explore the risk factors predicting haemoglobinuria after ultrasound-guided percutaneous microwave ablation (MWA) of liver tumours and discuss the treatments and outcomes.

MATERIALS AND METHODS

The present study comprised 2,829 patients admitted for liver tumours treated with MWA from Jan 2011 to April 2017. Ethics committee approval was waived and informed consent for treatment procedures were obtained from the patients. Haemoglobinuria after MWA was found in 149 patients. The influence of 19 risk factors was assessed. Binary logistic regression and receiver operating characteristic (ROC) curve analysis were used for statistical analysis. The treatments and outcomes of patients with haemoglobinuria were summarised.

RESULTS

By univariate analysis, histopathology, liver cirrhosis, MWA volume, MWA energy, and MWA duration were significant risk factors. By multivariate analysis and ROC curve, MWA energy, duration, and volume were identified as predictors of haemoglobinuria after MWA. Drug treatments including kidney protection, adequate hydration, alkalisation of urine, and diuresis were administrated to the patients with haemoglobinuria. One patient progressed to acute kidney injury (AKI) while others had good clinical outcomes.

CONCLUSION

Haemoglobinuria is a controllable side effect after MWA of liver tumours, which is related to high MWA energy, long MWA duration, and great MWA volume. It usually caused few side effects on renal function with correct treatment.

Prospective Comparison of Equations Based on Creatinine and Cystatin C for the Glomerular Filtration Rate Estimation in Chinese Renal Transplant Recipients

BACKGROUND

Currently, there is no dedicated equation to estimate glomerular filtration rate (GFR) for transplanted kidneys. This study aimed to compare the performance of serum creatinine (Scr)- and cystatin C (CysC)-based equations in Chinese renal transplant recipients.

METHODS

A total of 252 stable renal transplant recipients were enrolled in this study. The plasma clearance of ^99mTc-DTPA (rGFR) was used as a reference standard. The Scr, CysC, and rGFR of the patients were measured on the same day. The bias, precision, accuracy (percentage of estimates within 10%, 30%, and 50% of rGFR), and agreements of 8 Scr and 5 CysC eGFR equations were assessed. The factors affecting the accuracy were also evaluated.

RESULTS

Among the Scr-based equations, the Japanese Society of Nephrology-Chronic Kidney Disease Initiatives (JSN-CKDI) equation had the best overall performance with a bias of -6.2 mL/min/1.73 m², and 96.1% of its estimates were within 30% of the rGFR. For the CysC-based equations, the Filler equation had the best performance with a bias of -3.9 mL/min/1.73 m², and 93.7% of its estimates were within 30% of the rGFR. Overall, the CysC-based equations showed better performance than the Scr-based equations. In addition, significant differences were observed between bias and gender and between bias and rGFR value in some equations, whereas transplantation time and immunosuppressive regimens were not correlated with the bias.

CONCLUSION

The JSN-CKDI equation provides the best estimation of the GFR equations, and the CysC-based equations performed better than the Scr-based equations in this population.

Inhibition of thyroid carcinoma cells with YAP1 protein interference and its mechanism

OBJECTIVE

To investigate the effects and mechanism of yes-associated protein 1 (YAP1) on thyroid carcinoma cells.

MATERIALS AND METHODS

Quantitative Real-time PCR (qRT-PCR) and Western blot assay were used to detect the expression of YAP1 in normal thyroid cells (HT-ori3) and four types of thyroid carcinoma cells: FTC-133, IHH-4, TPC-1 and NPA. The cell lines with the highest expression of YAP1 were selected as the experimental materials. qRT-PCR and Western blot assay were used to detect the interference effect of si-YAP1. The cell proliferation and the effect on the PI3K-Akt signal pathway were examined by MTT and Western blot.

RESULTS

The expression of YAP1 significantly increased in the thyroid carcinoma cell line compared with normal thyroid cells, among which the expression of YAP1 in TPC-1 was the highest. Quantitative PCR and Western blot results showed significant interference effects. The MTT assay indicated that YAP1 interference suppressed the proliferation of cells and the expression of p-Akt.

CONCLUSIONS

The interference of YAP1 can inhibit the growth of thyroid cancer cells, and its mechanism may be associated with the PI3K-Akt signaling pathway.

miR-145 is critical for modulation of vascular smooth muscle cell proliferation in human carotid artery stenosis

miR-145 is highly expressed in vascular cells, where it regulates phenotypic switching and vascular homeostasis, but its role in carotid artery stenosis (CAS) is controversial. In the present study, the expression of miR-145 was assessed by real time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in human samples (both plasma and/or endarterectomy samples) from patients with symptomatic CAS and in controls without CAS. The mouse carotid artery ligation (CAL) model was used to determine the role of miR-145 on vascular smooth muscle cells in vivo (VSMCs) by using a mimic of or an inhibitor of miR-145. We found that miR-145 expression was significantly reduced in the plasma and plaque from patients with CAS (p less than 0.01). The expression of miR-145 in the mouse CAL model, as assessed by qRT-PCR, was significantly reduced compared to the carotid arteries of the control group (p less than 0.01). In vitro, enhancement or inhibition of miR-145 in VSMCs demonstrated that miR-145 significantly inhibited proliferation of VSMCs (p less than 0.05); in vivo, enhancement of miR-145 significantly inhibited neointimal formation in the CAL model (p less than 0.01). These results demonstrate that the expression of miR-145 is reduced in human CAS, miR-145 plays a critical role in CAS by modulation of VSMC proliferation, suggesting that MiR-145 may present a potential therapeutic option for treating CAS.

Relationship between environmental conditions, TRI5 gene expression and deoxynivalenol production in stored Lentinula edodes infected with Fusarium graminearum

This study made the first attempt to relate the production of deoxynivalenol (DON) to the expression of TRI5 gene in Fusarium graminearum as a function of interacting environmental factors (water activity (aw) (0.95-0.98), temperature (20-30 °C) and incubation time (7 day-28 day)), so as to investigate its production mechanisms in Lentinula edodes. Changes in temperature, water activity and incubation time could significantly (P<0.01) affect DON production and TRI5 gene expression. The highest DON concentration (793.5±27.4 μg/kg) and TRI5 gene expression (2−ΔΔCt=38.8±4.8) were observed when the cultures were incubated at 20 °C and 0.98 aw for 21 days. Multi-regression analysis was performed and nonlinear models based on polynomial equations were established to uncover the individual effects of temperature, water activity and incubation time as well as their interactions on DON production and TRI5 gene expression. The established model was further used to develop contour maps to predict the DON production and TRI5 gene expression in relation to storage conditions in L. edodes. Highly significant positive correlation between DON production and fold TRI5 gene expression (R=0.5534, P<0.0001) was observed in this commodity. The production mechanisms of DON in L. edodes revealed in the present study will be beneficial for developing more effective targeted control strategies.

Decreased Expression of MYPT1 Contributes to Tumor Angiogenesis and Poor Patient Prognosis in Human Prostate Cancer

BACKGROUND

Our previous study demonstrated that Myosin Phosphatase Targeting subunit 1 (MYPT1) may function as a direct target of microRNA-30d, which promotes tumor angiogenesis and tumor growth of prostate cancer (PCa). Here, we aimed to investigate the clinical significance of MYPT1 expression and its functions in PCa.

METHODS

Roles of MYPT1 deregulation in tumor angiogenesis of PCa was determined in vitro and in vivo experiments. Expression patterns of MYPT1 and CD31 proteins were examined by immunohistochemistry and immunofluorescence, respectively. Associations of MYPT1/CD31 combination with various clinicopathological features and patients' prognosis of PCa were also statistically evaluated.

RESULTS

Through gain- and loss-of-function experiments, MYPT1 inhibited capillary tube formation of endothelial cells and in vivo tumor angiogenesis in a mouse model with the downregulation of VEGF and CD31 expression. In addition, MYPT1 expression was significantly decreased, while CD31 expression was dramatically increased in PCa tissues compared to benign prostate tissues. Notably, MYPT1 expression levels in PCa tissues were negatively correlated with that of CD31. Statistically, MYPT1-low/CD31- high expression was distinctly associated with high Gleason score, positive biochemical recurrence, and reduced overall survival of PCa patients. Moreover, PCa patients with MYPT1-low/CD31-high expression more frequently had shorter overall, biochemical recurrence-free and metastasis-free survivals. MYPT1/CD31 combination was identified as an independent factor to predict biochemical recurrence-free and metastasis-free survivals of PCa patients.

CONCLUSIONS

Our findings indicate that MYPT1 may inhibit angiogenesis and contribute favorable prognosis in PCa patients, implying that MYPT1 might be a potential drug candidate in anticancer therapy.

Iron deficiency stress can induce MxNAS1 protein expression to facilitate iron redistribution in Malus xiaojinensis

Iron (Fe) is a vital trace element in plants, and deficiency of this element in apple trees can reduce fruit quality. Nicotianamine (NA) is known to play an important role in Fe transport and endogenous hormone balance. In the present study, we investigated the role of a nicotianamine synthase 1 gene (MxNas1) in an apple species, Malus xiaojinensis, that has a more Fe-efficient genotype than other apple species and ecotypes. To characterise the response of M. xiaojinensis to Fe deficiency, we used quantitative Q-PCR to determine the level of expression of MxNas1 and Western blot to measure protein levels. Immunohistochemical staining and GFP fluorescence localisation of the MxNAS1 protein were also carried out. HPLC and polarised absorption spectrophotometry were performed to investigate the effects of overexpression of MxNas1 in order to elucidate the role of MxNAS1 in the cellular uptake of active Fe in tobacco suspension cells. We found that MxNas1 expression and protein levels were higher under Fe deficiency stress than under Fe sufficiency. Immunohistochemical staining showed that MxNAS1 was localised mainly in the epidermal and vascular tissues of the roots, vascular tissues of the stem and palisade cells of mature leaves, and in parenchyma cells of young leaves. MxNAS1 was mainly localised in the plasma membranes and vesicles of protoplasts. In addition, overexpression of MxNas1 in stable transgenic tobacco cells increased NA and active Fe content under Fe sufficiency. The results suggest that MxNas1 expression in M. xiaojinensis is induced in response to Fe deficiency stress, resulting in higher levels of the protein. MxNAS1 may be involved in the redistribution of Fe in M. xiaojinensis under Fe deficiency.