Landscape of urine biomarkers for bladder cancer:molecular function,cell-of-origin,and bibliometric trend

Background:The effective management of bladder cancer(BCa)depends on the early diagnosis and surveillance.Previous studies have explored numerous urinary molecules as potential biomarkers of BCa.However,the molecular functions and cell-of-origin profiles of these biomarkers are yet to be elucidated.In this study,we aimed to provide a comprehensive overview of the landscape of urinary biomarker genes for BCa.Methods:We conducted an exhaustive literature search in PubMed,through which 555 biomarker genes were identified.We then analyzed the BCa single-cell atlas to infer the cellular origin of these BCa urine biomarker genes and performed functional enrichment analysis to gain insights into the functional molecular implications of these biomarkers.Results:These genes are involved in tumor proliferation,angiogenesis,cellmigration,and cell death and are predominantly expressed in epithelial and stromal cells.Interestingly,our analysis ofmultiomics tumor data revealed a discordance between tissue and urine in terms of differential methylation and RNA expression,suggesting that biomarker discovery for liquid biopsies should ideally begin with the analysis of bodily fluids rather than relying interest and that test strategies incorporating multiple molecular markers represent an ongoing trend.Conclusions:Collectively,our study has built a landscape of BCa urine biomarker genes,uncovered molecular insights into these biomarkers,and revealed the bibliometric trends in this field,which will contribute to the discovery of novel biomarkers in the future.

Molecular Functions of Oxygen-Evolving Complex Family Proteins in Photosynthetic Electron Flow

Oxygen-evolving complex （OEC） protein is the original name for membrane-peripheral subunits of photosystem （PS） II. Recently, multiple isoforms and homologs for OEC proteins have been iden- tified in the chloroplast thylakoid lumen, indicating that functional diversification has occurred in the OEC family. Gene expression profiles suggest that the Arabidopsis OEC proteins are roughly categorized into three groups： the authentic OEC group, the stressresponsive group, and the group including proteins related to the chloroplast NAD（P）H dehydrogenase （NDH） complex involved in cyclic electron transport around PSI. Based on the above gene expression profiles, molecular functions of the OEC family proteins are discussed together with our current knowledge about their functions.

Understanding biological functions through molecular networks

The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.

Fibroblast activation protein (FAP) as a prognostic biomarker in multiple tumors and its therapeutic potential in head and neck squamous cell carcinoma

Background:Fibroblast activation protein(FAP),a cell surface serine protease,plays roles in tumor invasion and immune regulation.However,there is currently no pan-cancer analysis of FAP.Objective:We aimed to assess the pan-cancer expression profile of FAP,its molecular function,and its potential role in head and neck squamous cell carcinoma(HNSC).Methods:We analyzed gene expression,survival status,immune infiltration,and molecular functional pathways of FAP in The Cancer Genome Atlas(TCGA)and Genotype Tissue Expression(GTEx)tumors.Furthermore,to elucidate the role of FAP in HNSC,we performed proliferation,migration,and invasion assays post-FAP overexpression or knock-down.Results:FAP expression was elevated in nine tumor types and was associated with poor survival in eight of them.In the context of immune infiltration,FAP expression negatively correlated with CD8+T-cell infiltration infive tumor types and positively with regulatory T-cell infiltration in four tumor types.Our enrichment analysis highlighted FAP’s involvement in the PI3K-Akt signaling pathway.In HNSC cells,FAP overexpression activated the PI3K-Akt pathway,promoting tumor proliferation,migration,and invasion.Conversely,FAP knockdown showed inhibitory effects.Conclusion:Our study unveils the association of FAP with poor tumor prognosis across multiple cancers and highlights its potential as a therapeutic target in HNSC.

Molecular Dynamics Study on Microstructure of Potassium Dihydrogen Phosphates Solution

Molecular dynamics simulations were carried out to study the internal energy and microstructure of potassium dihydrogen phosphates （KDP） solution at different temperatures. The water molecule was treated as a simple-point-charge model, while a seven-site model for the dihydrogen phosphate ion was adopted. The internal energy functions and the radial distribution functions of the solution were studied in detail. An unusually large local particle number density fluctuation was observed in the system at saturation temperature. It has been found that the specific heat of oversaturated solution is higher than that of unsaturated solution, which indicates the solution experiences a crystallization process below saturation temperature. The radial distribution function between the oxygen atom of water and the hydrogen atom of the dihydrogen phosphate ion shows a very strong hydrogen bond structure. There are strong interactions between potassium cation and oxygen atom of dihydrogen phosphate ion in KDP solution, and much more ion pairs were formed in saturated solution.

Proteomic Profiling and Protein-Protein Interaction Network Reveal the Molecular Mechanisms of Susceptibility to Drought Stress in Canola(Brassica napus L.)

Drought stress is one of the most important abiotic stresses that plants face frequently in nature.Under drought conditions,many morphological,physiological,and molecular aspects of plants are changed and as a result plants experience a remarkable reduction in growth,yield,and reproduction.To expand our understanding of the molecular basis of the plant response to drought stress,the proteomic profile and protein-protein network of canola(Brassica napus L.)were studied.The focus was to show molecular mechanisms related to canola susceptibility to drought stress.The experiment used a completely randomized design,implemented in a hydroponic system under greenhouse conditions.To impose drought stress,plants were exposed to Hoagland’s solution supplemented with polyethylene glycol(PEG)6000 for 7 days.The drought stress resulted in 161reproducible protein spots in twodimensional electrophoresis of canola leaves.The t-student test showed 21 differentially abundant proteins(DAP),of which 2 and 19 were up and down accumulated,respectively.Two spots identified as 1-aminocyclopropane-1-carboxylate oxidase and D-2-hydroxyglutarate dehydrogenase showed an increased abundance of 2.11 and 1.77,respectively.The extended protein-protein interaction of differentially abundant proteins and KEGG analysis showed 47 pathways directly and indirectly associated with canola response to drought stress.DAPs with increased abundance were associated with amino acid and signaling processes,whereas DAPs with decreased abundance were mostly connected with pathways responsible for energy production.The results of the study will help to elucidate further the molecular events associated with the susceptibility to drought stress in canola.

Ab initio calculation on accurate analytic potential energy functions and harmonic frequencies of c^3∑g^＋ and B^1-Пu states of dimer 7Li2

The comparison between single-point energy scanning （SPES） and geometry optimization （OPT） in determining the equilibrium geometries of c^3∑g^＋ and B^1-Пu states of dimer 7Li2 is made at numerous basis sets by using a symmetryadapted-cluster configuration-interaztion （SAC-CI） method in the Gaussian 03 program package. In this paper the difference of the equilibrium geometries obtained by SPES and by OPT is reported. The results obtained by SPES are found to be more reasonable than those obtained by OPT in full active space at the present SAC-CI level of theory. And the conclusion is attained that the cc-PVTZ is a most suitable basis set for these states. The calculated dissociation energies and equilibrium geometries are 0.8818 eV and 0.3090 nm for c^3∑g^＋ state, and 0.3668 eV and 0.2932 nm for B^1-Пu state respectively. The potential energy curves are calculated over a wide internuclear distance range from about 2.5α0 to 37α0 and have a least-squares fit into the Murrell-Sorbie function. According to the calculated analytic potential energy functions, the harmonic frequencies （We） and other spectroscopic data （ωeXe, Be and αe） are calculated. Comparison of the theoretical determinations at present work with the experiments and other theories clearly shows that the present work is the most complete effort and thus represents an improvement over previous theoretical results.

Interfacial Charge Transfer Induced Electronic Property Tuning of MoS_2 by Molecular Functionalization

The modulation of electrical properties of MoS_2 has attracted extensive research interest because of its potential applications in electronic and optoelectronic devices.Herein,interfacial charge transfer induced electronic property tuning of MoS_2 are investigated by in situ ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy measurements.A downward band-bending of MoS_2-related electronic states along with the decreasing work function,which are induced by the electron transfer from Cs overlayers to MoS_2,is observed after the functionalization of MoS_2 with Cs,leading to n-type doping.Meanwhile,when MoS_2 is modified with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane(F_4-TCNQ),an upward band-bending of MoS_2-related electronic states along with the increasing work function is observed at the interfaces.This is attributed to the electron depletion within MoS_2 due to the strong electron withdrawing property of F_4-TCNQ,indicating p-type doping of MoS_2.Our findings reveal that surface transfer doping is an effective approach for electronic property tuning of MoS_2 and paves the way to optimize its performance in electronic and optoelectronic devices.

Molecular cloning and functional analyses of low-temperature induced genes from Ammopiptanthus mongolicus

Studies on the cold-responsive genes and cold signaling of woody species drop far behind in comparison to herbaceous plants.Due to similar lignified structure,perennial characteristic,and enhanced tolerance,it seems much easier to find strongly antifreeze genes and obtain effective results in transgenic woody plants.In this study,Ammopiptanthus mongolicus,an evergreen,broadleaf and cold-resist leguminous shrub growing in the desert of Inner Mongolia,was used as a material for low-temperature induced gene isolation.Through differential expression analysis induced by low-temperature,thirteen up-regulated cDNAs were identified.One of them,AmEBP1,(accession number:DQ519359)confers enhanced cold-tolerance to both transgenic E.coli and transgenic Arabidopsis.Results suggest that AmEBP1 can stimulate the synthesis of ribosome and the dephosphyration of the α-subunit of initiation factor 2(eIF2α),and subsequently promote the translation process.By which the transgenic plants obtained increased cold-resistant ability.

Grain Shape Genes:Shaping the Future of Rice Breeding

The main goals of rice breeding nowadays include increasing yield,improving grain quality,and promoting complete mechanized production to save labor costs.Rice grain shape,specified by three dimensions,including grain length,width and thickness,has a more precise meaning than grain size,contributing to grain appearance quality as well as grain weight and thus yield.Furthermore,the divergence of grain shape characters could be utilized in mechanical seed sorting in hybrid rice breeding systems,which has been succeeded in utilizing heterosis to achieve substantial increase in rice yield in the past decades.Several signaling pathways that regulate rice grain shape have been elucidated,including G protein signaling,ubiquitination-related pathway,mitogen-activated protein kinase signaling,phytohormone biosynthesis and signaling,micro RNA process,and some other transcriptional regulatory pathways and regulators.This review summarized the recent progress on molecular mechanisms underlying rice grain shape determination and the potential of major genes in future breeding applications.

Molecular surface functionalization of In_(2)O_(3) to tune interfacial microenvironment for enhanced catalytic performance of CO_(2) electroreduction

Indium-based materials(e.g.,In_(2)O_(3))are a class of promising non-noble metal-based catalysts for electroreduction of carbon dioxide(CO_(2)).However,competitive hydrogen reduction reaction(HER)on indium-based catalysts hampers CO_(2) reduction reaction(CO_(2)RR)process.We herein tune the interfacial microenvironment of In_(2)O_(3) through chemical graft of alkyl phosphoric acid molecules using a facile solution-processed strategy for the first time,which is distinguished from other researches that tailor intrinsic activity of In_(2)O_(3) themselves.The surface functionalization of alkyl phosphoric acids over In_(2)O_(3) is demonstrated to remarkably boost CO_(2) conversion.For example,octadecylphosphonic acid modified In_(2)O_(3) exhibits Faraday efficiency for H_(2) H_(2) H_(2)(FE)of as low as 6.6%and FEHCOOH of 86.5%at-0.67 V vs.RHE,which are far superior to parent In_(2)O_(3) counterparts(FE of 24.0%and FEHCOOH of 63.1%).Moreover,the enhancing effect of alkyl phosphoric acid functionalization is found to be closely related to the length of alkyl chains.By virtue of comprehensive experimental characterizations and molecular dynamics simulations,it is revealed that the modification of alkyl phosphoric acids significantly alters the interface microenvironment of the electrocatalyst,which changes the electrocatalyst surface from hydrophilic and aerophobic to hydrophobic and aerophilic.In this case,the water molecules are pushed away and more CO_(2) molecules are trapped,increasing local CO_(2) concentration at In_(2)O_(3) active sites,thus leading to the significantly enhanced CO_(2)RR and suppressed HER.This work highlights the importance of regulating the interfacial microenvironment of inorganic catalysts by molecular surface functionalization as a means for promoting the electrochemical performance in electrosynthesis and beyond.

Screening of the Metastasis-Associated Genes by Gene Chip in High Metastatic Human Ovarian Cancer Cell Lines

Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio （SLR） ≥3], and 640 genes were downregulated （SLR≤-3）. Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes （115 genes, 9.3%）, followed by chromosome 2 （94 genes, 7.6%）, chromosome 12 （88 genes, 7.1%）, chromosome 11 （76 genes, 6.1%）, chromosomes X （71 genes, 5.7%）, and chromosomes l7 （69 genes, 5.6%）. These genes were localized on short-arm of chromosome （q）, which had 805 （65.1%） genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes （306 genes, 24.7%） belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes （144 genes, 11.6%）. The rest of the top two groups were signal transduction genes （137 genes, 11.1%） and proteins binding genes （116 genes, 9.4%）. These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown （16.7 %）. Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.

Gene and protein expression profiles of olfactory ensheathing cells from olfactory bulb versus olfactory mucosa

Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-derived OECs remains unclear. In this study, we extracted OECs from OB and OM and compared the gene and protein expression profiles of the cells using transcriptomics and non-quantitative proteomics techniques. The results revealed that both OB-derived OECs and OM-derived OECs highly expressed genes and proteins that regulate cell growth, proliferation, apoptosis and vascular endothelial cell regeneration. The differentially expressed genes and proteins of OB-derived OECs play a key role in regulation of nerve regeneration and axon regeneration and extension, transmission of nerve impulses and response to axon injury. The differentially expressed genes and proteins of OM-derived OECs mainly participate in the positive regulation of inflammatory response, defense response, cytokine binding, cell migration and wound healing. These findings suggest that differentially expressed genes and proteins may explain why OB-derived OECs and OM-derived OECs exhibit different therapeutic roles. This study was approved by the Animal Ethics Committee of the General Hospital of Ningxia Medical University(approval No. 2017-073) on February 13, 2017.

Structural, Electronic Properties and Chemical Bonding of Borate Li4CaB2O6 under High Pressure： an Ab Initio Investigation

We calculate structural, electronic properties and chemical bonding of borate Li4CaB2O6 under high pressure by means of the local density-functional pseudopotential approach. The equilibrium lattice constants, density of states, Mulliken population, bond lengths, bond angles as well as the pressure dependence of the band gap are presented. Analysis of the simulated high pressure band structure suggests that borate Li4CaB2O6 can be used as the semi-conductor optical material. Based on the Mulliken population analysis, it is found that the electron transfer of the Li atom is very different from that of other atoms in the studied range of high pressures. The charge populations of the Li atom decrease with the pressure up to 60 GPa, then increase with the pressure.

2D-and 3D-QSBR Studies on the Relationship between Structure and Biodegradability of Phthalates

Nine phthalates were calculated at the B3LYP/6-311G＊＊ level using DFT method. The corresponding linear relationship equations （R2 were 0.853 and 0.936 respectively） for the biodegradation rate （Kb） and half-life time （h/2） of biodegradation were obtained with the structural parameters as theoretical descriptors. Furthermore, CoMFA method was also applied to establish 3D models which revealed the fields influencing these properties. The relationship between the properties and the structure was obtained. The correlation coefficients of the models were 0.992 and 0.999, respectively. Analyses of 2D and 3D models demonstrated that the molecular volume was an important factor affecting the biodegradability of these compounds.

Mechanistic, Energetic and Structural Aspects of the Adsorption of Carmustine on the Functionalized Carbon Nanotubes

Using density functional theory, noncovalent interactions and two mechanisms of covalent functionalization of drug carmustine with functionalized carbon nanotube（CNT） have been investigated. Quantum molecular descriptors of noncovalent configurations were studied. It was specified that binding of drug carmustine with functionalized CNT is thermodynamically suitable. NTCOOH and NTCOCl can bond to the NH group of carmustine through OH（COOH mechanism） and Cl（COCl mechanism） groups, respectively. The activation energies, activation enthalpies and activation Gibbs free energies of two pathways were calculated and compared with each other. The activation parameters related to COOH mechanism are higher than those related to COCl mechanism, and therefore COCl mechanism is suitable for covalent functionalization. COOH functionalized CNT（NTCOOH） has more binding energy than COCl functionalized CNT（NTCOCl） and can act as a favorable system for carmustine drug delivery within biological and chemical systems（noncovalent）. These results could be generalized to other similar drugs.

Effect of demethyltransferase FTO on tumor progression

N6-methyladenosine(m6A)modification is the most widespread and conserved internal mRNA modification in mammalian cells.It greatly affects genetic regulation by enhancing the involvement of diverse cellular enzymes and thus,plays a significant role in basic life processes.Numerous studies on m6A modification identified FTO as a crucial demethylase that participates in various biological processes.Not only does FTO play a pivotal role in obesity-related conditions,but it also influences the occurrence,development,and prognosis of several cancers,such as acute myeloid leukemia,breast cancer,liver cancer,and lung cancer.Moreover,FTO also shows a close association with immunity and viral infections.This article summarized the molecular mechanism of FTO in tumorigenesis and tumor progression.

Analytical potential energy function for the electronic states ~2Π_(1/2) and ~2Π_(3/2) of O_2~x (x=+1,-1)

The splitting of potential energy levels for ground state X^2∏g of O^x2 （x = ＋1,-1） under spin-orbit coupling （SOC） has been calculated by using the spin-orbit （SO） multi-configuration quasi-degenerate perturbation theory （SO-MCQDPT）. Their Murrell-Sorbie （M S） potential functions are gained, and then the spectroscopic constants for electronic states 2^∏1/2 and 2^∏3/2 are derived from the M S function. The vertical excitation energies for O^x2 （x = ＋1,-1） are v[O2＋1^（2∏3/2→X^2∏1/2）] =195.652cm^-1, and v[O2^-1（2^∏1/2 →X^2∏3/2）] =182.568cm^-1, respectively. All the spectroscopic data for electronic states 2^∏1/2 and 2^∏3/2 are given for the first time.

Parkinson's disease: From genetics to molecular dysfunction and targeted therapeutic approaches

Parkinson's disease (PD) is the most common neurodegenerative movement disorder in the elderly. As the pathogenesis of PD is still not fully understood, medications with the capacity of halting the disease progression are currently unavailable. The discovery of genes that are causative for, or increase susceptibility to PD is pivotal for the development of novel therapeutic approaches, as they are critical for the onset of PD and the molecular pathways underlying its pathogenesis. By reviewing relevant data, we discuss causative genes, and those associated with PD susceptibility and quantitative traits. Through Gene Ontology database and STRING analysis, we emphasize the roles of inorganic cation transmembrane transport pathways and hypothalamic pituitary thyroid axis, in addition to the established roles of inflammation/oxidative stress and mitochondrial dysfunction in the pathogenesis of PD. It is hoped these insights 1) untangle the clinical complex presentations of PD, 2) reveal the interwoven molecular network leading to PD, and 3) identify critical molecular targets to facilitate novel PD drug discovery, with a view to providing improved consultation and personalized medicine for patients with PD in the future.