Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.

Deep learning has emerged as a powerful tool for investigating intricate biological processes in plants by harnessing the potential of large-scale data. Gene regulation is a complex process that transcription factors (TFs), cooperating with their target genes, participate in through various aspects of biological processes. Despite its significance, the study of gene regulation has primarily focused on a limited number of notable instances, leaving numerous aspects and interactions yet to be explored comprehensively. Here, we developed DEGRN (Deep learning on Expression for Gene Regulatory Network), an innovative deep learning model designed to decipher gene interactions by leveraging high-dimensional expression data obtained from bulk RNA-Seq and scRNA-Seq data in the model plant Arabidopsis. DEGRN exhibited a compared level of predictive power when applied to various datasets. Through the utilization of DEGRN, we successfully identified an extensive set of 3,053,363 high-quality interactions, encompassing 1430 TFs and 13,739 non-TF genes. Notably, DEGRN's predictive capabilities allowed us to uncover novel regulators involved in a range of complex biological processes, including development, metabolism, and stress responses. Using leaf senescence as an example, we revealed a complex network underpinning this process composed of diverse TF families, including bHLH, ERF, and MYB. We also identified a novel TF, named MAF5, whose expression showed a strong linear regression relation during the progression of senescence. The mutant maf5 showed early leaf decay compared to the wild type, indicating a potential role in the regulation of leaf senescence. This hypothesis was further supported by the expression patterns observed across four stages of leaf development, as well as transcriptomics analysis. Overall, the comprehensive coverage provided by DEGRN expands our understanding of gene regulatory networks and paves the way for further investigations into their functional implications.

Intraday relations between physical activity and energy intake among behavioral weight loss participants.

OBJECTIVE: Weight loss results from a negative energy balance, when energy intake (EI) is less than energy expended, e.g., from physical activity (PA). However, PA may impact energy balance beyond energy expenditure alone, through indirect effects on eating behavior. Yet, no research has examined if engaging in PA-a central component of most weight loss programs-is associated with same-day EI among individuals with overweight/obesity pursuing weight loss. METHOD: Adults (N = 101) with overweight/obesity in a weight loss program were prescribed a reduced-calorie diet and PA regimen (250 min of moderate-to-vigorous PA at midtreatment). For 3 weeks at midtreatment, PA and EI were measured via an accelerometer and self-monitoring app, respectively. Multilevel models examined within-person relations between PA and EI preceding PA ("pre-PA"), acutely following PA ("acute post-PA," the 2 hr following PA), in the time following the acute post-PA period ("remaining time in day"), and across entire PA days ("full-day"), relative to non-PA matched time periods. RESULTS: EI was higher in the pre-PA and acute post-PA periods. There were no reliable differences in EI during the remaining time in day nor across the full-day on PA days versus within-subject matched non-PA days. There also was insufficient evidence to suggest EI pre-PA, post-PA, or across entire PA days, relative to non-PA matched time periods, was associated with percent weight change. CONCLUSIONS: Findings suggest that engaging in PA was associated with different within-person EI patterns compared to non-PA days, though there was little evidence to support that these patterns relate to weight change. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Automated Messaging Delivered Alongside Behavioral Treatment for Weight Loss: Qualitative Study.

BACKGROUND: Mobile health interventions for weight loss frequently use automated messaging. However, this intervention modality appears to have limited weight loss efficacy. Furthermore, data on users' subjective experiences while receiving automated messaging-based interventions for weight loss are scarce, especially for more advanced messaging systems providing users with individually tailored, data-informed feedback. OBJECTIVE: The purpose of this study was to characterize the experiences of individuals with overweight or obesity who received automated messages for 6-12 months as part of a behavioral weight loss trial. METHODS: Participants (n=40) provided Likert-scale ratings of messaging acceptability and completed a structured qualitative interview (n=39) focused on their experiences with the messaging system and generating suggestions for improvement. Interview data were analyzed using thematic analysis. RESULTS: Participants found the messages most useful for summarizing goal progress and least useful for suggesting new behavioral strategies. Overall message acceptability was moderate (2.67 out of 5). From the interviews, 2 meta-themes emerged. Participants indicated that although the messages provided useful reminders of intervention goals and skills, they did not adequately capture their lived experiences while losing weight. CONCLUSIONS: Many participants found the automated messages insufficiently tailored to their personal weight loss experiences. Future studies should explore alternative methods for message tailoring (eg, allowing for a higher degree of participant input and interactivity) that may boost treatment engagement and efficacy. TRIAL REGISTRATION: ClinicalTrials.gov NCT05231824; https://clinicaltrials.gov/study/NCT05231824.

Adsorption Equilibrium and Diffusion of CH4, CO2, and N2 in Coal-Based Activated Carbon.

Coal-based activated carbon is an ideal adsorbent for concentrating CH4 from coalbed methane and recovering CO2 from industrial waste gas. In order to upgrade the environmentally protective preparation technology of coal-based activated carbons and clarify the adsorption equilibrium and diffusion rules of CH4, CO2, and N2 in these materials, we prepared granular activated carbon (GAC) via air oxidation, carbonization, and physical activation using anthracite as the raw material. Also, we measured the adsorption isotherms and adsorption kinetic data of GAC by the gravimetric method and characterized its surface chemical properties. According to the results, GAC had abundant micropore structures with a pore size mainly in the range of 5.0-10.0 Å, and its surface was covered with plentiful oxygen-containing functional groups. The specific pore structure and surface chemical properties could effectively improve the separation and purification effects of GAC on CH4 and CO2. In the temperature range of 278-318 K, the equilibrium separation of CH4/N2 by GAC with a coefficient between 3 and 4 could be achieved. Also, the CO2/CH4 separation coefficient decreased with the increase in temperature but remained around 3. The bivariate Langmuir equation could describe the adsorption behaviors of GAC on CH4/N2, CO2/N2, and CH4/CO2. With the increase in the concentrations of CH4 and CO2 in the gas phase, the difference between the adsorption capacity of CH4 or CO2 and that of N2 became greater. The change of the gas ratio did not affect the characteristics of preferential adsorption of CH4 and CO2. At different temperatures (278, 298, and 318 K), the diffusion coefficients of CH4, N2, and CO2 at various pressure points showed predominately a small variation without an obvious trend. These results demonstrated that the separation of CH4/N2, CO2/N2, and CH4/CO2 by the activated carbon could only rely on the equilibrium separation effect rather than the kinetic effect.

Using artificial intelligence to optimize delivery of weight loss treatment: Protocol for an efficacy and cost-effectiveness trial.

Gold standard behavioral weight loss (BWL) is limited by the availability of expert clinicians and high cost of delivery. The artificial intelligence (AI) technique of reinforcement learning (RL) is an optimization solution that tracks outcomes associated with specific actions and, over time, learns which actions yield a desired outcome. RL is increasingly utilized to optimize medical treatments (e.g., chemotherapy dosages), and has very recently started to be utilized by behavioral treatments. For example, we previously demonstrated that RL successfully optimized BWL by dynamically choosing between treatments of varying cost/intensity each week for each participant based on automatic monitoring of digital data (e.g., weight change). In that preliminary work, participants randomized to the AI condition required one-third the amount of coaching contact as those randomized to the gold standard condition but had nearly identical weight losses. The current protocol extends our pilot work and will be the first full-scale randomized controlled trial of a RL system for weight control. The primary aim is to evaluate the hypothesis that a RL-based 12-month BWL program will produce non-inferior weight losses to standard BWL treatment, but at lower costs. Secondary aims include testing mechanistic targets (calorie intake, physical activity) and predictors (depression, binge eating). As such, adults with overweight/obesity (N = 336) will be randomized to either a gold standard condition (12 months of weekly BWL groups) or AI-optimized weekly interventions that represent a combination of expert-led group, expert-led call, paraprofessional-led call, and automated message). Participants will be assessed at 0, 1, 6 and 12 months.

Crystal optics simulations for delineation of the three-dimensional cellular nuclear distribution using analyzer-based refraction-contrast computed tomography.

Refraction-contrast computed tomography (RCT) using a refractive angle analyzer of Si perfect crystal can reconstruct the three-dimensional structure of biological soft tissue with contrast comparable to that of stained two-dimensional pathological images. However, the blurring of X-ray beam by the analyzer has prevented improvement of the spatial resolution of RCT, and the currently possible observation of tissue structure at a scale of approximately 20 µm provides only limited medical information. As in pathology, to differentiate between benign and malignant forms of cancer, it is necessary to observe the distribution of the cell nucleus, which is approximately 5-10 µm in diameter. In this study, based on the X-ray dynamical diffraction theory using the Takagi-Taupin equation, which calculates the propagation of X-ray energy in crystals, an analyzer crystal optical system depicting the distribution of cell nuclei was investigated by RCT imaging simulation experiments in terms of the thickness of the Laue-case analyzer, the camera pixel size and the difference in spatial resolution between the Bragg-case and Laue-case analyzers.

Enhanced intestinal protein fermentation in schizophrenia.

BACKGROUND: Emerging findings highlighted the associations of mental illness to nutrition and dysbiosis in the intestinal microbiota, but the underlying mechanisms, especially in schizophrenia (SZ), remain unclarified. METHODS: We conducted a case-control study of SZ patients (case to control=100:52) by performing sequencing of the gut metagenome; measurement of fecal and plasma non-targeted metabolome; including short-, medium-, and long-chain fatty acids; and targeted metabolites, along with recorded details of daily intakes of food. RESULTS: The metagenome analysis uncovered enrichment of asaccharolytic species and reduced abundance of carbohydrate catabolism pathways and enzymes in the gut of SZ patients, but increased abundance of peptidases in contrast to their significantly reduced protein intake. Fecal metabolome analysis identified increased concentrations of many protein catabolism products, including amino acids (AAs), urea, branched short-chain fatty acids, and various nitrogenous derivates of aromatic AAs in SZ patients. Protein synthesis, represented by the abundance of AA-biosynthesis pathways and aminoacyl-tRNA transferases in metagenome, was significantly decreased. The AUCs (area under the curve) of the diagnostic random forest models based on their abundance achieved 85% and 91%, respectively. The fecal levels of AA-fermentative enzymes and products uniformly showed positive correlations with the severity of psychiatric symptoms. CONCLUSIONS: Our findings revealed apparent dysbiosis in the intestinal microbiome of SZ patients, where microbial metabolism is dominated by protein fermentation and shift from carbohydrate fermentation and protein synthesis in healthy conditions. The aberrant macronutrient metabolism by gut microbes highlights the importance of nutrition care and the potential for developing microbiota-targeted therapeutics in SZ.

Ring artifact removal for differential phase-contrast X-ray computed tomography using a conditional generative adversarial network.

PURPOSE: The integration process used as a pre-processing step in the reconstruction of differential phase-contrast X-ray CT (d-PCCT) causes the measurement noise to propagate throughout the projection image, which is leading to increased ring artifacts (RA) in the reconstructed image. It is difficult to eliminate the RA using conventional RA removal methods that were developed for the absorption-based CT field. We propose an effective method that can remove RA of d-PCCT images. METHODS: The proposed method uses Laplacian images reconstructed from second-derivative projections of d-PCCT. This method is based on a conditional generative adversarial network (cGAN), whose loss function is designed by adding the L1- and L2-norm to the original cGAN. The training data were taken from a numerical phantom generated by a d-PCCT imaging simulator. To validate the applicability of the trained network, we tested its RA removal effect on test data from numerical phantoms generated randomly and actual experimental data. RESULTS: The results of numerical validation using numerical phantoms showed that the proposed method improved the RA removal effect compared to conventional methods. In addition, image comparison by visual evaluation showed that only the proposed method was able to remove RA while preserving original structures in the actual biological d-PCCT images. CONCLUSION: We proposed a cGAN-based method for RA removal that exploits the physical properties of d-PCCT. The proposed method was able to completely remove RA from d-PCCT images on both simulated data and biological data. We believe that this method is useful for the observation of various types of biological soft tissue.

Computational and Experimental Approaches to Decipher the Binding Mechanism of General Odorant-Binding Protein 2 from Athetis lepigone to Chlorpyrifos and Phoxim.

Insect resistance to insecticides is an increasingly serious problem, and the resistant mechanisms are complicated. The resistance research based on the chemosensory pathway is one of the hot problems at present, but the specific binding mechanism of chemosensory genes and insecticides remains elusive. The binding mechanism of AlepGOBP2 (belong to insect chemosensory gene) with two insecticides was investigated by computational and experimental approaches. Our calculation results indicated that four key residues (Phe12, Ile52, Ile94, and Phe118) could steadily interact with these two insecticides and be assigned as hotspot sites responsible for their binding affinities. The significant alkyl-π and hydrophobic interactions involved by these four hotspot residues were found to be the driving forces for their binding affinities, especially for two residues (Phe12 and Ile94) that significantly contribute to the binding of chlorpyrifos, which were also validated by our binding assay results. Furthermore, we also found that the AlepGOBP2-chlorpyrifos/phoxim complexes can be more efficiently converged in the residue-specific force field-(RSFF2C) and its higher accuracy and repeatability in protein dynamics simulation, per-residue free energy decomposition, and computational alanine scanning calculations have also been achieved in this paper. These findings provided useful insights for efficient and reliable calculation of the binding mechanism of relevant AlepGOBPs with other insecticides, facilitating to develop new and efficient insecticides targeting the key sites of AlepGOBP2.

miR-101 suppresses colon cancer cell migration through the regulation of EZH2.

BACKGROUND: colorectal cancer (CRC) is one of the most prevalent types of malignancies worldwide. The incidence of CRC is steadily increasing due to extended life expectancy and aging-related genetic and epigenetic abnormalities. Dysregulation of microRNAs (miRNAs) has been implicated in CRC development. METHODS: the current study is a basic research study aimed at understanding the molecular mechanism of miR-101 in the pathogenesis of CRC using human samples in vivo and CRC cell lines in vitro. The miRNAs profile from human samples was analyzed by miRNA microarrays and the expression level of single miRNAs were confirmed by qRT-PCR. The validation of the direct target of miR-101 was performed by western blot assay. The cell mobility of CRC was assessed using the Transwell migration assay. RESULTS: downregulation of miR-101 was identified in 39 human CRC tissues and CRC cell lines (HT29 and SW620) when compared to their counterpart control. We further confirmed that the enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, is a direct target of miR-101. Overexpression of EZH2 promoted CRC cell line migration and this effect was inhibited by forcing the expression of miR-101. Thus, we conclude that miR-101 regulated colon cancer cell migration occurs at least partially, though targeting EZH2. CONCLUSION: our study suggests that miR-101 functions as a tumor suppressor in CRC, and miR-101 may be a potential therapeutic target for CRC treatment.

Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae.

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif 'ATAGA', an 18 bp poly-T stretch, three copies of a 12 bp 'TATATATATATA', and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae.

[Inhibition of the replication of H9N2 influenza virus in vivo by short-term repeated oral administration of chicken interferon α].

To evaluate the optimal administration frequency for interferon-α (IFN-α) and the effect of its combined use with inactive virus on chicken flocks, the prokaryotic expression plasmid pET-22b-ChIFN-α was constructed and transferred into Escherichia coli BL21(DE3) host bacteria to induce the expression of chicken IFN-α and to harvest recombinant proteins inclusion bodies. The expression of recombinant chicken IFN-α was confirmed by SDS-PAGE, and the results demonstrated that the chicken IFN-α (20 kDa) was highly expressed using the prokaryotic expression vector with a concentration of 0.2 mg/mL in the medium. Chicken IFN-α was diluted to 2.5×104 U/fowls and administered to immunized specific-pathogen-free chickens orally in combination with inactivated H9N2 subtype influenza virus. Chicken that received chicken IFN-α were safe after three repeated immunizations (96 h). In addition, chicken IFN-α could induce higher levels of antiviral-related inducible genes in peripheral blood, spleen, and thymus of chicken flocks. The results of a challenge assay revealed that the lowest detoxification rates of chicken IFN-α ranged from three to five days, suggesting a higher capacity to resist H9N2 subtype avian influenza virus. The present study obtained the optimal immune frequency and immunization period for chicken IFN-α to provide theoretical support for the optimal clinical application of IFN-α.

Mitochondrial genome characteristics of Somena scintillans (Lepidoptera: Erebidae) and comparation with other Noctuoidea insects.

In this study, mitogenome of Somena scintillans (Lepidoptera: Erebidae) were sequenced and compared with other Noctuoidea species. The mitogenome is 15,410 base pairs in length. All 13 protein-coding genes (PCGs) are initiated by ATN codons except cox1 with CGA and all of PCGs terminate with TAA except nad4 with TAG. The codons ACG and CGC are absent. All the tRNA genes could be folded into the typical cloverleaf secondary structure except the trnS1 which not only loses dihydrouridine (DHU) arm but also mutates its anticodon into TCT. In the AT-rich region of the mitogenome the motif 'ATAGA' mutates to 'ATATA' and two copies of 161 bp-tandem repeats and two 'TA' short tandem repeats are founded. Phylogenetic analyses showed that S. scintillans is clustered into subfamily Lymatriinae. The phylogenetic relationships within Noctuoidea is (((Nolidae + (Euteliidae + Noctuidae)) + Erebidae) + Notodontidae).

All-inorganic perovskite quantum dots stabilized blue phase liquid crystals.

All-inorganic perovskite quantum dots (PQDs) have been effectively incorporated in the three-dimensional ordered structure of blue phase liquid crystals (BPLCs) to stabilize the BPLCs. Uniform dispersion, reduced phase transition temperature, widened BP temperature range, dynamic and fast electro-optical response and static optical display of selective reflection mode and photoluminescence mode have been confirmed with a given concentration of PQDs. Such a novel strategy of assembling all-inorganic PQDs in BPLCs shows favorable prospects for wide-range and near room temperature BPLCs, responsive BPLCs, multifunctional display materials and tunable bandgap lasers.

Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae).

In the present study, the complete mitogenome of Theretra japonica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T. japonica, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species. All 13 protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome C oxidase subunit 1 gene (cox1) which is initiated by the codon CGA as observed in other lepidopteran insects. Cytochrome C oxidase subunit 2 gene (cox2) has the incomplete termination codon T and NADH dehydrogenase subunit 1 gene (nad1) terminates with TAG while the remainder terminates with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Ile and Leu2 are the most frequently used codon families and codons CGG, CGC, CCG, CAG, and AGG are absent. The 431 bp AT-rich region includes the motif ATAGA followed by a 23 bp poly-T stretch, short tandem repeats (STRs) of TC and TA, two copies of a 28 bp repeat 'ATTAAATTAATAAATTAA TATATTAATA' and a poly-A element. Phylogenetic analyses within Sphingidae confirmed that T. japonica belongs to the Macroglossinae and showed that the phylogenetic relationship of T. japonica is closer to Ampelophaga rubiginosa than Daphnis nerii. Phylogenetic analyses within Theretra demonstrate that T. japonica, T. jugurtha, T. suffusa, and T. capensis are clustered into one clade.

Chiral Photonic Crystalline Microcapsules with Strict Monodispersity, Ultrahigh Thermal Stability, and Reversible Response.

Tunable photonic crystals (TPCs) reflecting selected wavelengths of visible light and responding to external stimuli are widely applied to fabricate smart optical devices. Chiral nematic liquid crystals (CNLCs) possessing response to temperature, electric field, and magnetic field are considered as one-dimensional TPCs. The encapsulation of CNLCs provides responsive photonic devices with stand-alone macroscopic structure and excellent processability. However, when CNLCs as cores are wrapped by polymeric shells to form core-shell structured microcapsules, the polydispersity of microcapsule size, the irregular spatial geometry, and the low thermal stability inevitably result in a deterioration of the optical performance and limited application at high temperatures. Herein, a combination of microfluidic emulsification and interfacial polymerization is employed to fabricate polymer wrapped photonic crystalline microcapsules (PWPCMs). The sizes and reflected colors of PWPCMs can be simultaneously controlled by adjusting the flow rates in the microfluidic chips. PWPCMs possess strictly monodispersed sizes with coefficients of variation less than 1%. The free-standing PWPCMs have high thermal stability. The deformation temperature of PWPCMs is as high as 210 °C. The colored PWPCMs also exhibit a reversible thermochromic property between the chiral nematic phase and the isotropic phase. The highly stable and tunable PWPCMs provide new opportunities for a wide range of photonic applications, including smart optical window, tunable microlasers, responsive microsensors, and various photonic devices.

Mitochondrial genome characteristics of two Sphingidae insects (Psilogramma increta and Macroglossum stellatarum) and implications for their phylogeny.

In this study, complete mitogenomes of P. increta and M. stellatarum (Lepidoptera: Sphingidae) were sequenced and compared with other Sphingidae species. The mitogenomes containing 37 genes and a AT rich region are circular molecules with 15,252 and 15,290 base pairs in length respectively. Except cox1 all 13 protein-coding genes (PCGs) are initiated by ATN codons. Most of PCGs terminate with TAA except nad5 and cox1 in P. increta and nad5 and cox2 in M. stellatarum. Ile and Leu2 are the most frequently used codon families in both species and codons CGC, CCG, TCG and ACG are absent in P. increta while in M. stellatarum CGC, CCG, CTG, AGG are absent. All the tRNA genes could be folded into the typical cloverleaf secondary structure except the trnS1 of P. increta which lost dihydrouridine (DHU) stem. The AT-rich region of both insects includes the motif ATAGA followed by a 18-19bp polyT stretch and 2-3 short tandem repeats (STRs) of TA, and a poly-A element. Phylogenetic analyses showed that the phylogenetic relationships are (((Sphinx morio+Manduca sexta)+(P. increta+Notonagemia analis scribae))+(Agrius convolvuli)+(M. stellatarum+(Ampelophaga rubiginosa+Daphnis nerii)).

Complete mitochondrial genome of Cnidocampa flavescens (Lepidoptera: Limacodidae).

Cnidocampa flavescens, lives in Nepal, Bhutan, China, Far East of Russia, Korea, and Japan, belongs to the Lepidoptera family Limacodidae. In this study, we describe the genomic features of the mitogenome sequences of the insects. The mitogenome of C. flavescens is 15,406 bp long consisting a typical set of genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) and one major 415 bp non-coding A + T-rich region. All PCGs of C. flavescens start with ATN codons and end with TAA codons. The gene arrangement of C. flavescens mitogenome is same to Monema flavescens while the intergenic spacers and overlaps are different. The 415 bp A + T-rich region contains a conserved ATAGA motif followed a poly-T stretch.

Complete mitochondrial genome of Histia rhodope Cramer (Lepidoptera: Zygaenidae).

Histia rhodope Cramer, found in India, Chinese, Burma, Indonesia and other Southeast Asian regions, belongs to Lepidoptera family Zygaenidae. In this study, we describe the genomic features of the mitogenome sequences of these insects. The mitogenome of Histia rhodope Cramer is 15,205 bp long consisting a typical set of genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes) and one major 376 bp non-coding A + T-rich region. All PCGs of Histia rhodope Cramer start with ATN codons except cox1 which start with CGA codon and all PCGs stop at TAA codons. Phylogenetic analysis demonstrates that Histia rhodope Cramer and Rhodopsona rbiginosa are clustered together into a monophyletic group Zygaenidae. Zygaenidae is phylogenetically closer to Limacodiae than Tortricidea.

Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog.

Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues.