Systematic analysis of the Hippo pathway organization and oncogenic alteration in evolution.

The Hippo pathway is a central regulator of organ size and a key tumor suppressor via coordinating cell proliferation and death. Initially discovered in Drosophila, the Hippo pathway has been implicated as an evolutionarily conserved pathway in mammals; however, how this pathway was evolved to be functional from its origin is still largely unknown. In this study, we traced the Hippo pathway in premetazoan species, characterized the intrinsic functions of its ancestor components, and unveiled the evolutionary history of this key signaling pathway from its unicellular origin. In addition, we elucidated the paralogous gene history for the mammalian Hippo pathway components and characterized their cancer-derived somatic mutations from an evolutionary perspective. Taken together, our findings not only traced the conserved function of the Hippo pathway to its unicellular ancestor components, but also provided novel evolutionary insights into the Hippo pathway organization and oncogenic alteration

Evolution of digestive enzymes and dietary diversification in birds

As the most species-rich class of tetrapod vertebrates, Aves possesses diverse feeding habits, with multiple origins of insectivory, carnivory, frugivory, nectarivory, granivory and omnivory. Since digestive enzymes mediate and limit energy and nutrient uptake, we hypothesized that genes encoding digestive enzymes have undergone adaptive evolution in birds. To test this general hypothesis, we identified 16 digestive enzyme genes (including seven carbohydrase genes (hepatic amy, pancreatic amy, salivary amy, agl, g6pc, gaa and gck), three lipase genes (cyp7a1, lipf and pnlip), two protease genes (ctrc and pgc), two lysozyme genes (lyz and lyg) and two chitinase genes (chia and chit1)) from the available genomes of 48 bird species. Among these 16 genes, three (salivary amy, lipf and chit1) were not found in all 48 avian genomes, which was further supported by our synteny analysis. Of the remaining 13 genes, eight were single-copy and five (chia, gaa, lyz, lyg and pgc) were multi-copy. Moreover, the multi-copy genes gaa, lyg and pgc were predicted to exhibit functional divergence among copies. Positively selected sites were detected in all of the analyzed digestive enzyme genes, except agl, g6pc, gaa and gck, suggesting that different diets may have favored differences in catalytic capacities of these enzymes. Furthermore, the analysis also revealed that the pancreatic amylase gene and one of the lipase genes (cyp7a1) have higher ω (the ratio of nonsynonymous to the synonymous substitution rates) values in species consuming a larger amount of seeds and meat, respectively, indicating an intense selection. In addition, the gck carbohydrase gene in species consuming a smaller amount of seeds, fruits or nectar, and a lipase gene (pnlip) in species consuming less meat were found to be under relaxed selection. Thus, gene loss, gene duplication, functional divergence, positive selection and relaxed selection have collectively shaped the evolution of digestive enzymes in birds, and the evolutionary flexibility of these enzymes may have facilitated their dietary diversification

Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

BACKGROUND: Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incongruence of molecular evidence, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performed de novo transcriptome sequencing of four RNA-seq libraries prepared from brain and liver tissues of a plateau zokor (Eospalax baileyi) and a hoary bamboo rat (Rhizomys pruinosus), and analyzed the transcriptome sequences alongside a published transcriptome of the Middle East blind mole rat (Spalax galili). We characterize the transcriptome assemblies of the two spalacids, and recover the phylogeny of the three subfamilies using a phylogenomic approach. RESULTS: Approximately 50.3 million clean reads from the zokor and 140.8 million clean reads from the bamboo ratwere generated by Illumina paired-end RNA-seq technology. All clean reads were assembled into 138,872 (the zokor) and 157,167 (the bamboo rat) unigenes, which were annotated by the public databases: the Swiss-prot, Trembl, NCBI non-redundant protein (NR), NCBI nucleotide sequence (NT), Gene Ontology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 5,116 nuclear orthologous genes were identified in the three spalacids and mouse, which was used as an outgroup. Phylogenetic analysis revealed a sister group relationship between the zokor and the bamboo rat, which is supported by the majority of gene trees inferred from individual orthologous genes, suggesting subfamily Myospalacinae is more closely related to subfamily Rhizomyinae. The same topology was recovered from concatenated sequences of 5,116 nuclear genes, fourfold degenerate sites of the 5,116 nuclear genes and concatenated sequences of 13 protein coding mitochondrial genes. CONCLUSIONS: This is the first report of transcriptome sequencing in zokors and bamboo rats, representing a valuable resource for future studies of comparative genomics in subterranean mammals. Phylogenomic analysis provides a conclusive resolution of interrelationships of the three subfamilies within the family Spalacidae, and highlights the power of phylogenomic approach to dissect the evolutionary history of rapid radiations in the tree of life

Use acupuncture to relieve perimenopausal syndrome: study protocol of a randomized controlled trial

Law Number 11 / 2008 on Information and Electronic Transaction (UU ITE) is the regulation concerning on criminal law in addition to the Criminal Code (KUHP). UU ITE is commonly regarded additional regulation of the Criminal Code as a special law (lex specialis) in which Penal Code is deemed as lex generalis. It is based on the principle of lex specialis derogate legi generalis. This article uses legal research to review the decision of District Court in Bandung Number 1033/PID.B/2014/PN.BDG where it comprises legislation and cases. It concludes that the judge is not frugal in applying the principle lex specialis derogat legi generalis in the consideration. This is associated with the indictment of public prosecutor which only prejudges with article 303 paragraph (1) to 2. In contrast, the indictment which does not meet the requirement of a careful, clear, and complete description asserts to become void by law. Keywords: Online Gambling, Criminal Principle, Indictmen

Effects of epigallocatechin-3-gallate on bovine oocytes matured

Objective Epigallocatechin-3-gallate (EGCG) is a major ingredient of catechin polyphenols and is considered one of the most promising bioactive compounds in green tea because of its strong antioxidant properties. However, the protective role of EGCG in bovine oocyte in vitro maturation (IVM) has not been investigated. Therefore, we aimed to study the effects of EGCG on IVM of bovine oocytes. Methods Bovine oocytes were treated with different concentrations of EGCG (0, 25, 50, 100, and 200 μM), and the nuclear and cytoplasmic maturation, cumulus cell expansion, intracellular reactive oxygen species (ROS) levels, total antioxidant capacity, the early apoptosis and the developmental competence of in vitro fertilized embryos were measured. The mRNA abundances of antioxidant genes (nuclear factor erythriod-2 related factor 2 [NRF2], superoxide dismutase 1 [SOD1], catalase [CAT], and glutathione peroxidase 4 [GPX4]) in matured bovine oocytes were also quantified. Results Nuclear maturation which is characterized by first polar body extrusion, and cytoplasmic maturation characterized by peripheral and cortical distribution of cortical granules and homogeneous mitochondrial distribution were significantly improved in the 50 μM EGCG-treated group compared with the control group. Adding 50 μM EGCG to the maturation medium significantly increased the cumulus cell expansion index and upregulated the mRNA levels of cumulus cell expansion-related genes (hyaluronan synthase 2, tumor necrosis factor alpha induced protein 6, pentraxin 3, and prostaglandin 2). Both the intracellular ROS level and the early apoptotic rate of matured oocytes were significantly decreased in the 50 μM EGCG group, and the total antioxidant ability was markedly enhanced. Additionally, both the cleavage and blastocyst rates were significantly higher in the 50 μM EGCG-treated oocytes after in vitro fertilization than in the control oocytes. The mRNA abundance of NRF2, SOD1, CAT, and GPX4 were significantly increased in the 50 μM EGCG-treated oocytes. Conclusion In conclusion, 50 μM EGCG can improve the bovine oocyte maturation, and the protective role of EGCG may be correlated with its antioxidative property

Applications of Catalytic Hairpin Assembly Reaction in Biosensing.

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered

Identification ferroptosis-related hub genes and diagnostic model in Alzheimer’s disease

BackgroundFerroptosis is a newly defined form of programmed cell death and plays an important role in Alzheimer’s disease (AD) pathology. This study aimed to integrate bioinformatics techniques to explore biomarkers to support the correlation between ferroptosis and AD. In addition, further investigation of ferroptosis-related biomarkers was conducted on the transcriptome characteristics in the asymptomatic AD (AsymAD).MethodsThe microarray datasets GSE118553, GSE132903, GSE33000, and GSE157239 on AD were downloaded from the GEO database. The list of ferroptosis-related genes was extracted from the FerrDb website. Differentially expressed genes (DEGs) were identified by R “limma” package and used to screen ferroptosis-related hub genes. The random forest algorithm was used to construct the diagnostic model through hub genes. The immune cell infiltration was also analyzed by CIBERSORTx. The miRNet and DGIdb database were used to identify microRNAs (miRNAs) and drugs which targeting hub genes.ResultsWe identified 18 ferroptosis-related hub genes anomalously expressed in AD, and consistent expression trends had been observed in both AsymAD The random forest diagnosis model had good prediction results in both training set (AUC = 0.824) and validation set (AUC = 0.734). Immune cell infiltration was analyzed and the results showed that CD4+ T cells resting memory, macrophages M2 and neutrophils were significantly higher in AD. A significant correlation of hub genes with immune infiltration was observed, such as DDIT4 showed strong positive correlation with CD4+ T cells memory resting and AKR1C2 had positive correlation with Macrophages M2. Additionally, the microRNAs (miRNAs) and drugs which targeting hub genes were screened.ConclusionThese results suggest that ferroptosis-related hub genes we screened played a part in the pathological progression of AD. We explored the potential of these genes as diagnostic markers and their relevance to immune cells which will help in understanding the development of AD. Targeting miRNAs and drugs provides new research clues for preventing the development of AD

Simultaneous Formation of CH₃NH₃PbI₃ and electron transport layers using antisolvent method for efficient perovskite solar cells

A new antisolvent method was developed to prepare CH₃NH₃PbI₃ and electron transport layers for making efficient hybrid perovskite solar cells. By directly using [6,6]-phenyl-C61-butyric acid methyl ester in chlorobenzene solution as antisolvent, CH₃NH₃PbI₃ and electron transport layers were simultaneously formed in the films. This method not only simplifies the fabrication process of devices, but also produces uniform perovskite films and improves the interfacial structures between CH₃NH₃PbI₃ and electron transport layers. Large perovskite grains were observed in these films, with the average grain size of >1 μm. The so-formed CH₃NH₃PbI₃/electron transport layers demonstrated good optical and charge transport properties. And perovskite solar cells fabricated using these simultaneously-formed layers achieved a higher power conversion efficiency of 16.58% compared to conventional antisolvent method (14.92%). This method reduces nearly 80% usage of chlorobenzene during the fabrication, offering a more facile and environment-friendly approach to fabricate efficient perovskite solar cells than the conventional antisolvent method