Extensive characterization of peptides from Panax ginseng C. A. Meyer using mass spectrometric approach

Panax ginseng is an important herb that has clear effects on the treatment of diverse diseases. Until now, the natural peptide constitution of this herb remains unclear. Here, we conduct an extensive characterization of Ginseng peptidome using MS‐based data mining and sequencing. The screen on the charge states of precursor ions indicated that Ginseng is a peptide‐rich herb in comparison of a number of commonly used herbs. The Ginseng peptides were then extracted and submitted to nano‐LC‐MS/MS analysis using different fragmentation modes, including CID, high‐energy collisional dissociation, and electron transfer dissociation. Further database search and de novo sequencing allowed the identification of total 308 peptides, some of which might have important biological activities. This study illustrates the abundance and sequences of endogenous Ginseng peptides, thus providing the information of more candidates for the screening of active compounds for future biological research and drug discovery studies.     

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures

LC-MS/MS has emerged as the method of choice for the identification and quantification of protein sample mixtures. For very complex samples such as complete proteomes, the most commonly used LC-MS/MS method, data-dependent acquisition (DDA) precursor selection, is of limited utility. The limited scan speed of current mass spectrometers along with the highly redundant selection of the most intense precursor ions generates a bias in the pool of identified proteins toward those of higher abundance. A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented. In the first stage of the strategy, all detectable peptide ion signals are extracted from high resolution LC-MS feature maps or aligned sets of feature maps. The selected features or a subset thereof are subsequently sequenced in sequential, non-redundant directed LC-MS/MS experiments, and the MS/MS data are mapped back to the original LC-MS feature map in a fully automated manner. The strategy, implemented on an LTQ-FT MS platform, allowed the specific sequencing of 2,000 features per analysis and enabled the identification of more than 1,600 phosphorylation sites using a single reversed phase separation dimension without the need for time-consuming prefractionation steps. Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions.     

中缅树鼩能量代谢的季节变化

小型哺乳动物的体重和产热特征的季节调节对其生存至关重要。为探讨中缅树鼩的能量代谢适应特征随季节的变化,采用耗氧量测定、食物平衡法、形态测量等方法,分别对其冬季和夏季的基础代谢率(BMR)、非颤抖性产热(NST)、体温、体重、蒸发失水、能量收支和消化道的长度和重量进行了测定。中缅树鼩冬季体温、体重、基础代谢率、NST、蒸发失水散热分别为37. 9℃ ± 0.14℃ ,126.1 ± 2.1 g,42. 94 ± 2.65 J/g· h,54. 97 ±2.14 J/ g·h,5. 69 ±0.33 J/ g·h;夏季体温、体重、基础代谢率、NST、蒸发失水散热分别为38.5℃ ± 0. 27℃ ,106.9 ±5.1 g,28. 69 ±3.06 J/ g·h,47.43 ± 2.45 J / g·h,7.12 ±0. 57 J/ g·h;中缅树鼩的每日摄入能、消化能、可代谢能冬季均比夏季显著增加,消化道特征冬季和夏季存在变化,随着温度降低、食物质量下降,小肠长度和重量增加。这些结果表明:中缅树鼩在冬季,通过增加体重、基础代谢率和NST、能量摄入、消化能和可代谢能,降低蒸发失水等方式应对季节性环境变化。代谢产热和消化生理调节在季节性适应过程中具有重要地位。     

The morphogenesis of the scapula of Tupaia belangeri

The therian scapula was until now thought to show very primitive features during early morphogenesis, as are found in the scapula of adult monotremes (elevated position of the scapula, lack of a spina and a fossa supraspinata, laterally directed cavitas glenoidalis). A morphogenetic study of the scapula of Tupaia belangeri has proved some of these assumptions to be wrong. The scapula undergoes a tilting which shifts its angulus articularis cranially, but no descent of the scapula could be found. The supraspinous fossa, which was supposed to develop very late in ontogeny from the anterior border of the scapula (Lewis 1902, Cheng 1955), is present in Tapaiai from the start. Part of it ossifies in membrane. The scapular spine does not develop as a cartilaginous outgrowth from the anterior border, but is formed mainly as an appositional bone along the lateral surface of the scapula. The glenoid cavity and the humerus are initially directed laterally. They attain their definitive form after the heart has migrated downward and the arms have been adducted. This represents a true plesiomorphous character state in therian ontogeny.     

Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach

We present a comprehensive mass spectrometric approach that integrates intact protein molecular mass measurement ("top-down") and proteolytic fragment identification ("bottom-up") to characterize the 70S ribosome from Rhodopseudomonas palustris. Forty-two intact protein identifications were obtained by the top-down approach and 53 out of the 54 orthologs to Escherichia coli ribosomal proteins were identified from bottom-up analysis. This integrated approach simplified the assignment of post-translational modifications by increasing the confidence of identifications, distinguishing between isoforms, and identifying the amino acid positions at which particular post-translational modifications occurred. Our combined mass spectrometry data also allowed us to check and validate the gene annotations for three ribosomal proteins predicted to possess extended C-termini. In particular, we identified a highly repetitive C-terminal "alanine tail" on L25. This type of low complexity sequence, common to eukaryotic proteins, has previously not been reported in prokaryotic proteins. To our knowledge, this is the most comprehensive protein complex analysis to date that integrates two MS techniques.     

The ontogenesis of the manubrium sterni in Tupaia belangeri

The morphogenesis of the manubrium sterni was studied in a series of dated embryos of Tupaia belangeri. In addition to the sternal bands, the "paired suprasternal Anlage" takes part in the shaping of the manubrium sterni as reported by Klima (1968) for other mammals. It forms skeletal elements that mediate between the clavicle and the manubrium: the sternocalvicular ligament and the paired prominence on the dorsal surface of the manubrium, which underlies the clavicles. The paired prominence corresponds to the praeclavium present in some therians. Very probably, the discus articularis of the sternoclavicular articulation of some primates can be attributed to the suprasternal Anlage. There was, however, no indication that the ossa suprasternalia of primates develop from the suprasternal Anlagen: In Tupaia these Anlagen do not form the cranial part of the manubrium. Klima's "unpaired Anlage" develops differently in Tupaia than in other therians. It consists of connective tissue and is not integrated into the manubrium. It presents an insertion surface for the M. pectoralis major, which shifts its origin onto the manubrium, after the sternal bands have fused. The homology of the "unpaired Anlage" and the "pars chondralis interclaviculae" is doubtful.     

Pathogenesis of Hepatitis C Virus Infection in Tupaia belangeri

The lack of a small-animal model has hampered the analysis of hepatitis C virus (HCV) pathogenesis. The tupaia (Tupaia belangeri), a tree shrew, has shown susceptibility to HCV infection and has been considered a possible candidate for a small experimental model of HCV infection. However, a longitudinal analysis of HCV-infected tupaias has yet to be described. Here, we provide an analysis of HCV pathogenesis during the course of infection in tupaias over a 3-year period. The animals were inoculated with hepatitis C patient serum HCR6 or viral particles reconstituted from full-length cDNA. In either case, inoculation caused mild hepatitis and intermittent viremia during the acute phase of infection. Histological analysis of infected livers revealed that HCV caused chronic hepatitis that worsened in a time-dependent manner. Liver steatosis, cirrhotic nodules, and accompanying tumorigenesis were also detected. To examine whether infectious virus particles were produced in tupaia livers, naive animals were inoculated with sera from HCV-infected tupaias, which had been confirmed positive for HCV RNA. As a result, the recipient animals also displayed mild hepatitis and intermittent viremia. Quasispecies were also observed in the NS5A region, signaling phylogenic lineage from the original inoculating sequence. Taken together, these data suggest that the tupaia is a practical animal model for experimental studies of HCV infection.Hepatitis C virus (HCV) is a small enveloped virus that causes chronic hepatitis worldwide (32). HCV belongs to the genus Hepacivirus of the family Flaviviridae. Its genome comprises 9.6 kb of single-stranded RNA of positive polarity flanked by highly conserved untranslated regions at both the 5′ and 3′ ends (4, 27, 29). The 5′ untranslated region harbors an internal ribosomal entry site (29) that initiates translation of a single open reading frame encoding a large polyprotein comprising about 3,010 amino acids (35). The encoded polyprotein is co- and posttranslationally processed into 10 individual viral proteins (15).In most cases of human infection, HCV is highly potent and establishes lifelong persistent infection, which progressively leads to chronic hepatitis, liver steatosis, cirrhosis, and hepatocellular carcinoma (9, 16, 21). The most effective therapy for treatment of HCV infection is administration of pegylated interferon combined with ribavirin. However, the combination therapy is an arduous regimen for patients; furthermore, HCV genotype 1b does not respond efficiently (19). The prevailing scientific opinion is that a more viable option than interferon treatment is needed.The chimpanzee is the only validated animal model for in vivo studies of HCV infection, and it is capable of reproducing most aspects of human infection (5, 18, 23, 28, 35, 36). The chimpanzee is also the only validated animal for testing the authenticity and infectivity of cloned viral sequences (8, 14, 35, 36). However, chimpanzees are relatively rare and expensive experimental subjects. Cross-species transmission from infected chimpanzees to other nonhuman primates has been tested but has proven unsuccessful for all species evaluated (1).The tupaia (Tupaia belangeri), a tree shrew, is a small nonprimate mammal indigenous to certain areas of Southeast Asia (6). It is susceptible to infection with a wide range of human-pathogenic viruses, including hepatitis B viruses (13, 20, 31), and appears to be permissive for HCV infection (33, 34). In an initial report, approximately one-third of inoculated animals exhibited acute, transient infection, although none developed the high-titer sustained viremia characteristic of infection in humans and chimpanzees (33). The short duration of follow-up precluded any observation of liver pathology. In addition to the putative in vivo model, cultured primary hepatocytes from tupaias can be infected with HCV, leading to de novo synthesis of HCV RNA (37). These reports strongly support tupaias as a valid model for experimental studies of HCV infection. However, longitudinal analyses evaluating the clinical development and pathology of HCV-infected tupaias have yet to be examined. In the present study, we describe the clinical development and pathology of HCV-infected tupaias over an approximately 3-year time course.     

阿尔茨海默病树鼩模型建立的探索

目的探索建立树鼩阿尔茨海默病(AD)动物模型的可行性。方法将30只成年雄性树鼩Tupaia belangeri随机分成3组,模型组腹腔注射D-半乳糖(D-gal)造成急性衰老后,对树鼩双侧海马内一次性注射β淀粉样蛋白1~42片段(Aβ1~42)和鹅膏蕈氨酸(IBO)的混合液,对照(生理盐水)组将所有药物替换为等剂量生理盐水,空白组不做处理。用Morris水迷宫对3组树鼩进行行为学测试,用苏木精-伊红染色法和镀银染色法进行病理检测分析。结果 Morris水迷宫测试结果提示,模型树鼩出现了明显的学习记忆功能障碍。病理检测结果显示,模型组脑海马区出现明显胶质细胞增生和神经纤维缠结。对照组和空白组无明显病理改变。结论腹腔注射D-gal,双侧海马注射Aβ1~42和IBO混合液的方法可以造成树鼩学习记忆能力下降,并出现神经胶质细胞增生和神经纤维缠结,是一种可行的树鼩AD模型造模方法。     

Rhombomere-specific patterns of apoptosis in the tree shrew Tupaia belangeri

Whether rhombomere-specific patterns of apoptosis exist in the developing hindbrain of vertebrates is under debate. We have investigated the sequence of apoptotic events in three-dimensionally reconstructed hindbrains of Tupaia belangeri (8- to 19-somite embryos). Apoptotic cells were identified by structural criteria and by applying an in situ tailing technique to visualize DNA fragmentation. Seven rhombomeres originated from three pro-rhombomeres. Among pre-migratory neural crest cells in the dorsal thirds of the neural folds, the earliest apoptotic concentrations appeared in the developing third rhombomere (r3). Dorsal apoptotic maxima then persisted in r3, extended from r3 to r2, and also arose in r5. Transverse apoptotic bands increased the total amount of apoptotic cells in odd-numbered rhombomeres first in r3 and, with a delay, also in r5. This sequence of apoptotic events was paralleled by an approximate rostrocaudal sequence of neural crest cell delamination from the even-numbered rhombomeres. Thus, large-scale apoptosis in r3 and r5 helped to establish crest-free zones that segregated streams of migrating neural crest cells adjacent to r2, r4, and r6. The sequence of apoptotic events observed in the dorsal thirds of rhombomeres matches that reported for the chick embryo. Other shared features are apoptotic peaks in the position of a circumscribed ventricular protrusion of fusing parts of the neural folds in r1 and r2, and Y-shaped apoptotic patterns composed of apoptotic maxima in the dorsal and lateral thirds of r1, r2, and r3. These rhombomere-specific patterns of apoptosis may therefore represent a conserved character, at least in amniotes.This work was supported by the Deutsche Forschungsgemeinschaft (KN 525/1–1, KN 525/1–2, BR 1185/4–1, and former Sonderforschungsbereich 89: Cardiology)     

中缅树鼩自然感染六种病毒的血清流行病学

中缅树鼩作为一种新型实验动物,在医学生物学上,尤其是病毒学方面的应用受到越来越多的重视.实验动物自身病毒感染会影响动物健康和干扰实验结果,甚至危害实验人员生命安全.所以,实验动物病毒检测一直是动物质量控制的重要部分.中缅树鼩研究迄今缺乏清晰的病毒自然感染资料.为调查中缅树鼩的病毒感染状况,采集野生俘获和人工繁殖的中缅树鼩血清样本272份,全部血清样本通过ELISA方法对乙型肝炎病毒(HBV)表面抗原,丙型肝炎病毒(HCV)总抗体,以及戊型肝炎病毒(HEV)、腺病毒(ADV)、单纯疱疹病毒1型(HSV-1)和2型(HSV-2)的IgG抗体进行了检测.结果表明,ELISA初筛HBV表面抗原有3份阳性样本,但通过乙型肝炎两对半定量检测进一步确认为阴性:抗HCV抗体和抗HEV、ADV、HSV-1 IgO抗体检测均为阴性;抗HSV-2 IgG检测有1份阳性样本.提示仪抗原或抗体血清学指标检测树鼩肝炎结果并不能反应个体携带病毒的状态,应该再进行病毒学指标确认.同时建议中缅树嗣繁殖群应进行HSV-2的筛选,以便杜绝和控制该病毒的感染.     

Disk formation in retinal cones of Tupaia belangeri (Scandentia)

Existing hypotheses on the mode of disk formation in the photoreceptor cells of mammals appear to be incompatible: (1) plasma membranes of adjacent evaginations form a disk which, subsequently, is internalized by a disk rim; (2) pinocytotic vesicles are pinched off from the plasma membrane and fuse into a larger vesicle, which flattens and forms a disk. We have studied the development of the cone outer segment and the disk formation in Tupaia belangeri by transmission electron microscopy. During the first two postnatal weeks, the distal part of the single cilium, which is inserted apically on the inner segment, becomes balloon-shaped. Apical to the axoneme, it contains tubular and vesicular material, which, most probably, has been detached from the axonemal microtubules. These tubules and vesicles do not contribute to disks. The balloon-shaped expansion, later retained as the ciliary backbone, establishes the contact with the pigment epithelium. Formation of disks, from the 12-day-old Tupaia onwards, occurs between adjacent evaginations at the outer segment base. The initial disk rims are “hooked” to the ciliary axonemal microtubules. The axonemal microtubules are involved in the initiation and in the alignment of the disks. Disk rim formation and, thus, internalization of disks proceeds from the base to the apex of the outer segment, that is, from the younger to the older disks. In the adult Tupaia, an uneven progression of disk rim formation on both sides of the axoneme is found among consecutive disks. The seemingly incompatible hypotheses on the mode of disk formation reflect a heterochrony of the internalization of membranes and of the disk formation among different mammals and, possibly, between cones and rods. Received: 24 July 1997 / Accepted: 10 September 1997     

Mass spectrometric elucidation of the neuropeptidome of a crustacean neuroendocrine organ

Elucidating how neuropeptides affect physiology may result in delineating peptidergic mechanisms and identifying antagonists for application in basic and translational science. Human neuropeptide Y (NPY) regulates cardiac activity; frequently invertebrates contain orthologs of vertebrate peptides. We report invertebrate NPY-like neuropeptide F (NPF) arrested the signal frequency of the slow phase of the cardiac cycle (EC50 = 1 pM); however, signal frequency of the fast phase was affected only minimally. Neuropeptide F decreased the duration of the slow phase by ~70% (EC50 = 0.6 pM), but increased the duration of the fast phase by ~57% (EC50 = 10nM). Short NPF-1 (sNPF-1) decreased the signal frequency of the slow phase by ~70% (EC50 = 9 nM); yet, signal frequency of the fast phase was unaffected. Short NPF-1 decreased the duration of the slow phase ~55% (EC50 ~50 nM), but increased the duration of the fast phase ~20% without dose dependency. Neuropeptide F and sNPF-1 increased isoelectric period duration. This novel report demonstrated NPY-like peptides are cardioactive but functionally unique. These data contribute to understanding how invertebrate orthologs affect cardiovascular activity. Dipteran fast and slow phases may be generated from separate pacemakers in the abdominal heart and in the anterior thoracocephalic aorta, respectively. Thus, our research suggests NPF and sNPF-1 act through different mechanisms to regulate cardiac activity. Invertebrate NPY-like peptides act in olfaction and feeding yet mechanisms which are associated with their cardioactive effects remain unknown; our work may provide evidence linking their roles in sensory response and cardiac activity.     

Body temperature rhythm of the tree shrew, Tupaia belangeri.

The circadian rhythm of body temperature of the tree shrew Tupaia belangeri was studied by telemetry. The amplitude of the daily (or circadian) variation was found to be much larger than that of most endotherms (amplitude approximately 5 degrees C) and the bimodal shape of the rhythm differed from the cosine waveform that characterizes the temperature rhythms of most other species. In free-running conditions, as well as in the entrained state, the temperature rhythm remained synchronized to the rhythm of locomotor activity.     

Direct mass spectrometric characterization of disulfide linkages

Disulfide linkage is critical to protein folding and structural stability. The location of disulfide linkages for antibodies is routinely discovered by comparing the chromatograms of the reduced and non-reduced peptide mapping with location identification confirmed by collision-induced dissociation (CID) mass spectrometry (MS)/MS. However, CID product spectra of disulfide-linked peptides can be difficult to interpret, and provide limited information on the backbone region within the disulfide loop. Here, we applied an electron-transfer dissociation (ETD)/CID combined fragmentation method that identifies the disulfide linkage without intensive LC comparison, and yet maps the disulfide location accurately. The native protein samples were digested using trypsin for proteolysis. The method uses RapiGest SF Surfactant and obviates the need for reduction/alkylation and extensive sample manipulation. An aliquot of the digest was loaded onto a C₄ analytical column. Peptides were gradient-eluted and analyzed using a Thermo Scientific LTQ Orbitrap Elite mass spectrometer for the ETD-triggered CID MS³ Wypych J, Li M, Guo A, Zhang Z, Martinez T, Allen MJ, Fodor S, Kelner DN, Flynn GC, Liu YD, et al. Human IgG2 antibodies display disulfide-mediated structural isoforms. J Biol Chem. 2008;283:16194–205. doi:10.1074/jbc.M709987200. PMID:18339624[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] experiment. Survey MS scans were followed by data-dependent scans consisting of ETD MS² scans on the most intense ion in the survey scan, followed by 5 MS³ CID scans on the 5 most intense ions in the ETD MS² scan. We were able to identify the disulfide-mediated structural variants A and A/B forms and their corresponding disulfide linkages in an immunoglobulin G2 monoclonal antibody with λ light chain (IgG2λ), where the location of cysteine linkages were unambiguously determined.     

中缅树鼩微卫星分子标记的筛选

目的 筛选中缅树鼩微卫星分子标记,逐步填补中缅树鼩特异性遗传标记的空白.方法 建立中缅树鼩基因小片段插入文库,利用5’端地高辛标记的(CA)15探针从约1500个菌落中选出36个阳性克隆.对这些克隆进行测序,发现其中15个含有重复序列,其中1个为重复克隆,1个因两端序列太短而不能设计引物.结果 用Primer3软件设计...     

Cryopreservation of epididymal sperm in tree shrews (Tupaia belangeri)

Cryopreservation of sperm from tree shrews, which are considered primitive primates, would enhance genetic management and breeding programs. Epididymal sperm were surgically harvested from male tree shrews, cryopreserved in two Tes-Tris-based cryodiluents, and used in four experiments. In Experiment 1, there were no significant differences in motility and acrosome integrity among five concentrations of egg yolk in TTE after cooling to 4 °C. However, sperm frozen in TTE containing 20% egg yolk at −172 °C/min had better (P < 0.05) post-thaw motility and acrosome integrity. In Experiment 2, sperm held for 10 min prior to storage in liquid nitrogen had greater motility than those held for 5 or 15 min (P < 0.05), but acrosome integrity was not different (P > 0.05) among treatments. In Experiment 3, sperm frozen in TTE diluent had higher (P < 0.05) motility and acrosome integrity than those in TEST diluent. In Experiment 4, there were no differences (P > 0.05) in the fertilization rate of oocytes and the proportion of tree shrews yielding fertilized oocytes, following AI with fresh versus frozen sperm. In conclusion, tree shrew epididymal sperm were successfully cryopreserved, as assessed by post-thaw motility, acrosome integrity, and fertilizing ability.