Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)

Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in virus, bacteria and mammals. Our results support the hypothesis that the molecular clock for proteins has two pointers existing separately in DNA and protein sequences. It is more accurate to read the molecular clock by combination (additive) of these two pointers, since the ticking rates of them are sometimes consistent, sometimes different. CAUSA software were released as Open Source under GNU/GPL license, and are downloadable free of charge from the website www.dnapluspro.com

Transcriptome and network analyses reveal key pathways and genes involved in response to carotenoid deposition in scallop muscle

Carotenoids are essential nutrients for humans and animals, and carotenoid content has become an important trait to evaluate the nutritional value of many cultured animals. Marine animals provide humans with diverse carotenoids, and developing carotenoid-enriched varieties has been the focus of marine animal breeding. Understanding the molecular mechanism of carotenoid deposition could benefit marine animal breeding for carotenoid content improvement. In the present study, transcriptomic analysis of adductor muscle was performed between Yesso scallop (Patinopecten yessoensis) with white muscle (WM) and carotenoid-enriched orange muscle (OM). A total of 683 differentially expressed genes (DEGs) were identified, with 302 and 381 genes being up- and down-regulated in OM scallop. Gene co-expression network analysis identified four carotenoid accumulation−related modules, including three up-regulated modules and one down-regulated module. The genes in up-regulated modules mainly participate in the pathways of translation and transcription (MEgreen), immune system (MElightyellow), and lipid metabolism (MEpink), while the down-regulated module is mainly enriched with genes involved in various metabolic pathways (MEturquoise). As the causal gene responsible for muscle coloration in scallop, PyBCO-like 1 is the hub gene of MEturquoise and showed strong connectivity with NR2F1A, a transcriptional factor involved in the regulation of retinoic acid. In addition, the up-regulated DEGs, including WDR3, RPP29, TBL3, RIOK2, and NOB1 from “ribosome biogenesis”, HSP70s and HSP702Bs from “antigen processing and presentation”, and ACOX1 from “PPAR signaling pathway” were identified as hub genes, indicating the potential regulatory role of these genes and pathways in response to carotenoid accumulation. Our data contribute to a deeper understanding of the regulatory and response mechanisms of carotenoid accumulation in marine animals

Insight into the chemical adsorption properties of CO molecules supported on Au or Cu and hybridized Au-CuO nanoparticles

Although nanosized Au clusters have been well developed for many applications, fundamental understanding of their adsorption/activation behaviors in catalytic applications is still lacking, especially when other elements provide promotion or hybridization functions. Au hybridized with Cu element is a highly investigated system; Cu is in the same element group as Au and thus displays similar physicochemical properties. However, their hybrids are not well understood in terms of their chemical states and adsorption/ activation properties. In this work, typical gamma-Al2O3-supported Au and CuO as well as Au-CuO nanoparticles were prepared and characterized to explore their adsorption/activation properties in depth using CO as a probe molecule using advanced techniques, such as XPS, HR-TEM, temperature programmed experiments and operando DRIFT combined with mass spectra. It was found that gold and copper can both act as active sites during CO adsorption and activation. The CO-TPD and operando DRIFT results also revealed that CO molecules were able to react with surface oxygenated species, resulting in the direct formation of CO2 over the three samples in the absence of gaseous O-2. The gold step sites (Austep) participated more readily in the reaction, especially under gaseous O-2-free conditions. During adsorption, CO molecules were more preferentially adsorbed on Au-0 sites at lower temperature comparing with those on the Cu-0 sites. However, competitive adsorption occurred between CO adsorbed on Au-0 and Cu-0 with increased reaction temperature, and the synergy between the Au and Cu compositions was too strong to suppress the adsorption and activation of the CO molecules. The dynamic adsorption equilibrium over 120 degrees C to 200 degrees C resulted in the appearance of a hysteresis performance platform

Single nucleotide polymorphism in the 3′ untranslated region of LPP is a risk factor for lung cancer: a case-control study

Abstract Background Single nucleotide polymorphisms (SNPs) in 3′-untranslated region (UTR) of genes related with cell-matrix adhesions and migration might affect miRNA binding and potentially affect the risk of cancer. The present study aimed to screen SNPs in 3′ UTR of cancer-related genes and investigate their contribution to the susceptibility of lung cancer. Methods Seven SNPs were selected and genotyped in a case-control study (322 lung cancer patients and 384 controls) among Chinese Han population. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated by logistic regression adjusted for age and gender in multiple genetic models. Results In stratified analyses by gender, three (rs1064607, rs3796283 and rs2378456) of LPP gene were associated with a significantly increased susceptibility for lung cancer among male population. Besides, LPP rs2378456 weakened lung cancer risk in female. LPP rs1064607 polymorphism was significantly correlated with increased risk of lung adenocarcinoma. Furthermore, AA genotype of TNS3 rs9876 polymorphism was associated with lymphatic metastasis. Conclusion Our results provides evidence for the impact of LPP polymorphisms on the susceptibility to lung cancer in Chinese population

Single-Crystalline Pyramidal TiCxParticles Grown by Biphase Diffusion Synthesis

© 2022 American Chemical Society.In this study, we present single-crystalline pyramid-shaped (SP) TiCx particles synthesized on a stacked melt (copper)-solid (titanium) substrate using a biphase diffusion synthesis (BDS) method, in which different sizes ranging from nano- to micrometer scale were obtained within the copper melt with the {100} planes exposed to air. Direct observation and further plasma treatment of the pyramids at different self-assembly stages facilitated the investigation of their growth mode, especially in the horizontal plane. The dendritic growth mode along with the edge and corner-shared modes of the SP TiCx particles frozen on the copper surface was investigated. With SP TiCx particles stacked on top, MoS2-based phototransistors exhibited an up to 6-fold photocurrent increase under laser illumination at different wavelengths, which was attributed to the localized surface plasmonic resonance (LSPR) effect. The BDS method is applied for the synthesis of SP TiCx particles, with a detailed investigation of the relevant growth mode and related applications, such as decoration for high-performance photodevices.11Nsciescopu

Dual‐logic‐in‐memory implementation with orthogonal polarization of van der Waals ferroelectric heterostructure

Abstract The rapid advancement of AI‐enabled applications has resulted in an increasing need for energy‐efficient computing hardware. Logic‐in‐memory is a promising approach for processing the data stored in memory, wherein fast and efficient computations are possible owing to the parallel execution of reconfigurable logic operations. In this study, a dual‐logic‐in‐memory device, which can simultaneously perform two logic operations in four states, is demonstrated using van der Waals ferroelectric field‐effect transistors (vdW FeFETs). The proposed dual‐logic‐in‐memory device, which also acts as a two‐bit storage device, is a single bidirectional polarization‐integrated ferroelectric field‐effect transistor (BPI‐FeFET). It is fabricated by integrating an in‐plane vdW ferroelectric semiconductor SnS and an out‐of‐plane vdW ferroelectric gate dielectric material—CuInP2S6. Four reliable resistance states with excellent endurance and retention characteristics were achieved. The two‐bit storage mechanism in a BPI‐FeFET was analyzed from two perspectives: carrier density and carrier injection controls, which originated from the out‐of‐plane polarization of the gate dielectric and in‐plane polarization of the semiconductor, respectively. Unlike conventional multilevel FeFETs, the proposed BPI‐FeFET does not require additional pre‐examination or erasing steps to switch from/to an intermediate polarization, enabling direct switching between the four memory states. To utilize the fabricated BPI‐FeFET as a dual‐logic‐in‐memory device, two logical operations were selected (XOR and AND), and their parallel execution was demonstrated. Different types of logic operations could be implemented by selecting different initial states, demonstrating various types of functions required for numerous neural network operations. The flexibility and efficiency of the proposed dual‐logic‐in‐memory device appear promising in the realization of next‐generation low‐power computing systems