The evolution and application progress of non-modified drug target discovery CETSA technology / 药学学报

Understanding the research methods for drug protein targets is crucial for the development of new drugs, clinical applications of drugs, drug mechanisms, and the pathogenesis of diseases. Cellular thermal shift assay (CETSA), a target research method without modification, has been widely used since its development. Now, there are various CETSA-based technology combinations, such as mass spectrometry-based cellular thermal shift assay (MS-CETSA), isothermal dose response-cellular thermal shift assay (ITDR-CETSA), amplified luminescent proximity homogeneous assay-cellular thermal shift assay (Alpha-CETSA), etc., which combine their respective advantages and further expand the application scope of CETSA. These technologies are suitable for the entire drug development chain, from drug screening to monitoring the target binding and off-target toxicity of drugs in patients. Based on the author's research experience, this paper reviews the principles of CETSA and related binding technologies, their application in target discovery, and the progress of data processing and analysis in recent years, aiming to provide reference and reference for the further application of CETSA.

Discovery of the mechanisms of acupuncture in the treatment of migraine based on functional magnetic resonance imaging and omics / 医学前沿

Migraine is one of the most prevalent and disabling neurological disease, but the current pharmacotherapies show limited efficacy and often accompanied by adverse effects. Acupuncture is a promising complementary therapy, but further clinical evidence is needed. The influence of acupuncture on migraine is not an immediate effect, and its mechanism remains unclear. This study aims to provide further clinical evidence for the anti-migraine effects of acupuncture and explore the mechanism involved. A randomized controlled trial was performed among 10 normal controls and 38 migraineurs. The migraineurs were divided into blank control, sham acupuncture, and acupuncture groups. Patients were subjected to two courses of treatment, and each treatment lasted for 5 days, with an interval of 1 day between the two courses. The effectiveness of treatment was evaluated using pain questionnaire. The functional magnetic resonance imaging (fMRI) data were analyzed for investigating brain changes induced by treatments. Blood plasma was collected for metabolomics and proteomics studies. Correlation and mediation analyses were performed to investigate the interaction between clinical, fMRI and omics changes. Results showed that acupuncture effectively relieved migraine symptoms in a way different from sham acupuncture in terms of curative effect, affected brain regions, and signaling pathways. The anti-migraine mechanism involves a complex network related to the regulation of the response to hypoxic stress, reversal of brain energy imbalance, and regulation of inflammation. The brain regions of migraineurs affected by acupuncture include the lingual gyrus, default mode network, and cerebellum. The effect of acupuncture on patients' metabolites/proteins may precede that of the brain.

Alterações sistêmicas na assinatura do ciclo celular de pacientes com COVID-19 / Systemic changes in the cell cycle signature of patients with COVID-19

Com base nas perturbações fosfoproteômicas de moléculas associadas ao ciclo celular em células infectadas pelo coronavírus causador da síndrome respiratória aguda grave (SARSCoV)-2, a hipótese de inibidores do ciclo celular como uma terapia potencial para a doença de coronavírus 2019 (COVID-19) foi proposta. No entanto, o cenário das alterações do ciclo celular em COVID-19 permanece inexplorado. Aqui, realizamos uma análise integrativa de sistemas imunológicos de proteoma publicamente disponível (espectrometria de massa) e dados de transcriptoma (sequenciamento de RNA em massa e de célula única [scRNAseq]), com o objetivo de caracterizar mudanças globais na assinatura do ciclo celular de pacientes com COVID-19. Além de módulos de co-expressão de genes significativos enriquecidos associados ao ciclo celular, encontramos uma rede interconectada de proteínas diferencialmente expressas associadas ao ciclo celular (DEPs) e genes (DEGs) integrando dados moleculares de 1.480 indivíduos (974 pacientes infectados por SARS-CoV-2 e 506 controles [controles saudáveis ou indivíduos com outras doenças respiratórias]). Entre esses DEPs e DEGs estão várias ciclinas (CCNs), ciclo de divisão celular (CDCs), quinases dependentes de ciclinas (CDKs) e proteínas de manutenção de minicromossomos (MCMs). Embora os pacientes com COVID-19 compartilhem parcialmente o padrão de expressão de algumas moléculas associadas ao ciclo celular com outras doenças respiratórias, eles exibiram uma expressão significativamente maior de moléculas associadas ao ciclo celular relacionadas à gravidade da doença. Notavelmente, a assinatura do ciclo celular predominou nos leucócitos do sangue dos pacientes, mas não nas vias aéreas superiores. Os dados de scRNAseq de 229 indivíduos (159 pacientes com COVID- 19 e 70 controles) revelaram que as alterações das assinaturas do ciclo celular predominam nas células B, T e NK. Esses resultados fornecem uma compreensão global única das alterações nas moléculas associadas ao ciclo celular em pacientes com COVID-19, sugerindo novas vias putativas para intervenção terapêutica

Based on phosphoproteomics perturbations of cell cycle-associated molecules in severe acute respiratory syndrome coronavirus (SARS-CoV)-2-infected cells, the hypothesis of cell cycle inhibitors as a potential therapy for Coronavirus disease 2019 (COVID-19) has been proposed. However, the landscape of cell cycle alterations in COVID-19 remains mostly unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome (mass spectrometry) and transcriptome data (bulk and single-cell RNA sequencing [scRNAseq]), aiming to characterize global changes in the cell cycle signature of COVID-19 patients. Beyond significant enriched cell cycle-associated gene co-expression modules, we found an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating molecular data of 1,480 individuals (974 SARS-CoV- 2 infected patients and 506 controls [either healthy controls or individuals with other respiratory illness]). Among these DEPs and DEGs are several cyclins (CCNs), cell division cycle (CDCs), cyclin-dependent kinases (CDKs), and mini-chromosome maintenance proteins (MCMs). Although COVID-19 patients partially shared the expression pattern of some cell cycleassociated molecules with other respiratory illnesses, they exhibited a significantly higher expression of cell cycle-associated molecules associated with disease severity. Notably, the cell cycle signature predominated in the patients blood leukocytes but not in the upper airways. The scRNAseq data from 229 individuals (159 COVID-19 patients and 70 controls) revealed that the alterations of cell cycle signatures predominate in B, T, and NK cells. These results provide a unique global comprehension of the alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention

Screening for host proteins interacting with Mycobacterium tuberculosis Rv1705c by human proteome microarray / 中华微生物学和免疫学杂志

Objective:To investigate the proteins interacting with Mycobacterium tuberculosis Rv1705c in human body. Methods:Rv1705c was prokaryotically expressed and inclusion bodies were collected for further lysis and the purification of Rv1705c. ELISA assay was used to detect the secretion of IFN-γ after stimulating macrophages with Rv1705c protein. Purified and biotin-labeled Rv1705c sample was incubated on the HuProt? human proteome microarray to screen the interacting proteins. GenePix Pro 6.0 software was used to extract all features of the data obtained from the scanned images and further analysis was performed based on bioinformatics databases such as GO and KEGG. GST pull-down was performed to verify the interaction of Rv1705c with PSMA3 and RSAD2.Results:The purification results showed that Rv1705c was expressed in endosomes. The secretion of IFN-γ increased significantly after stimulating macrophages with Rv1705c. A total of 29 potential Rv1705c-interacting proteins were screened, and nine of them showed signal-to-noise ratio (SNR)>1.6, namely PSMA3, NLN, THOP1, UPF3A, RSAD2, OMG, PNKD, STEAP3 and MED8. Further bioinformatics analysis revealed that PSMA3, RSAD2 and C1QBP were involved in innate immune signaling pathway, and there were interactions of PSMA3 and RSAD2 with IFN. GST pull-down assay validated that PSMA3 and RSAD2 interacted with Rv1705c.Conclusions:This study showed that PSMA3 and RSAD2 interacted with Rv1705c, providing reference for further investigation on the mechanism of Mycobacterium tuberculosis infection.

Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia

Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI- LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein familiesin T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusions: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom's toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.(AU)

Proteoma urinario en la enfermedad renal diabética. Estado del arte

La enfermedad renal diabética (ERD) es la principal complicación microvascular de los pacientes con diabetes mellitus; esta es una entidad que genera un aumento significativo en la mortalidad de origen cardiovascular de este grupo de pacientes, aunque su diagnóstico temprano impacta de forma significativa en la evolución a enfermedad renal terminal y, por lo tanto, en la mortalidad. La detección de albuminuria en la orina y el deterioro de la tasa de filtración glomerular estimada son las principales técnicas diagnósticas que se utilizan en la práctica clínica para establecer la presencia de ERD; sin embargo, estas tienen limitaciones y por lo tanto es importante resaltar que el daño renal suele ser irreversible una vez están presentes. Durante los últimos años, numerosos estudios se han enfocado en detectar nuevos biomarcadores para detectar ERD y es aquí donde aparece como nueva herramienta la proteómica urinaria, una tecnología emergente que permite identificar en una muestra de orina proteínas que sugieren la presencia de esta enfermedad de manera temprana. Asimismo, el descubrimiento de biomarcadores basados en proteómicos representa una estrategia novedosa para mejorar el diagnóstico, pronóstico y tratamiento de la nefropatía diabética; sin embargo, los enfoques basados en la proteómica aún no están disponibles en la mayoría de los laboratorios de química clínica.

Diabetic kidney disease (DKD) is the main microvascular complication in patients with diabetes mellitus; it is an entity that generates a significant increase in mortality of cardiovascular origin in this group of patients, although its early diagnosis has a significant impact on the evolution to end-stage kidney disease and, therefore, on mortality. The detection of albuminuria in urine and the deterioration of the estimated glomerular filtration rate are the main diagnostic techniques that are used in clinical practice to establish the presence of DKD; however, they have limitations and therefore it is important to note that kidney damage is usually irreversible once they are present. Over the last few years, numerous studies have focused on the discovery of new biomarkers to detect DKD and this is where the urinary proteomics appears as a new tool, an emerging technology that allows the identification of proteins in a urine sample that strongly suggest the early presence of this disease. Likewise, the discovery of proteomic-based biomarkers represents a novel strategy to improve the diagnosis, prognosis and treatment of diabetic nephropathy; however, proteomics-based approaches are not yet available in the majority of clinical chemistry laboratories.

Modelo ideal de nefroprevención para Colombia

La enfermedad renal crónica (ERC) es una patología altamente prevalente en países en vía de desarrollo como Colombia, en donde afecta a gran parte de la población. Esta es una enfermedad que afecta la calidad de vida y la longevidad de los pacientes, así como los costos del sistema de salud. La ERC tiene un carácter progresivo e irreversible, por lo que intervenirla en etapas tempranas resulta ser una medida altamente costo-efectiva; a partir de esto surge el concepto de nefroprevención, mediante la cual, teniendo en cuenta los niveles de prevención primaria, secundaria y terciaria, se puede lograr una identificación precoz y la interrupción o enlentecimiento de la progresión, y además se puede implementar un manejo oportuno e integral del daño renal según el estadio de la enfermedad. Esto es posible haciendo una búsqueda activa de casos, realizando pruebas de cribado y haciendo intervenciones interdisciplinarias que incluyan educación de la población y del personal en salud, para así promover el autocuidado y realizar un seguimiento que impacte de forma positiva en la calidad de vida de los pacientes, en los desenlaces de la enfermedad y en la economía de los países en vía de desarrollo, los cuales deben optimizar sus limitados recursos e invertir en los procesos que generen mayor costo-efectividad.

Chronic kidney disease (CKD) is a highly prevalent entity in developing countries, affecting a large part of the Colombian population, which affects the quality of life, longevity and health costs. It has a progressive and irreversible character, so that intervening in early stages, turns out to be a highly cost-effective measure, from this, the concept of nephro-prevention arises, in which taking into account the levels of primary, secondary and tertiary prevention, it is possible to obtain an early identification, interruption or slowing down of progression, and timely and comprehensive management of kidney damage according to the stage of their disease; taking into account an active search for cases, carrying out screening tests and an interdisciplinary intervention that includes education of the population and health personnel, in order to generate self-care and follow-up that positively impacts quality of life, outcomes and finally the economy of developing countries, which those who, with limited resources, must optimize and invest in the processes that generate greater cost-effectiveness.

Identification techniques of small molecule drug target proteins without chemical modification and its applications: a review / 生物工程学报

Identification of the target proteins of small molecule drugs is crucial for understanding the mechanisms of drug actions and its side effects. Conventional methods require chemical modification, which might alter the activities of the drugs. Various label-free techniques have been developed to identify drug target proteins without chemical modifications. This includes drug affinity responsive target stability (DARTS), stability of proteins from rates of oxidation (SPROX), cellular thermal shift assay (CETSA), thermal proteome profiling (TPP) and many others. Here we review the principles and applications of these label-free techniques, their advantages and limitations, as well as the most recent advances.

Application of omics technology in oleaginous microorganisms / 生物工程学报

Microbial oils are potential resources of fuels and food oils in the future. In recent years, with the rapid development of systems biology technology, understanding the physiological metabolism and lipid accumulation characteristics of oleaginous microorganisms from a global perspective has become a research focus. As an important tool for systems biology research, omics technology has been widely used to reveal the mechanism of high-efficiency production of oils by oleaginous microorganisms. This provides a basis for rational genetic modification and fermentation process control of oleaginous microorganisms. In this article, we summarize the application of omics technology in oleaginous microorganisms, introduced the commonly used sample pre-processing and data analysis methods for omics analysis of oleaginous microorganisms, reviewe the researches for revealing the mechanism of efficient lipid production by oleaginous microorganisms based on omics technologies including genomics, transcriptomics, proteomics (modification) and metabolomics (lipidomics), as well as mathematical models based on omics data. The future development and application of omics technology for microbial oil production are also proposed.

Comparison of urine proteome in rats intraperitoneally infected by different microorganisms / 生物工程学报

Different microorganisms can cause intraperitoneal infection. This study was to distinguish different microbial infections by urine analysis. Rats were intraperitoneally injected with Escherichia coli, Staphylococcus aureus, and Candida albicans, separately. Urine samples were collected from rats at 0, 12, 36 and 72 h after infection. Urinary proteins were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with the control (without infection), a total of 69 differential proteins were identified in rats injected with E. coli. A total of 31 differences proteins were identified in rats injected with S. aureus. A total of 38 differential proteins were identified in rats injected with C. albicans. Urine proteome was different when rats were infected by different microorganisms, suggesting that urine may have the potential for differential diagnosis of different intraperitoneal infections.

Proteome and Acetylome Profiling of Livers in C57BL/6J Male Mice during Normal Aging / 中国医学科学院学报

Objective To obtain the proteome and acetylome profiles of livers in mice during normal aging.Methods We applied tandem mass tag labeling and liquid chromatography tandem mass spectrometry and achieved proteome and acetylome data in C57BL/6J male mice aged 2 and 18 months under physiological conditions.Results A total of 4712 proteins were quantified by proteome profiling,and 4818 acetylated sites in 1367 proteins by acetylome profiling.The proteome and acetylome revealed moderate differences in the livers of young and old mice.There were 195 differentially expressed proteins in the proteome and 113 differentially expressed acetylated sites corresponding to 76 proteins in the acetylome.Functional enrichment analysis for the proteome showed that aging-associated upregulated proteins were mainly involved in fatty acid metabolism,epoxygenase P450 pathway,drug catabolic process,organic hydroxy compound metabolic process,and arachidonic acid metabolic process,while the downregulated proteins were related to regulation of gene silencing,nucleosome assembly,protein heterotetramerization,response to interferon,protein-DNA complex assembly and other processes.For the acetylome,the proteins with aging-associated upregulated acetylated sites mainly participated in cofactor metabolism,small molecule catabolic process,ribose phosphate metabolic process,ribonucleotide metabolic process,and purine-containing compound metabolic process,while the proteins with downregulated acetylated sites were associated with sulfur compound metabolic process,response to unfolded protein,and amino acid metabolic process.Conclusion We profiled the proteome and acetylome of livers in mice during normal aging and generated datasets for further research on aging.

Proteomic characterization of Naja mandalayensis venom

Background Naja mandalayensis is a spitting cobra from Myanmar. To the best of our knowledge, no studies on this venom composition have been conducted so far. On the other hand, few envenomation descriptions state that it elicits mainly local inflammation in the victims' eyes, the preferred target of this spiting cobra. Symptoms would typically include burning and painful sensation, conjunctivitis, edema and temporary loss of vision. Methods We have performed a liquid-chromatography (C18-RP-HPLC) mass spectrometry (ESI-IT-TOF/MS) based approach in order to biochemically characterize N. mandalayensis venom. Results A wide variety of three-finger toxins (cardiotoxins) and metallopeptidases were detected. Less abundant, but still representative, were cysteine-rich secretory proteins, L-amino-acid oxidases, phospholipases A2, venom 5'-nucleotidase and a serine peptidase inhibitor. Other proteins were present, but were detected in a relatively small concentration. Conclusion The present study set the basis for a better comprehension of the envenomation from a molecular perspective and, by increasing the interest and information available for this species, allows future venom comparisons among cobras and their diverse venom proteins.(AU)

Comparative transcriptome and proteome profiling of chlorophyll metabolism pathway in four types of Magnolia officinalis / 中国中药杂志

Magnolia officinalis is a traditional Chinese medicine,with many years of cultivating process, M. officinalis leaves show more differentiation types due to the exchange of seeds from different provenances. "Da Ao"(DA), "Xiao Ao"(XA), "Chuan Hou"(CH),and "Liu Ye"(LY)are the main types of M. officinalis in Sichuan province of China,and there were obvious differences in growth rate,chemical composition,leaf shape and leaf colour. This study selected different types of M. officinalis leaves(DA,XA,LY and CH)from Sichuan to determine their chlorophyll content. Transcriptomic level sequencing of different types of M. officinalis leaf tissues was by high-throughput sequencing analysis and proteomics used an integrated approach involving TMT labelling and LC-MS/MS to quantify the dynamic changes of the whole proteome of M. officinalis. The results showed that CH had the lowest chlorophyll content while DA had the highest chlorophyll content. Furthermore,transcriptome and proteomics results showed that chlorophyll synthesis pathway in DA glutamine-tRNA reductase,urinary porphyrins decarboxylase(UROD),oxygen-dependent protoporphyrin(ODCO),the original-Ⅲ oxidase protoporphyrin oxidase(PPO),magnesium chelating enzyme subunit ChlD,protoporphyrin magnesium Ⅸ monomethyl ester [oxidative] cyclase(MPPMC)were significantly higher than CH,XA and LY,consistent in the results of determination of chlorophyll content(chlorophyll content was highest of 37.56 mg·g~(-1) FW). Some rate-limiting enzymes related to the chlorophyll synthesis,such as ODCO,PPO and MPPMC were tested by Parallel Reaction Monitoring(PRM),and the results showed that the rate-limiting enzyme content in DA was higher than that in other three types. Therefore,based on the differences in leaf color of four types of M. officinalis,the research conducted a preliminary study on the chlorophyll metabolism pathway in leaves of different types of M. officinalis,and explored relevant genes and proteins causing leaf color differences from the molecular level,so as to lay a foundation for studying the differences in growth and development of different types of M. officinalis.

Proteomic Classification and Identification of Proteins Related to Tissue Healing of Platelet-Rich Plasma

BACKGROUND: Platelet-rich plasma (PRP) is a plasma component of autologous blood containing a high concentration of platelets. PRP is used to promote healing of damaged tissues. However, there are not many studies on the composition and expression patterns of active proteins in PRP. The purpose of this study was to identify unknown factors that contribute to tissue healing by proteomic analysis of proteins in PRP.METHODS: Three men in their 30s with no basal disease participated in this study. All identified proteins were classified for tissue healing-related functions on the basis of the gene ontology analysis of adhesion molecule with Ig-like domain 2 (AmiGO2). PRP was prepared by using the ACP kit and GPS III kit.RESULTS: We identified a total of 125 proteins related to wound healing, along with three proteins for angiogenesis involved in wound healing, two proteins for fibroblast migration, four proteins for collagen biosynthesis process, two proteins for glycosaminoglycan biosynthesis process, and 13 proteins for glycosaminoglycan binding. So, in addition to the growth factors that have been already known to be involved in tissue healing, 25 new proteins were identified.CONCLUSIONS: We identified the unknown proteins associated with tissue healing in PRP. Our findings may serve as a foundation for the establishment of basic medical evidence for PRP applications.

Comparison of protein profiles of the pellicle, gingival crevicular fluid, and saliva: possible origin of pellicle proteins

BACKGROUND: The pellicle, the acellular organic material deposited on the surface of tooth enamel, has been thought to be derived from saliva. In this study, protein compositions of the pellicle, gingival crevicular fluid, and saliva collected from healthy adults were compared to elucidate the origin of pellicle proteins. RESULTS: The pellicle, gingival crevicular fluid, and saliva from the parotid gland or mixed gland were collected; subsequently, protein expression in samples from the respective individual was compared by SDS-PAGE and mass spectrometry. Following SDS-PAGE, proteins in the major bands were identified by mass spectrometry. The band pattern of pellicle proteins appeared different from those of gingival crevicular fluid, or saliva samples. Using mass spectrometry, 13 proteins in these samples were identified. The relative abundance of the proteins was quantitatively analyzed using mass spectrometry coupled with stable isotope labeling and by western blot. Cystatin S and α-amylase detected in pellicle were enriched in saliva samples, but not in gingival crevicular fluid, by western blot, and their abundance ratios were high in saliva and low in gingival crevicular fluid when analyzed by stable isotope labeling. Serotransferrin, however, was found only in the pellicle and gingival crevicular fluid by western blot and its abundance ratio was low in saliva. CONCLUSIONS: Our study revealed that the gingival crevicular fluid appears to contribute to pellicle formation in addition to saliva.

Differences in Proteomic Profiles Between Caries Free and Caries Affected Children

Abstract Objective: To determine if there are differences in protein profiles in saliva depending if children of caries-free versus caries affected. Material and Methods: A cohort of 91 children with ages between 6 and 19 years, along clinical status of caries experience. Protein profiles in saliva were determined using electrophoresis and the calculation of the percentage of a specific band at a specific molecular weight in relationship to the total protein in that sample (% of total) using molecular weight standards. This quantification was repeated for each protein band across a range of molecular weights for each sample. Chi-square, Fisher's exact, and Student t-tests were used to compare the distributions between caries-free and caries affected children (α=0.05). Results: Histatin was more likely to be non-detectable or reduced in caries-free children (OR=7.56; 95% CI 1.62-35.13) and these children had on average one less gel band detected by the assay we used. Conclusion: We have found differences in proteins between caries affected and caries-free children, suggesting that this line of investigation holds the promise of providing new tools for caries management.

Oxidative stress and antioxidant defense in detoxification systems of snake venom-induced toxicity

Snakebites remain a major life-threatening event worldwide. It is still difficult to make a positive identification of snake species by clinicians in both Western medicine and Chinese medicine. The main reason for this is a shortage of diagnostic biomarkers and lack of knowledge about pathways of venom-induced toxicity. In traditional Chinese medicine, snakebites are considered to be treated with wind, fire, and wind-fire toxin, but additional studies are required. Methods: Cases of snakebite seen at the Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine were grouped as follows: fire toxin - including four cases of bites by Agkistrodon acutus and three bites by Trimeresurus stejnegeri - and wind-fire toxin - four cases of bites by vipers and three bites by cobras. Serum protein quantification was performed using LC-MS/MS. Differential abundance proteins (DAPs) were identified from comparison of snakebites of each snake species and healthy controls. The protein interaction network was constructed using STITCH database. Results: Principal component analysis and hierarchical clustering of 474 unique proteins exhibited protein expression profiles of wind-fire toxins that are distinct from that of fire toxins. Ninety-three DAPs were identified in each snakebite subgroup as compared with healthy control, of which 38 proteins were found to have significantly different expression levels and 55 proteins displayed no expression in one subgroup, by subgroup comparison. GO analysis revealed that the DAPs participated in bicarbonate/oxygen transport and hydrogen peroxide catabolic process, and affected carbon-oxygen lyase activity and heme binding. Thirty DAPs directly or indirectly acted on hydrogen peroxide in the interaction network of proteins and drug compounds. The network was clustered into four groups: lipid metabolism and transport; IGF-mediated growth; oxygen transport; and innate immunity. Conclusions: Our results show that the pathways of snake venom-induced toxicity may form a protein network of antioxidant defense by regulating oxidative stress through interaction with hydrogen peroxide.(AU)

Protein fingerprinting with digital sequences of linear protein subsequence volumes: a computational study

Proteins in a proteome can be identified from a sequence of K integers equal to the digitized volumes of subsequences withL residues from the primary sequence of a stretched protein. Exhaustive computations on the proteins of Helicobacterpylori (UniProt id UP000000210) with L and K in the range 4–8 show that *90% of the proteins can be identified uniquelyin this manner. This computational result can be translated into practice with a nanopore, an emerging technology that doesnot require analyte immobilization, proteolysis or labeling. Unlike other methods, most of which focus on a specific targetprotein, nanopore-based methods enable the identification of multiple proteins from a sample in a single run. Recent workby Kennedy, Kolmogorov and associates shows that the blockade current due to a protein molecule translocating through ananopore is roughly proportional to one or more contiguous residues. The present study points to a modified version inwhich the volumes of subsequences (rather than of single residues) may be obtained by integrating the blockade current dueto L contiguous residues. The advantages arising from this include lower detector bandwidth, elimination of thehomopolymer problem and reduced noise. Because an identifier is based on near as well as distant (up to 2KL-L) residues,this approach uses more global information than an approach based on single residues and short-range correlations. Theresults of the study, which are available in a data supplement, are discussed in detail. Potential implementation issues areaddressed.

Transcriptome and proteome analyses of resistant preharvest peanut seed coat in response to Aspergillus flavus infection

BACKGROUND: The infection of peanut (Arachis hypogaea L.) seed coat by the pathogenic fungus Aspergillus flavus has highly negative economic and health impacts. However, the molecular mechanism underlying such defense response remains poorly understood. This study aims to address this issue by profiling the transcriptomic and proteomic changes that occur during the infection of the resistant peanut cultivar J11 by A. flavus. RESULTS: Transcriptomic study led to the detection of 13,539 genes, among which 663 exhibited differential expression. Further functional analysis found the differentially expressed genes to encode a wide range of pathogenesis- and/or defense-related proteins such as transcription factors, pathogenesis-related proteins, and chitinases. Changes in the expression patterns of these genes might contribute to peanut resistance to A. flavus. On the other hand, the proteomic profiling showed that 314 of the 1382 detected protein candidates were aberrantly expressed as a result of A. flavus invasion. However, the correlation between the transcriptomic and proteomic data was poor. We further demonstrated by in vitro fungistasis tests that hevamine-A, which was enriched at both transcript and protein levels, could directly inhibit the growth of A. flavus. Conclusions: The results demonstrate the power of complementary transcriptomic and proteomic analyses in the study of pathogen defense and resistance in plants and the chitinase could play an important role in the defense response of peanut to A. flavus. The current study also constitutes the first step toward building an integrated omics data platform for the development of Aspergillus-resistant peanut cultivars

Effect of ketamine anesthesia on proteome in hippocampus of aged rats / 中华麻醉学杂志

Objective@#To evaluate the effects of ketamine anesthesia on proteome in hippocampus in aged rats.@*Methods@#Thirty healthy male Wistar rats, aged 20 months, weighing 560-610 g, were divided into 2 groups (n=15 each) using a random number table method: control group (group C) and ketamine group (group K). In group K, ketamine 80 mg/kg was intraperitoneally injected, additional 1/2 initial dose was given when the righting reflex was recovered, and anesthesia was maintained for 3 h. Morris water maze test was performed starting from 1st day after the end of anesthesia.Five rats were selected at days 1 and 7 after the end of anesthesia and sacrificed, and hippocampal tissues were obtained to extract proteins.Proteins extracted from rat hippocampi were identified by 2-dimensional electrophoresis (2-DE). The differentially expressed proteins were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and biological information system.@*Results@#Compared with group C, the escape latency and total swimming distance to find the submerged platform in Morris water maze at the 1st day after anesthesia were significantly prolonged in group K (P<0.05 or 0.01). The MALDI-TOF-MS analysis showed that there were 21 differentially expressed proteins at 1st day after ketamine anesthesia, of which 6 proteins (involving maintenance of intracellular protein homeostasis, energy metabolism, etc.) presented with up-regulated expression and 15 proteins (involving synaptic vesicle transport efficiency, synaptic structural and functional plasticity, maintenance of intracellular protein homeostasis, NMDA-mediated Ca2+ signal transport, energy metabolism, etc.) presented with down-regulated expression.There were 8 differentially expressed proteins at 7th day, including 3 proteins with up-regulated expression and 5 proteins with down-regulated expression (P<0.05).@*Conclusion@#Ketamine anesthesia can induce 21 differentially expressed proteins in hippocampi of aged rats, involving synaptic vesicle transport efficiency, synaptic structural and functional plasticity, intracellular protein homeostasis, NMDA-mediated Ca2+ signal transport, energy metabolism, and etc.which may be involved in the mechanism of ketamine-induced temporary cognitive dysfunction.