A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections.

Although numerous studies have been conducted on hybrid speciation, our understanding of this process remains limited. Through an 18-year systematic investigation of all taxa of Populus on the Qinghai-Tibet Plateau, we discovered three new taxa with clear characteristics of sect. Leucoides. Further evidence was gathered from morphology, whole-genome bioinformatics, biogeography, and breeding to demonstrate synthetically that they all originated from distant hybridization between sect. Leucoides and sect. Tacamahaca. P. gonggaensis originated from the hybridization of P. lasiocarpa with P. cathayana, P. butuoensis from the hybridization of P. wilsonii with P. szechuanica, and P. dafengensis from the hybridization of P. lasiocarpa with P. szechuanica. Due to heterosis, the three hybrid taxa possess greater ecological adaptability than their ancestral species. We propose a hybrid speciation process model that incorporates orthogonal, reverse, and backcrossing events. This model can adequately explain some crucial evolutionary concerns, such as the nuclear-cytoplasmic conflict on phylogeny and the extinction of ancestral species within the distribution range of hybrid species.

A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau.

While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides, species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata, naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata, resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys.

A WRKY transcription factor, PyWRKY75, enhanced cadmium accumulation and tolerance in poplar.

Cadmium (Cd) pollution has detrimental effects on the ecological environment and human health. Currently, phytoremediation is considered an environmentally friendly way to remediate Cd pollution. The application of transgenic plants to remediate soil pollution is a new technology that has emerged in recent years. In this study, PyWRKY75 was isolated and cloned from Populus yunnanensis, and the functionality of PyWRKY75 in woody plants (poplar) under Cd stress was verified. The increase in plant height of the OE-41 line (overexpression poplar) was 33.2% higher than that of the wild type (WT). Moreover, PyWRKY75 significantly promoted the absorption and accumulation of Cd in poplar, which increased by 51.32% in the OE-41 line when compared with the WT. The chlorophyll content of transgenic poplar leaves was higher than that of the WT, which reflected a protective mechanism of PyWRKY75. Other antioxidants, such as POD, SOD, CAT, APX, AsA, GSH and PCs, also made the transgenic poplars more tolerant to Cd, and they behaved differently in roots, stems and leaves. In general, PyWRKY75 played a potential role in regulating plant tolerance to Cd stress. This study provides a scientific basis and a new type of modified poplar for Cd pollution remediation.

Changes in Proteome and Protein Phosphorylation Reveal the Protective Roles of Exogenous Nitrogen in Alleviating Cadmium Toxicity in Poplar Plants.

Phytoremediation soil polluted by cadmium has drawn worldwide attention. However, how to improve the efficiency of plant remediation of cadmium contaminated soil remains unknown. Previous studies showed that nitrogen (N) significantly enhances cadmium uptake and accumulation in poplar plants. In order to explore the important role of nitrogen in plants' responses to cadmium stress, this study investigates the poplar proteome and phosphoproteome difference between Cd stress and Cd + N treatment. In total, 6573 proteins were identified, and 5838 of them were quantified. With a fold-change threshold of > 1.3, and a p-value < 0.05, 375 and 108 proteins were up- and down-regulated by Cd stress when compared to the control, respectively. Compared to the Cd stress group, 42 and 89 proteins were up- and down-regulated by Cd + N treatment, respectively. Moreover, 522 and 127 proteins were up- and down-regulated by Cd + N treatment compared to the CK group. In addition, 1471 phosphosites in 721 proteins were identified. Based on a fold-change threshold of > 1.2, and a p-value < 0.05, the Cd stress up-regulated eight proteins containing eight phosphosites, and down-regulated 58 proteins containing 69 phosphosites, whereas N + Cd treatment up-regulated 86 proteins containing 95 phosphosites, and down-regulated 17 proteins containing 17 phosphosites, when compared to Cd stress alone. N + Cd treatment up-regulated 60 proteins containing 74 phosphosites and down-regulated 37 proteins containing 42 phosphosites, when compared to the control. Several putative responses to stress proteins, as well as transcriptional and translational regulation factors, were up-regulated by the addition of exogenous nitrogen following Cd stress. Especially, heat shock protein 70 (HSP70), 14-3-3 protein, peroxidase (POD), zinc finger protein (ZFP), ABC transporter protein, eukaryotic translation initiation factor (elF) and splicing factor 3 B subunit 1-like (SF3BI) were up-regulated by Cd + N treatment at both the proteome and the phosphoproteome levels. Combing the proteomic data and phosphoproteomics data, the mechanism by which exogenous nitrogen can alleviate cadmium toxicity in poplar plants was explained at the molecular level. The results of this study will establish the solid molecular foundation of the phytoremediation method to improve cadmium-contaminated soil.

TAK-242 suppresses lipopolysaccharide-induced inflammation in human coronary artery endothelial cells.

TAK-242 (resatorvid), a novel small-molecule cyclohexene derivative, inhibits TLR4 signaling selectively. TAK-242 blocked the Toll-like receptor (TLR) 4-triggered inflammatory signaling by binding directly to a specific amino acid Cys747 in the intracellular domain of TLR4. The present study was designed to examine the effects of TAK-242 on vascular inflammatory responses in human coronary artery endothelial cells (HCAECs) challenged by lipopolysaccharide (LPS, a TLR4 ligand). The results show that TAK-242 attenuated the LPS-induced expression of interleukin (IL)-6, IL-8 and monocyte chemoattractant protein 1 both at the transcription and translation levels in HCAECs. LPS-induced endothelial cell adhesion molecules, intercellular adhesion molecular-1 and vascular cell adhesion molecule-1 expressions were also reduced by treatment with TAK-242. In addition, coincubation with TAK-242 did not effect the expression of TLR4 in LPS-activated HCAECs. Furthermore, TAK-242 efficiently suppressed LPS-induced phosphorylation of nuclear factor κB (NF-κB) and IL-1 associated kinase-1 (IRAK-1) in HCAECs. These findings show that TAK-242 can suppress endothelial cell inflammation, suggesting that TAK-242 might be suitable for development as a therapeutic agent for inflammatory cardiovascular disease.

The small-molecule inhibitor selectivity between IKKα and IKKß kinases in NF-κB signaling pathway.

The enzyme complex IκB kinase (IKK) is an essential activator of NF-κB signaling pathway involved in propagating the cellular response to inflammation. The complex contains two functional subunits IKKα and IKKß, which are structurally conserved kinases and selective inhibition of them would result in distinct biological effects. However, most existing IKK inhibitors show moderate or high promiscuity for the two homologous kinases. Understanding of the molecular mechanism and biological implication underlying the specific interactions in IKK-ligand recognition is thus fundamentally important for the rational design of selective IKK inhibitors. In the current work, we integrated molecular docking, quantum mechanics/molecular mechanics calculation and Poisson-Boltzmann/surface area analysis to investigate the structural basis and energetic property of the selective binding of small-molecule ligands to IKKα and IKKß. It was found that the selectivity is primarily determined by the size and topology difference in ATP-binding pocket of IKKα and IKKß kinase domains; bulky inhibitor molecules commonly have, respectively, low and appropriate affinities towards IKKα and IKKß, and thus exhibit relatively high selectivity for IKKß over IKKα, whereas small ligands can only bind weakly to both the two kinases with low selectivity. In addition, the conformation, arrangement and distribution of residues in IKK pockets are also responsible for constituting the exquisite specificity of ligand binding to KKα and IKKß. Next, a novel quantitative structure-selectivity relationship model was developed to characterize the relative contribution of each kinase residue to inhibitor selectivity and to predict the selectivity and specificity for a number of known IKK inhibitors. Results showed that the active-site residues contribute significantly to the selectivity by directly interacting with inhibitor ligands, while those protein portions far away from the kinase active sites may also play an important role in determining the selectivity through long-range non-bonded forces and indirect allosteric effect.

Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth.

Grape hyacinth (Muscari) is an important ornamental bulbous plant with an extraordinary blue colour. Muscari armeniacum, whose flowers can be naturally white, provides an opportunity to unravel the complex metabolic networks underlying certain biochemical traits, especially colour. A blue flower cDNA library of M. armeniacum and a white flower library of M. armeniacum f. album were used for transcriptome sequencing. A total of 89 926 uni-transcripts were isolated, 143 of which could be identified as putative homologues of colour-related genes in other species. Based on a comprehensive analysis relating colour compounds to gene expression profiles, the mechanism of colour biosynthesis was studied in M. armeniacum. Furthermore, a new hypothesis explaining the lack of colour phenotype of the grape hyacinth flower is proposed. Alteration of the substrate competition between flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) may lead to elimination of blue pigmentation while the multishunt from the limited flux in the cyanidin (Cy) synthesis pathway seems to be the most likely reason for the colour change in the white flowers of M. armeniacum. Moreover, mass sequence data obtained by the deep sequencing of M. armeniacum and its white variant provided a platform for future function and molecular biological research on M. armeniacum.

Simultaneous determination of trace migration of phthalate esters in honey and royal jelly by GC-MS.

A simple, rapid, and reliable liquid-liquid extraction coupled to GC-MS method was developed and validated for the quantification of 22 phthalate esters (PAEs) in honey and royal jelly. Instrument parameters for GC-MS were tested to obtain the satisfactory separation between 22 PAEs with high sensitivity. The extraction procedure was optimized in order to achieve the best recovery. The following criteria were used to validate the developed method: linearity, LOD, lower LOQ, precision, accuracy, matrix effect and carry-over. Correlation coefficients were >0.999 by applying the linear regression model based on the least-squares method with a weighting factor (1/x). The intra- and interday precision were within 12.7% in terms of RSD, and the accuracy was within -11.8% in terms of relative error. The mean extraction recoveries ranged between 80.1 and 110.9% for honey and royal jelly. No significant matrix effect and carry-over for PAEs were observed for the analysis of honey and royal jelly samples. A total of 20 real samples were analyzed for a mini-survey using the developed method. Seven PAEs in honey samples and five PAEs in royal jelly samples were found, indicating potential contamination with several PAEs.

Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.

Quantitative structure-activity relationship (QSAR), a regression modeling methodology that establishes statistical correlation between structure feature and apparent behavior for a series of congeneric molecules quantitatively, has been widely used to evaluate the activity, toxicity and property of various small-molecule compounds such as drugs, toxicants and surfactants. However, it is surprising to see that such useful technique has only very limited applications to biomacromolecules, albeit the solved 3D atom-resolution structures of proteins, nucleic acids and their complexes have accumulated rapidly in past decades. Here, we present a proof-of-concept paradigm for the modeling, prediction and interpretation of the binding affinity of 144 sequence-nonredundant, structure-available and affinity-known protein complexes (Kastritis et al. Protein Sci 20:482-491, 2011) using a biomacromolecular QSAR (BioQSAR) scheme. We demonstrate that the modeling performance and predictive power of BioQSAR are comparable to or even better than that of traditional knowledge-based strategies, mechanism-type methods and empirical scoring algorithms, while BioQSAR possesses certain additional features compared to the traditional methods, such as adaptability, interpretability, deep-validation and high-efficiency. The BioQSAR scheme could be readily modified to infer the biological behavior and functions of other biomacromolecules, if their X-ray crystal structures, NMR conformation assemblies or computationally modeled structures are available.

Elevated expression of TNFRSF4 impacts immune cell infiltration and gene mutation in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, which makes prognostic prediction challenging.We aimed to investigate association of TNFRSF4 expression with the immune infiltration and gene mutation in HCC. METHODS: In this study, the expression profiles and corresponding clinical data of HCC patients were downloaded from the Cancer Genome Atlas (TCGA) database.Kaplan-Meier and Cox regression were used to evaluate the clinical value of TNFRSF4. ESTIMATE and CIBERSORT algorithms were applied to investigate the infiltration ratio of 22 immune cells. The WGCNA and LASSO COX algorithms were performed, establishing a prognostic risk model that was then validated by HCC samples from GEO. Finally, the effects on gene mutation occurring in HCC patients of TNFRSF4 expression and risk score were appraised. RESULTS: In HCC tissues, it was found the TNFRSF4 expression profile was significantly different with age, gender, tumor grade, disease stage, prominently affecting the survival outcome and prognosis of patients. Univariate and multivariate COX regression analysis suggested that TNFRSF4 was an independent prognostic marker. Samples of high/low expression of TNFRSF4 were screened for differential genes, and then the WGCNA and LASSO COX constructed a 13-gene signature, excellently dividing samples into hign/low risk groups. Compared with the low-risk group, the overall survival (OS) of high-risk group was markedly lower, with P< 0.0001. By ROC curve analysis, the predictive ability of the 13-gene signature was further confirmed. Both the high/low TNFRSF4 expression and the high/low risk score were demonstrated to exert effects on the frequency of gene mutation in HCC. CONCLUSIONS: As an independent prognostic marker of HCC, TNFRSF4 was found simultaneously to affect the immune infiltration of cells and the frequency of gene mutations.

Parapapillary ßBM and γ Zones Played Different Roles in Axial Elongation Among Young Adolescents Using Optical Coherence Tomography.

Purpose: To evaluate the influencing factors of parapapillary ßBM and γ zones incidence in young adolescents and to explore their associations with axial length progression. Methods: In this prospective cohort study, 976 seventh-grade students from nine secondary schools in Beijing, China, were enrolled and followed up 1 year later. Parapapillary ßBM zone was defined as retinal pigment epithelium loss while Bruch's membrane was present. Parapapillary γ zone was defined as the absence of retinal pigment epithelium and Bruch's membrane. Logistic regression model was used to analyze the influencing factors of ßBM and γ zone incidence. A linear mixed model was used to analyze the associations between parapapillary zones and axial elongation. Results: Of the 976 participants, 139 (14.2%) had only ßBM zone, 398 (40.8%) had only γ zone, and 171 (17.5%) had both. At follow-up, the incidence of ßBM zone was 11.5% (76/659), and the incidence of γ zone was 9.7% (39/404). Optic disc tilt, thinner subfoveal choroid, and longer axial length at baseline showed a higher risk of γ zone incidence. The absence of γ zone at baseline showed a faster axial length progression. When the baseline axial length was 25 mm or longer, the ßBM zone was also related to the axial elongation. Conclusions: The γ zone was associated with axial length progression, and the ßBM zone was also associated with the axial length progression when the axial length exceeded 25 mm, which was consistent with the notion that excessive axial length growth not only is the extension of the eyeball but also has its own pathologic changes.

Integrating physiological and transcriptome analyses clarified the molecular regulation mechanism of PyWRKY48 in poplar under cadmium stress.

WRKY transcription factors (TFs) play an important role in regulating plant growth and responses to environmental stress. However, the molecular mechanism of WRKY to cadmium (Cd) stress is unclear, which prevents phytoremediation of Cd-contaminated soil from widely application. To determine the underlying mechanism, PyWRKY48-overexpressing poplars were obtained (OE-32 and OE-67) to study the Cd tolerance and accumulation in poplars. Results showed that the Cd content in the aboveground part of the two transgenic poplar lines were 1.57 and 1.99 times higher than that of wild type (WT), and lateral roots, GSH, PCs content and GST activity increased significantly. RNA-seq. data about transgenic and WT poplars revealed that 2074 differentially expressed genes (DEGs) in roots, 4325 in leaves, and 499 in both tissues. And these DEGs were mainly concentrated in ABC transport protein (PaABC), heavy-metal binding protein (PaHIPP), and transportation and loading of xylem (PaNPF, PaBSP) proteins, and they enhanced Cd accumulation. Meanwhile, PyWRKY48 increased the Cd tolerance of transgenic poplars by up-regulating the expression of PaGRP, PaPER and PaPHOS, which encode cell wall proteins, antioxidant enzyme, and heavy metal-associated proteins, respectively. In addition, overexpression PyWRKY48 promoted poplar growth by increasing the chlorophyll and carotenoid content. ENVIRONMENTAL IMPLICATION: This study generated PyWRKY48-overexpressing poplars and functionally verified them in Cd-contaminated soil, to analyze the effects of the gene on poplar growth, Cd tolerance and Cd accumulation. RNA seq. data revealed that several genes are involved in Cd exposure. This may provide a strong molecular basis and new ideas for improving the phytoremediation efficiency of Cd-contaminated soils. Importantly, the transgenic poplars grew better and accumulated more Cd than the wild-type. Therefore, PyWRKY48-overexpressing poplars could be considered useful for mitigating environmental pollution.

Structure-based prediction of protein-protein binding affinity with consideration of allosteric effect.

The conformational change upon protein-protein binding is largely ignored for a long time in the affinity prediction community. However, it is widely recognized that allosteric effect does play an important role in biomolecular recognition and association. In this article, we describe a new quantitative structure-activity relationship (QSAR)-based strategy to capture the structural and nonbonding information relating to not only the direct noncovalent interactions between protein binding partners, but also the indirect allosteric effect associated with binding. This method is then employed to quantitatively model and predict the protein-protein binding affinities compiled in a recently published benchmark consisting of 144 functionally diverse protein complexes with their structures available in both bound and unbound states (Kastritis et al. Protein Sci 20:482-491, 2011). With incorporating genetic algorithm and partial least squares regression (GA-PLS) into this method, a significant linear relationship between structural information descriptors and experimentally measured affinities is readily emerged and, on this basis, detailed discussions of physicochemical properties and structural implications underlying protein binding process, as well as the contribution of allosteric effect to the binding are addressed. We also give an empirical estimation of the prediction limit r(pred)(2) = 0.80 for structure-based method used to determine protein-protein binding affinity.

Comparative In Vitro and In Vivo Hydroxylation Metabolization of Polychlorinated Biphenyl 101 in Laying Hens: A Pilot Study.

Polychlorinated biphenyls (PCBs) can be metabolized into hydroxylated PCBs (OH-PCBs) that exhibit greater toxicity than their parent compounds. In particular, 2,2',4,5,5'-pentachlorobiphenyl (PCB 101) is commonly found in chicken feeds and breeding environments, although information on the biotransformation of this PCB in chickens is lacking. In this study, the hydroxylation metabolization of PCB 101 was assessed based on in vitro trials with Sanhuang chicken liver microsomes and in vivo experiments with Hy-Line Brown hens. The para-substituted metabolite 4'-OH-PCB 101 is the predominant metabolite of PCB 101. 4'-OH-PCB 101 is preferentially retained in the chicken bloodstream and partly distributed into different tissues of laying hens. The blood-brain barrier can effectively prevent the OH-PCB from entering the brain, and the adipose tissue contains a relatively low residue concentration of the OH-PCB. The laying hen can deplete the OH-PCB via laying eggs and excrement. The ratio of 4'-OH-PCB 101/PCB 101 in egg yolk is about 1:2. These results first provide definite evidence for the previous hypothesis of the PCB 101 metabolism by chickens. They could assist in predicting the environmental fate of PCBs, and in the risk assessment of PCBs and OH-PCBs in chicken-based foodstuffs.

Genome-Wide Investigation of the PtrCHLP Family Reveals That PtrCHLP3 Actively Mediates Poplar Growth and Development by Regulating Photosynthesis.

Chlorophyll (Chl) plays a crucial role in plant photosynthesis. The geranylgeraniol reductase gene (CHLP) participates in the terminal hydrogenation of chlorophyll biosynthesis. Although there are many studies related to the genome-wide analysis of Populus trichocarpa, little research has been conducted on CHLP family genes, especially those concerning growth and photosynthesis. In this study, three CHLP genes were identified in Populus. The evolutionary tree indicated that the CHLP family genes were divided into six groups. Moreover, one pair of genes was derived from segmental duplications in Populus. Many elements related to growth were detected by cis-acting element analysis of the promoters of diverse PtrCHLPs. Furthermore, PtrCHLPs exhibit different tissue expression patterns. In addition, PtrCHLP3 is preferentially expressed in the leaves and plays an important role in regulating chlorophyll biosynthesis. Silencing of PtrCHLP3 in poplar resulted in a decrease in chlorophyll synthesis in plants, thus blocking electron transport during photosynthesis. Furthermore, inhibition of PtrCHLP3 expression in poplar can inhibit plant growth through the downregulation of photosynthesis. Ultimately, PtrCHLP3 formed a co-expression network with photosynthesis and chlorophyll biosynthesis-related genes, which synergistically affected the growth and photosynthesis of poplars. Thus, this study provides genetic resources for the improved breeding of fast-growing tree traits.

PscCYP716A1-Mediated Brassinolide Biosynthesis Increases Cadmium Tolerance and Enrichment in Poplar.

Cadmium (Cd), as one of the heavy metals with biological poisonousness, seriously suppresses plant growth and does harm to human health. Hence, phytoremediation was proposed to mitigate the negative effects from Cd and restore contaminated soil. However, the internal mechanisms of detoxification of Cd used in phytoremediation are not completely revealed. In this study, we cloned the cytochrome P450 gene PscCYP716A1 from hybrid poplar "Chuanxiang No. 1" and found that the PscCYP716A1 was transcriptionally upregulated by Cd stress and downregulated by the exogenous brassinolide (BR). Meanwhile, PscCYP716A1 significantly promoted the poplar growth and enhanced the Cd accumulation in poplar. Compared to wild-type poplars, overexpressed PscCYP716A1 lines produced higher levels of endogenous BR and showed a stronger tolerance to Cd, which revealed that PscCYP716A1 may reduce the oxidative stress damage induced by Cd stress through accelerating BR synthesis. In general, PscCYP716A1 has a potential superiority in regulating the plant's tolerance to Cd stress, which will provide a scientific basis and a new type of gene-modified poplar for Cd-pollution remediation.

Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses.

Periplasmic oligopeptide-binding protein (OppA) is the initial receptor in the ATP-binding cassette (ABC) system of bacteria, which exhibits a broad specificity in binding oligopeptides without regard to sequence. Here, we present a computational study on the structural properties and energetic landscapes of OppA protein interacting with its cognate ligands on the basis of 28 structure/affinity-known OppA-tripeptide complexes. By employing a well-designed protocol that couples the hybrid quantum mechanical/molecular mechanical (QM/MM) scheme and the sophisticated Poisson-Boltzmann/surface area (PB/SA) solvent model together to analyze and decompose the energy components associated with the OppA-peptide binding, we demonstrate that the broad specificity of OppA-recognizing peptides is originated from a series of exquisite balances between the free energy contributions from, for example, the direct nonbonded interactions and indirect desolvation effects, the main chains and side chains, and the different residue positions of the tripeptide ligands. We also show that, in a framework of structure-based quantitative structure-activity relationship (SB-QSAR) methodology, the QM/MM-PB/SA-derived energy terms could be used as a good descriptor to characterize the interaction profile of OppA with peptides and correlate pretty well with the experimentally measured affinities of the binding.

Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses.

Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains. Characterizing the interaction interface of domain-peptide complexes and analyzing binding specificity for modular domains are critical for deciphering protein-protein interaction networks. In this article, we report the successful use of an integrated computational protocol to dissect the energetic profile and structural basis of peptide binding to third PDZ domain (PDZ3) from the PSD-95 protein. This protocol employs rigorous quantum mechanics/molecular mechanics (QM/MM), semi-empirical Poisson-Boltzmann/surface area (PB/SA), and empirical conformational free energy analysis (CFEA) to quantitatively describe and decompose systematic energy changes arising from, respectively, noncovalent interaction, desolvation effect, and conformational entropy loss associated with the formation of 30 affinity-known PDZ3-peptide complexes. We show that the QM/MM-, PB/SA-, and CFEA-derived energy components can work together fairly well in reproducing experimentally measured affinity after a linearly weighting treatment, albeit they are not compatible with each other directly. We also demonstrate that: (1) noncovalent interaction and desolvation effect donate, respectively, stability and specificity to complex architecture, while entropy loss contributes modestly to binding; (2) P(0) and P(-2) of peptide ligand are the most important positions for determining both the stability and specificity of the PDZ3-peptide complex, P(-1) and P(-3) can confer substantial stability (but not specificity) for the complex, and N-terminal P(-4) and P(-5) have only a very limited effect on binding.

A dual immune signature of CD8+ T cells and MMP9 improves the survival of patients with hepatocellular carcinoma.

The 5-year survival of hepatocellular carcinoma (HCC) is difficult due to the high recurrence rate and metastasis. Tumor infiltrating immune cells (TICs) and immune-related genes (IRGs) bring hope to improve survival and treatment of HCC patients. However, there are problems in predicting immune signatures and identifying novel therapeutic targets. In the study, the CIBERSORT algorithm was used to evaluate 22 immune cell infiltration patterns in gene expression omnibus (GEO) and the cancer genome atlas (TCGA) data. Eight immune cells were found to have significant infiltration differences between the tumor and normal groups. The CD8+ T cells immune signature was constructed by least absolute shrinkage and selection operator (LASSO) algorithm. The high infiltration level of CD8+ T cells could significantly improve survival of patients. The weighted gene co-expression network analysis (WGCNA) algorithm identified MMP9 was closely related to the overall survival of HCC patients. K-M survival and tROC analysis confirmed that MMP9 had an excellent prognostic prediction. Cox regression showed that a dual immune signature of CD8+ T cells and MMP9 was independent survival factor in HCC. Therefore, a dual prognostic immune signature could improve the survival of patient and may provide a new strategy for the immunotherapy of HCC.

The Role of C-Reactive Protein and Fibrinogen in the Development of Intracerebral Hemorrhage: A Mendelian Randomization Study in European Population.

Background: The causal association of C-reactive protein (CRP) and fibrinogen on intracerebral hemorrhage (ICH) remains uncertain. We investigated the causal associations of CRP and fibrinogen with ICH using two-sample Mendelian randomization. Method: We used single-nucleotide polymorphisms associated with CRP and fibrinogen as instrumental variables. The summary data on ICH were obtained from the International Stroke Genetics Consortium (1,545 cases and 1,481 controls). Two-sample Mendelian randomization estimates were performed to assess with inverse-variance weighted and sensitive analyses methods including the weighted median, the penalized weighted median, pleiotropy residual sum and outlier (MR-PRESSO) approaches. MR-Egger regression was used to explore the pleiotropy. Results: The MR analyses indicated that genetically predicted CRP concentration was not associated with ICH, with an odds ratio (OR) of 1.263 (95% CI = 0.935-1.704, p = 0.127). Besides, genetically predicted fibrinogen concentration was not associated with an increased risk of ICH, with an OR of 0.879 (95% CI = 0.060-18.281; p = 0.933). No evidence of pleiotropic bias was detected by MR-Egger. The findings were overall robust in sensitivity analyses. Conclusions: Our findings did not support that CRP and fibrinogen are causally associated with the risk of ICH.