The Citron homology domain of MAP4Ks improves outcomes of traumatic brain injury

The mitogen-activated protein kinase kinase kinase kinases(MAP4Ks)signaling pathway plays a pivotal role in axonal regrowth and neuronal degeneration following insults.Whether targeting this pathway is beneficial to brain injury remains unclear.In this study,we showed that adeno-associated virus-delivery of the Citron homology domain of MAP4Ks effectively reduces traumatic brain injury-induced reactive gliosis,tauopathy,lesion size,and behavioral deficits.Pharmacological inhibition of MAP4Ks replicated the ameliorative effects observed with expression of the Citron homology domain.Mechanistically,the Citron homology domain acted as a dominant-negative mutant,impeding MAP4K-mediated phosphorylation of the dishevelled proteins and thereby controlling the Wnt/β-catenin pathway.These findings implicate a therapeutic potential of targeting MAP4Ks to alleviate the detrimental effects of traumatic brain injury.

Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model

Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2(SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.

Sine oculis homeobox homolog family function in gastrointestinal cancer:Progression and comprehensive analysis

The sine oculis homeobox homolog(SIX)family,a group of transcription factors characterized by a conserved DNA-binding homology domain,plays a critical role in orchestrating embryonic development and organogenesis across various organisms,including humans.Comprising six distinct members,from SIX1 to SIX6,each member contributes uniquely to the development and differentiation of diverse tissues and organs,underscoring the versatility of the SIX family.Dysregulation or mutations in SIX genes have been implicated in a spectrum of developmental disorders,as well as in tumor initiation and progression,highlighting their pivotal role in maintaining normal developmental trajectories and cellular functions.Efforts to target the transcriptional complex of the SIX gene family have emerged as a promising strategy to inhibit tumor development.While the development of inhibitors targeting this gene family is still in its early stages,the significant potential of such interventions holds promise for future therapeutic advances.Therefore,this review aimed to comprehensively explore the advancements in understanding the SIX family within gastrointestinal cancers,focusing on its critical role in normal organ development and its implications in gastrointestinal cancers,including gastric,pancreatic,colorectal cancer,and hepatocellular carcinomas.In conclusion,this review deepened the understanding of the functional roles of the SIX family and explored the potential of utilizing this gene family for the diagnosis,prognosis,and treatment of gastrointestinal cancers.

Rodent epididymal cDNAs identified by sequence homology to human and canine counterparts

<abstract>Aim: Identification of the rodent counterparts of human and canine epididymal cDNAs HE3, HE4 and Ce8/Ly6G5C by sequence homology and analysis of their expression patterns and regulation level in the rat. Methods: 'Electronic screening' of Expressed Sequence Tag (EST) and genomic databases, followed by RT-PCR and Northern blot analysis. Results: Rodent ESTs and genomic sequences homologous to HE3, HE4 and Ce8/Ly6G5C were identified in the public databases and the 'full-length' rat cDNAs cloned. To emphasise their homology to the human and canine genes, they were named Me3/Re3, Me4/Re4 and Re8 for mouse and rat counterparts, respectively. mRNA expression patterns were analysed in rats, including rat HEl and HE5/CD52 counterparts as controls. Re3 and Re8 mRNAs were only found in the rat epididymis, while Re4 showed a broader tissue distribution. Within the epididymis, Re3 and Re4 mRNAs were detected in all regions; Re8, on the other hand, was restricted to the caput. During postnatal development, Re3 and control mRNAs were found from the earliest stages investigated, while Re8 mRNA was observed only from day 24 postnatum, corresponding to the onset of spermatogenesis in the prepubertal testis. Castration and testosterone supplementation of adult male rats suggested that none of the cloned mRNAs was directly androgen-regulated. Efferent duct ligation, however, showed that Re8 mRNA levels depended on testicular factors other than androgens. Conclusion: The novel rodent cDNAs can now be used to monitor epididymal gene expression more closely and to set up various regulatory and functional studies.

Expression,Purification,Characteristics and Homology Modeling of the HMGS from Streptococcus pneumoniae

Objective To understand the molecular basis for a potential reaction mechanism and develop novel antibiotics with homology modeling for 3-hydroxy-3-methylglutaryl coenzyme A （HMG-CoA） synthase （HMGS）. Methods The genetic engineering technology and the composer module of SYBYL7.0 program were used, while the HMGS three-dimensional structure was analyzed by homology modeling. Results The mvaS gene was cloned from Streptococcus pneumoniae and overexpressed in Escherichia coli from a pET28 vector. The expressed enzyme （about 46 kDa） was purified by affinity chromatography with a specific activity of 3.24 μmol/min/mg. Optimal conditions were pH 9.75 and 10 mmol/L MgCl2 at 37 ℃ The Vmax and Km were 4.69 μmol/min/mg and 213 μmol/L respectively. The 3D model of S.pneumoniae HMGS was established based on structure template of HMGS of Enterococcus faecalis. Conelusion The structure of HMGS will facilitate the structure-based design of alternative drugs to cholesterol-lowering therapies or to novel antibiotics to the Gram-positive cocci, whereas the recombinant HMGS will prove useful for drug development against a different enzyme in the mevalonate pathway.

Cloning and Homology Comparison of S Gene for Isolate TH-98 of Porcine Transmissible Gastroenteritis Virus

TH-98 isolate of transmissible gastroenteritis virus (TGEV) was propagated and harvested on swine testicle (ST) monolayer cell. Two pairs of primers were designed to amplify S gene by RT-PCR according to the published sequence of TGEV'S gene cDNA with Oligo version 4.1 and DNasis software. The products of PCR were named Sa and Sb, of 2.3 kb and 2.1 kb respectively. Sa was inserted in EcoR I and Kpn I sites after Sb was cloned in Kpn I and Pst I multiple cloning sites of the same pUC18 plasmid. The recombinant pUC-S plasmid was identified and analyzed by corresponding restriction endonuclease and nested PCR on the basis of the genetic sites of S gene and pUC18 plasmid, which was identified as S gene of TGEV. Recombinant pUC-S was sequenced and analyzed in comparison with the other strains. Gene sequence comparison indicated that TH-98 shared 99, 97, 98, 97 and 94% identities with Purdue-115(US), Miller(US), TO14(Japan), FS772(British), 96-1933(British), respectively, their deduced amino acid homology was 99, 97, 97, 96 and 93% correspondingly. In addition, the analysis report verified that pUC-S owned a complete open reading frame (ORF) including initiation codon, signal sequences, remaining sequences and termination codon as well. Therefore, the results affirmed that S gene of TGEV TH-98 was extremely conservative.

Homology Modelling and Structural Comparisons of Capsid-Associated Proteins from Circoviruses Reveal Important Virus-Specific Surface Antigens

Circoviridae represent a growing family of small animal viruses. Some of these viruses have veterinary and medical importance, although, a vast amount of these newly discovered viruses have unknown effects on their hosts. The capsid-associated protein (Cap) of circoviruses is of interest because of its role in viral structure, immune evasion, host cell entry, and nuclear shuttling of viral components. The structure of the porcine circovirus 2 (PCV2) Cap has been solved and offered insight to these functions. Based on the crystallographic PCV2 Cap structure, models from circoviruses isolated from avian, fish, and mammalian hosts have been constructed and analyzed to better understand the roles of these proteins in the virus family. A high degree of conservation is observed in the models, however, the surface antigens differ among viruses. This is likely a reflection of the small genome harbored by circoviruses, and therefore the requirement of their few proteins to carry out specific vital functions, while maintaining enough variation to successfully infect their hosts. Here we describe the putative structures of a range of Cap proteins from circoviruses based on the crystallographic determination of porcine Cap, identifying key regions for function and inhibition of crystal formation.

Poisson (Co)homology of a Class of Frobenius Poisson Algbras

In this paper, we study the truncated polynomial algebra L in n variables, and discuss the following four problems in detail: 1) Homology complex and homology group of Poisson algebra L;2) Given a new Poisson bracket by calculation modular derivation of Frobenius Poisson algebra;3) Calculate the twisted homology group of Poisson algebra L;4) Verify the theorem of twisted Poincaré duality between twisted Poisson homology and Poisson Cohomology.

A method to synthesize cDNA constructs by homology based recombination cloning

We introduce a homology-based recombination approach for generating a cDNA construct. This method depends on amplifying several exon fragments and their fusions by the homology-based recombination. This method provides a way to generate the cDNA sequence of any gene without any need for its mRNA. The paper describes the strategy by assembling cDNA of the MYB1 and MYB2 genes of Arabidopsis thaliana.

Homology Curve Complex

A homological analogue of curve complex of a closed connected orientable surface is developed and studied. The dis-tance in this complex is shown to be quite computable and an algorithm given (Theorem 3.5). As an application of this complex it is shown that for a closed orientable 3-manifold, and any of its Heegaard splittings, one can give an algorithm to decide whether the manifold contains a 2-sided, non-separating, closed incompressible surface (Theorem 1.1).

<i>Blastomyces dermatitidis</i>: Chitinase Homology Model, <i>in Silico</i>Docking, and Inhibition Assay

Blastomyces dermatitidis is a thermally dimorphic fungus that causes the disease blastomycosis. Currently there are a limited number of effective treatments, many of which have harsh side effects. Chitin, a component of the fungal cell wall is often broken down and recycled for cell wall remodeling and growth. Chitinase is the digestive enzyme capable of chitin hydrolysis. By inhibiting the chitinase we predicted that cells wouldn’t be able to divide and multiply normally, thereby leading to possible anti-fungal treatments. For this study we modeled the structure of B. dermatitidis chitinase, using homology modeling. By predicting a three-dimensional structure we were able to do additional analyses of the active site of the chitinase and predict the binding of a possible small molecule, acetazolamide, in silico. This binding allowed us to predict that this molecule might be capable of inhibiting the chitinase of B. dermatitidis. This inhibition was tested in vivo. No difference in the growth curves of the test and control organisms was observed, however there was a difference within the cell walls of the yeast cells. The cell walls appeared thicker with additional differences in cell wall orderly growth. These changes are consistent with changes that may occur as B. dermatitidis chitinases are inhibited.

Homology Modeling of Human Alpha-Glucosidase Catalytic Domains and SAR Study of Salacinol Derivatives

Maltase-glucoamylase (MGAM) and sucrase-isomaltase (SI) belong to human intestinal alpha-glucosidase and their N-terminal side catalytic domains are called NtMGAM and NtSI, and their C-terminal side catalytic domains are called CtMGAM and CtSI. As an antidiabetic, alpha-glucosidase inhibitor is required to bind to all of these domains to inhibit disaccharides hydrolysis. Salacinol and kotalanol isolated from Salacia reticulata are novel seed compounds for al-pha-glucosidase inhibitor. Even though the complex structures of NtMGAM or NtSI have been determined experimen-tally, those of CtMGAM and CtSI have not been revealed. Thus, homology modeling for CtMGAM and CtSI has been performed to predict the binding mode of salacinol and its derivatives for each domain. The binding affinities for these compounds were also calculated to explain the experimental structure-activity relationships (SARs). After a docking study of the derivatives to each catalytic domain, the MM/PBSA method has been applied to predict the binding affinities. The predicted binding affinities were almost consistent with the experimental SARs. The comparison of the complex structures and binding affinities provided insights for designing novel compounds, which inhibit all catalytic domains.

Homology modeling and functional annotation of bubaline pregnancy associated glycoprotein 2

Background： Pregnancy associated glycoproteins form a diverse family of glycoproteins that are variably expressed at different stages of gestation. They are probably involved in immunosuppression of the dam against the fetomaternal placentome. The presence of the products of binucleate cells in maternal circulation has also been correlated with placentogenesis and placental re-modeling. The exact structure and function of the gene product is unknown due to limitations on obtaining purified pregnancy associated glycoprotein preparations.Results： Our study describes an in silico derived 3D model for bubaline pregnancy associated glycoprotein 2. Structure-activity features of the protein were characterized, and functional studies predict bubaline pregnancy associated glycoprotein 2 as an inducible, extra-cellular, non-essential, N-glycosylated, aspartic pro-endopeptidase that is involved in down-regulation of complement pathway and immunity during pregnancy. The protein is also predicted to be involved in nutritional processes, and apoptotic processes underlying fetal morphogenesis and remodeling of feto-maternal tissues.Conclusion： The structural and functional annotation of buPAG2 shall allow the designing of mutants and inhibitors for dissection of the exact physiological role of the protein.

A Global Reduction Based Algorithm for Computing Homology of Chain Complexes

In this paper, we propose a new algorithm to compute the homology of a finitely generated chain complex. Our method is based on grouping several reductions into structures that can be encoded as directed acyclic graphs. The organized reduction pairs lead to sequences of projection maps that reduce the number of generators while preserving the homology groups of the original chain complex. This sequencing of reduction pairs allows updating the boundary information in a single step for a whole set of reductions, which shows impressive gains in computational performance compared to existing methods. In addition, our method gives the homology generators for a small additional cost.

The Tianma 65 m radio telescope antenna

The Tianma 65 m radio telescope(TMRT)at Shanghai is a fully steerable single-dish radio telescope in China,operating at centimeter to millimeter wavelengths(1.25 GHz to 50 GHz).This paper presents details on the main specifications,design,performance analysis,testing,and construction of the telescope antenna.The measured total efficiency is better than 50%over the whole elevation angle range,first sidelobe levels are less than−20 dB,antenna system noise temperatures are less than 70 K at 30°elevation angle,and pointing accuracy is less than 3″.The measured and calculated results are in good agreement,verifying the effectiveness of the design and analysis.

Using Chou’s Pseudo Amino Acid Composition for Protein Remote Homology Detection

Protein remote homology detection is a key problem in bioinformatics. Currently, the discriminative methods, such as Support Vector Machine (SVM), can achieve the best performance. The most efficient approach to improve the performance of the SVM-based methods is to find a general protein representation method that is able to convert proteins with different lengths into fixed length vectors and captures the different properties of the proteins for the discrimination. The bottleneck of designing the protein representation method is that native proteins have different lengths. Motivated by the success of the pseudo amino acid composition (PseAAC) proposed by Chou, we applied this approach for protein remote homology detection. Some new indices derived from the amino acid index (AAIndex) database are incorporated into the PseAAC to improve the generalization ability of this method. Our experiments on a well-known benchmark show this method achieves superior or comparable performance with current state-of-the-art methods.

Homology Model and Ligand Binding Interactions of the Extracellular Domain of the Human α4β2 Nicotinic Acetylcholine Receptor

Addiction to nicotine, and possibly other tobacco constituents, is a major factor that contributes to the difficulties smokers face when attempting to quit smoking. Amongst the various subtypes of nicotinic acetylcholine receptors (nAChRs), the α4β2 subtype plays an important role in mediating the addiction process. The characterization of human α4β2-ligand binding interactions provides a molecular framework for understanding ligand-receptor interactions, rendering insights into mechanisms of nicotine addiction and may furnish a tool for efficiently identifying ligands that can bind the nicotine receptor. Therefore, we constructed a homology model of human α4β2 nAChR and performed molecular docking and molecular dynamics (MD) simulations to elucidate the potential human α4β2-ligand binding modes for eleven compounds known to bind to this receptor. Residues V96, L97 and F151 of the α4 subunit and L111, F119 and F121 of the β2 subunit were found to be involved in hydrophobic interactions while residues S153 and W154 of the α4 subunit were involved in the formation of hydrogen bonds between the receptor and respective ligands. The homology model and its eleven ligand-bound structures will be used to develop a virtual screening program for identifying tobacco constituents that are potentially addictive.

SARS-CoV-2重组痘苗病毒疫苗rVTT△TK-RBD的构建、筛选及免疫原性研究

目的 构建重组痘苗病毒载体疫苗rVTT△TK-RBD,并评价其安全性和免疫原性。方法 参考严重急性呼吸综合征冠状病毒2(SARS-CoV-2)基因序列合成受体结合域(RBD)基因,并将其插入自主构建的重组质粒pSTKE的多克隆位点上,构建重组痘苗病毒穿梭载体pSTKE-RBD,并转染到预先感染天坛株痘苗病毒(VTT)的BHK-21细胞内,经多轮的荧光噬斑筛选成功获得重组痘苗病毒rVTT△TK-RBD;通过滴鼻方式免疫小鼠后,检测rVTT△TK-RBD对BALB/c小鼠体质量的影响;通过肌肉免疫小鼠后,分析rVTT△TK-RBD对BALB/c小鼠产生的特异性抗体和中和抗体的水平;通过流式细胞术检测rVTT△TK-RBD对BALB/c小鼠T细胞亚群的影响。结果 利用同源重组、增强型绿色荧光蛋白(EGFP)筛选标记和多次荧光噬斑筛选,成功筛选获得了表达RBD的胸腺激酶(TK)基因缺失型重组痘苗病毒rVTT△TK-RBD,且PCR验证成功。BALB/c小鼠体内实验表明rVTT△TK-RBD具有较好的抗SARS-CoV-2的免疫原性且相比于亲本株VTT明显降低了对机体的毒性作用。结论 成功构建并获得SARS-CoV-2重组痘苗病毒疫苗rVTT△TK-RBD并通过各项试验证明其安全性和免疫原性。

Subcellular Distribution and Chemical Forms of Cadmium in the Medicine Food Homology Plant Platycodon grandiflorum(Jacq.)A.DC.

Although Platycodon grandiflorum(Jacq.)A.DC.is a renowned medicine food homology plant,reports of excessive cadmium(Cd)levels are common,which affects its safety for clinical use and food consumption.To enable its Cd levels to be regulated or reduced,it is necessary to first elucidate the mechanism of Cd uptake and accumulation in the plant,in addition to its detoxification mechanisms.This present study used inductively couple plasma-mass-spectrometry to analyze the subcellular distribution and chemical forms of Cd in different tissues of P.grandiflorum.The experimental results showed that Cd was mainly accumulated in the roots[predominantly in the cell wall(50.96%-61.42%)],and it was found primarily in hypomobile and hypotoxic forms.The proportion of Cd in the soluble fraction increased after Cd exposure,and the proportion of insoluble phosphate Cd and oxalate Cd increased in roots and leaves,with a higher increase in oxalate Cd.Therefore,it is likely that root retention mechanisms,cell wall deposition,vacuole sequestration,and the formation of low mobility and low toxicity forms are tolerance strategies for Cd detoxification used by P.grandiflorum.The results of this study provide a theoretical grounding for the study of Cd accumulation and detoxification mechanisms in P.grandiflorum,and they can be used as a reference for developing Cd limits and standards for other medicine food homology plants.

Histological Assessment of Bone Regeneration in the Maxilla with Homologous Bone Graft:A Feasible Option for Maxillary Bone Reconstruction

Bone biomaterials have been increasingly used to reconstruct maxillary atrophic ridges.Thus,the aim of this study was to evaluate bone reconstruction in the maxilla using a homologous cortico-cancellous FFB(lyophilized)graft and verify its reliability.Eight individuals were included from 2014 to 2018.The first surgery was performed to install homologous bone blocks in the maxilla.The period of the second intervention varied between 5 months and 15 days to 11 months(≈7.93 months).The biopsies were taken from the central region of the matured graft during the surgery for implant placement.All patients presented clinical and radiographic conditions for the installation of dental implants.There was a 100%of survival rate.The histological assessment showed that the homologous block bone graft was an osteoconductive biomaterial,with connective tissue present,and newly formed bone juxtaposed on its surface.There were bone trabeculae with osteocytes and active osteoblasts with connective tissue in the mineralization process;the remodeling process can be found through the reverse lines.A limited focus of necrosis with fibrosis was detected,with small resorption and areas of inflammatory infiltrate,but without clinical significance.The homologous block bone graft can be considered a feasible option to substitute the autogenous bone graft(gold standard),with predictable clinical and favorable histological results.The patients had a shorter surgical period,low morbidity,and an unlimited amount of biomaterial available at an accessible cost.