A Chinese Medicine Formula “Xian-Jia-Tang” for Treating Bladder Outlet Obstruction by Improving Urodynamics and Inhibiting Oxidative Stress through Potassium Channels

The aim of this study is to investigate efficacy of a traditional Chinese medicine formula (named Xian-Jia-Tang, XJT) on bladder outlet obstruction (BOO) in rats and explore its mechanisms. Total 80 BOO model rats were established and randomly divided into 4 groups: physiological saline, XJT, Cesium Chloride (CC), and XJT and CC groups. Meanwhile, 12 rats were used as normal control. Bladder weight and urodynamics were measured. Oxidative stress level and mRNA expressions of potassium channels gene were detected in detrusor. The mRNA and protein levels of hypoxia inducible factor-α (HIF-α) in detrusor were detected by RT-PCR and Western blot. BOO model rats showed significantly higher bladder weight and abnormal urodynamics. XJT significantly improved the abnormal urodynamics and inhibited the oxidative stress and changes of mRNA levels of potassium channels genes in detrusor of BOO model rats. Moreover, KATP and SK2/3 mRNA were overexpressed in BOO model rats treated by XJT. Besides, the significantly increased levels of HIF-α mRNA and protein were also inhibited by XJT. However, these inhibition effects of XJT were weakened by CC. XJT could effectively improve the urodynamics and inhibit the oxidative stress caused by hypoxia through suppressing the role of potassium channels in BOO model rats

A Novel Cold-Regulated Cold Shock Domain Containing Protein from Scallop Chlamys farreri with Nucleic Acid-Binding Activity

Background: The cold shock domain (CSD) containing proteins (CSDPs) are one group of the evolutionarily conserved nucleic acid-binding proteins widely distributed in bacteria, plants, animals, and involved in various cellular processes, including adaptation to low temperature, cellular growth, nutrient stress and stationary phase. Methodology: The cDNA of a novel CSDP was cloned from Zhikong scallop Chlamys farreri (designated as CfCSP) by expressed sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The full length cDNA of CfCSP was of 1735 bp containing a 927 bp open reading frame which encoded an N-terminal CSD with conserved nucleic acids binding motif and a C-terminal domain with four Arg-Gly-Gly (RGG) repeats. The CSD of CfCSP shared high homology with the CSDs from other CSDPs in vertebrate, invertebrate and bacteria. The mRNA transcripts of CfCSP were mainly detected in the tissue of adductor and also marginally detectable in gill, hepatopancreas, hemocytes, kidney, mantle and gonad of healthy scallop. The relative expression level of CfCSP was up-regulated significantly in adductor and hemocytes at 1 h and 24 h respectively after low temperature treatment (P,0.05). The recombinant CfCSP protein (rCfCSP) could bind ssDNA and in vitro transcribed mRNA, but it could not bind dsDNA. BX04, a cold sensitive Escherichia coli CSP quadruple-deletion mutant, was used to examine the cold adaptation ability of CfCSP. After incubation at 17uC for 120 h, the strain of BX04 containing the vector pINIII showed growth defect and failed to form colonies, while strain containing pINIII-CSPA or pINIII

The Relative Distance Prediction of Transmembrane Protein Surface Residue Based on Improved Residual Networks

(1) Background: Transmembrane proteins (TMPs) act as gateways connecting the intra- and extra-biomembrane environments, exchanging material and signals crossing the biofilm. Relevant evidence shows that corresponding interactions mostly happen on the TMPs’ surface. Therefore, knowledge of the relative distance among surface residues is critically helpful in discovering the potential local structural characters and setting the foundation for the protein’s interaction with other molecules. However, the prediction of fine-grained distances among residues with sequences remains challenging; (2) Methods: In this study, we proposed a deep-learning method called TMP-SurResD, which capitalized on the combination of the Residual Block (RB) and Squeeze-and-Excitation (SE) for simultaneously predicting the relative distance of functional surface residues based on sequences’ information; (3) Results: The comprehensive evaluation demonstrated that TMP-SurResD could successfully capture the relative distance between residues, with a Pearson Correlation Coefficient (PCC) of 0.7105 and 0.6999 on the validation and independent sets, respectively. In addition, TMP-SurResD outperformed other methods when applied to TMPs surface residue contact prediction, and the maximum Matthews Correlation Coefficient (MCC) reached 0.602 by setting a threshold to the predicted distance of 10; (4) Conclusions: TMP-SurResD can serve as a useful tool in supporting a sequence-based local structural feature construction and exploring the function and biological mechanisms of structure determination in TMPs, which can thus significantly facilitate the research direction of molecular drug action, target design, and disease treatment

The Relative Distance Prediction of Transmembrane Protein Surface Residue Based on Improved Residual Networks

(1) Background: Transmembrane proteins (TMPs) act as gateways connecting the intra- and extra-biomembrane environments, exchanging material and signals crossing the biofilm. Relevant evidence shows that corresponding interactions mostly happen on the TMPs’ surface. Therefore, knowledge of the relative distance among surface residues is critically helpful in discovering the potential local structural characters and setting the foundation for the protein’s interaction with other molecules. However, the prediction of fine-grained distances among residues with sequences remains challenging; (2) Methods: In this study, we proposed a deep-learning method called TMP-SurResD, which capitalized on the combination of the Residual Block (RB) and Squeeze-and-Excitation (SE) for simultaneously predicting the relative distance of functional surface residues based on sequences’ information; (3) Results: The comprehensive evaluation demonstrated that TMP-SurResD could successfully capture the relative distance between residues, with a Pearson Correlation Coefficient (PCC) of 0.7105 and 0.6999 on the validation and independent sets, respectively. In addition, TMP-SurResD outperformed other methods when applied to TMPs surface residue contact prediction, and the maximum Matthews Correlation Coefficient (MCC) reached 0.602 by setting a threshold to the predicted distance of 10; (4) Conclusions: TMP-SurResD can serve as a useful tool in supporting a sequence-based local structural feature construction and exploring the function and biological mechanisms of structure determination in TMPs, which can thus significantly facilitate the research direction of molecular drug action, target design, and disease treatment

Control of tectonic differentiation on the formation of large oil and gas fields in craton basins: A case study of Sinian–Triassic of the Sichuan Basin

Craton basins are the main sites where marine carbonate oil and gas reservoirs develop in China. However, the previous studies scarcely focused on the controlling effects of tectonic differentiation on the formation of large oil and gas fields in the ancient craton basins. In such circumstances, it is difficult to evaluate and select the favorable zones for exploring carbonate oil and gas. In this paper, based on the research results of the Sinian–Triassic prototype basin and lithofacies paleogeography of the Sichuan Basin, the tectonic differentiation pattern of craton basins and its controls on the accumulation elements and the distribution of hydrocarbons were analyzed with reference to the concept that structures control the sedimentation and distribution of oil and gas. The study reveals the results in three aspects. First, the intra-cratonic graben controls the high-quality source rocks and the hydrocarbon generation center, which forms good source-reservoir assemblage with the high-quality reservoir in the platform margin at the flank, showing excellent near-source accumulation conditions. Second, the three types of paleo-uplifts (i.e. differential denudation, syn-sedimentary, and folding) and the deep-large faults developed in the craton are favorable for the formation and distribution of large-scale carbonate reservoirs. Third, the superimposed areas with tectonic differentiation in multiple periods and multiple types are favorable for forming large oil and gas fields. It is concluded that the marine carbonate rocks show a huge oil and gas exploration potential in the Sichuan Basin. Attention should be paid to the new exploration targets of natural gas, such as the Sinian Dengying Fm. in the platform margin at the east flank of Deyang–Anyue graben, the Lower Cambrian Longwangmiao Fm. on the slope of paleo-uplift in central Sichuan Basin, and the Middle Permian Maokou Fm. in central–west Sichuan Basin, where oil and gas accumulation conditions are favorable

Calculation and inducement of lacuna in the Mid-Permian Maokou Fm of Sichuan Basin

Erosion of carbonate strata not only can reflect the karst landform, but also can reveal the characteristics of carbonate karst reservoirs indirectly. In Sichuan Basin, the quantity and root causes of lacuna in the top strata of the Maokou Fm are unclear. In this paper, the features of such stratigraphic lacuna were analyzed qualitatively. Then, in accordance with the spectral transformation of GR logs and the characteristics of cycle in the Maokou Fm penetrated by four typical wells, the Milankovich cycles of the logs were identified. Then they were used for quantitative calculation of erosion quantity and for highlighting the root causes for the stratigraphic lacuna. According to the research results, the Mao-4 Member is residual in the Yibin–Ya'an–Jiangyou area and the Shizhu area, but missing in the other parts of Sichuan Basin with a stratigraphic lacuna intensity gradually increasing from the southern part to the central part and to the northern parts of the basin. Besides, the stratigraphic lacuna of the Maokou Fm varies from 0 to 200 m – for example, 0–60 m in the southwestern and northeastern parts of the basin, and 140–200 m in the southern, central and northern parts of the basin. Moreover, formation denudation occurred at the end of the Maokou Period was induced predominantly by erosion generated as the sea level fell during the glacial age, especially in the northern part of the basin. Also, the Mid-Permian karst landform inherited the sedimentary features of being high in the southwest and low in the northeast. In the areas from the southwestern to central and to the northern Sichuan Basin, the karst landform transits from erosion highlands to karst upper and lower slopes, coinciding well with the sedimentary features of the Wujiaping Period. In conclusion, the Milankovich cycles can be used to calculate the stratigraphic erosion in carbonate formations efficiently and accurately. The technique can be extended to the restoration of stratigraphic erosion in other marine basins. Keywords: Sichuan basin, Mid-Permian, Maokou Fm, Milankovich cycle, Stratigraphic erosion, Quantitative calculation, Glacial age, Genesis discussion, Karst landfor

Data from: The neuroendocrine immunomodulatory axis-like pathway mediated by circulating haemocytes in pacific oyster Crassostrea gigas

The neuroendocrine-immune (NEI) regulatory network is a complex system, which plays an indispensable role in the immunity of host. In this study, a neuroendocrine immunomodulatory axis (NIA)-like pathway mediated by the nervous system and haemocytes was characterized in the oyster Crassostrea gigas. Once invaded pathogen was recognized by the host, the nervous system would temporally release neurotransmitters to modulate the immune response. Instead of acting passively, oyster haemocytes were able to mediate neuronal immunomodulation promptly by controlling the expression of specific neurotransmitter receptors on cell surface and modulating their binding sensitivities, thus regulating intracellular concentration of Ca2+. This neural immunomodulation mediated by the nervous system and haemocytes could influence cellular immunity in oyster by affecting mRNA expression level of TNF genes, and humoral immunity by affecting the activities of key immune-related enzymes. In summary, though simple in structure, the ‘nervous-haemocyte’ NIA-like pathway regulates both cellular and humoral immunity in oyster, meaning a world to the effective immune regulation of the NEI network

A scallop nitric oxide synthase (NOS) with structure similar to neuronal NOS and its involvement in the immune defense.

BACKGROUND: Nitric oxide synthase (NOS) is responsible for synthesizing nitric oxide (NO) from L-arginine, and involved in multiple physiological functions. However, its immunological role in mollusc was seldom reported. METHODOLOGY: In the present study, an NOS (CfNOS) gene was identified from the scallop Chlamys farreri encoding a polypeptide of 1486 amino acids. Its amino acid sequence shared 50.0~54.7, 40.7~47.0 and 42.5~44.5% similarities with vertebrate neuronal (n), endothelial (e) and inducible (i) NOSs, respectively. CfNOS contained PDZ, oxygenase and reductase domains, which resembled those in nNOS. The CfNOS mRNA transcripts expressed in all embryos and larvae after the 2-cell embryo stage, and were detectable in all tested tissues with the highest level in the gonad, and with the immune tissues hepatopancreas and haemocytes included. Moreover, the immunoreactive area of CfNOS distributed over the haemocyte cytoplasm and cell membrane. After LPS, β-glucan and PGN stimulation, the expression level of CfNOS mRNA in haemocytes increased significantly at 3 h (4.0-, 4.8- and 2.7-fold, respectively, P < 0.01), and reached the peak at 12 h (15.3- and 27.6-fold for LPS and β-glucan respectively, P < 0.01) and 24 h (17.3-fold for PGN, P < 0.01). In addition, TNF-α also induced the expression of CfNOS, which started to increase at 1 h (5.2-fold, P < 0.05) and peaked at 6 h (19.9-fold, P < 0.01). The catalytic activity of the native CfNOS protein was 30.3 ± 0.3 U mgprot(-1), and it decreased significantly after the addition of the selective inhibitors of nNOS and iNOS (26.9 ± 0.4 and 29.3 ± 0.1 U mgprot(-1), respectively, P < 0.01). CONCLUSIONS: These results suggested that CfNOS, with identical structure with nNOS and similar enzymatic characteristics to nNOS and iNOS, played the immunological role of iNOS to be involved in the scallop immune defense against PAMPs and TNF-α

Discovery of Xuanhan-Kaijiang Paleouplift and its significance in the Sichuan Basin, SW China

A large inherited paleouplift from Pre-Sinian to Early Cambrian, named Xuanhan-Kaijiang paleouplift, has been discovered based on multiple geological information in the eastern Sichuan Basin: firstly, onlap deposition of Upper Sinian Dengying Formation and Lower Cambrian is observed from peripheral zone to central Xuanhan-Kaijiang area from the seismic profile; secondly, Dengying Formation thickness distribution map shows that this formation is thinnest in Xuanhan-Kaijiang area, and thickens towards the surrounding areas; thirdly, terrigenous clastic rock is observed in Upper Sinian Dengying Formation on outcrops in Chengkou County and Wuxi County etc., indicating the development of a paleouplift. The analysis of the characteristics, formation and evolution of the paleouplift reveals that the plane distribution of the paleouplift shows an arched structure, stretching in a north-south trend. The area of the paleouplift is around 16 000 km2. Vertically, the paleouplift can be divided into three parts: platform in the middle, steep slope in the west and ramp in the east. Originally, the paleouplift was an erosion-type uplift above the water level during the early stage of the Late Sinian; and gradually transformed into deposition-type uplift under water level during the late stage of the Late Sinian to the Early Cambrian. The formation of the paleouplift was controlled by several factors, including basement uplift, intracratonic rift, basement faults and regional uplifting. The paleouplift and its slope areas, favorable for the development of high energy facies and karst weathering reservoirs, are important exploration target areas in the eastern Sichuan Basin in the near future. Key words: Sichuan Basin, eastern Sichuan, paleouplift, Xuanhan-Kaijiang paleouplift, Sinian to Early Cambrian, intracratonic rift, onlap depositio

The Polymorphism in the Promoter of HSP70 Gene Is Associated with Heat Tolerance of Two Congener Endemic Bay Scallops (<i>Argopecten irradians irradians</i> and <i>A. i. concentricus</i>)

<div><p>Background</p><p>The heat shock protein 70 (HSP70) is one kind of molecular chaperones, which plays a key role in protein metabolism under normal and stress conditions.</p><p>Methodology</p><p>In the present study, the mRNA expressions of HSP70 under normal physiological condition and after acute heat stress were investigated in gills of two bay scallop populations (<i>Argopecten irradians irradians</i> and <i>A. i. concentricus</i>). The heat resistant scallops <i>A. i. concentricus</i> showed significantly lower basal level and higher induction of HSP70 compared with that of the heat sensitive scallops <i>A. i. irradians</i>. The promoter sequence of HSP70 gene from bay scallop (AiHSP70) was cloned and the polymorphisms within this region were investigated to analyze their association with heat tolerance. Totally 11 single nucleotide polymorphisms (SNPs) were identified, and four of them (−967, −480, −408 and −83) were associated with heat tolerance after HWE analysis and association analysis. Based on the result of linkage disequilibrium analysis, the <i>in vitro</i> transcriptional activities of AiHSP70 promoters with different genotype were further determined, and the results showed that promoter from <i>A. i. concentricus</i> exhibited higher transcriptional activity than that from <i>A. i. irradians</i> (<i>P</i><0.05).</p><p>Conclusions</p><p>The results provided insights into the molecular mechanisms underlying the thermal adaptation of different congener endemic bay scallops, which suggested that the increased heat tolerance of <i>A. i. concentricus</i> (compared with <i>A. i. irradians</i>) was associated with the higher expression of AiHSP70. Meanwhile, the −967 GG, −480 AA, −408 TT and −83 AG genotypes could be potential markers for scallop selection breeding with higher heat tolerance.</p></div