中华刺鳅消化系统形态与组织学研究

应用活体解剖和光镜技术对中华刺鳅消化系统形态与组织学特征进行了研究。结果显示:中华刺鳅属典型的无鳔管、有胃鱼类,消化道较短,约为体长的45%,整体呈“Z”字形。食道很短,后与胃相联,胃呈“V”型,胃分为贲门部、胃底部和幽门部,贲门胃自食道末端到胃的底部都具有丰富的腺组织分布,其长度也是胃部最长的,约占中华刺鳅消化管长度的23%。胃底部的肌肉发达较厚,但仅贲门部有丰富的腺组织。消化道各段在组织结构上差异显著。胃前,消化道肌肉层内环肌与外纵肌厚度之比自前向后逐渐增大,杯状细胞数量自前向后逐渐减少;胃后,肠道肌肉层内环肌与外纵肌厚度之比则逐渐减小,杯状细胞数量逐渐增多。消化腺分为肝脏和胰腺,肝脏与胰脏为独立的两个器官,胰脏分散分布于胃与肠道周围的系膜内,肉眼可见。未发现类似鲤科鱼类弥撒于肝脏或脾脏内的胰腺结构。中华刺鳅以日本沼虾和秀丽白虾为主要摄食对象,性凶猛,为典型的肉食性鱼类。     

香鱼消化道及肝脏的形态结构特征

采用解剖及石蜡切片显微技术观察了香鱼消化道及肝脏的组织学结构。香鱼消化道由口咽腔、食道、胃及肠构成。口咽腔大且狭长,其底壁前部有一对粘膜褶,两颌边缘着生宽扁梳状齿,腭骨及舌骨具齿,犁骨无齿;舌由基舌骨突出部分覆盖粘膜构成,舌粘膜上皮为复层扁平上皮,含有较多的杯状细胞和味蕾。食道、胃及肠均由粘膜层、粘膜下层、肌层及外膜构成。食道粘膜层上皮为复层扁平上皮,杯状细胞发达。胃呈V形,由贲门部、胃体部及幽门部组成,胃壁粘膜上皮为单层柱状上皮,贲门部与胃体部的固有层中有胃腺。肠较短,由前、中、后肠构成,肠壁粘膜上皮为单层柱状上皮,其游离面具微绒毛;上皮细胞间有杯状细胞。幽门盲囊有350～400条,其组织学结构与肠相同。肝脏单叶,外被浆膜;肝细胞形态不规则,肝小叶界限不明显。     

美洲黑石斑鱼消化道的形态结构

采用解剖和光镜技术观察了美洲黑石斑鱼消化道的形态及组织学结构。消化道由口咽腔、食道、胃、肠构成。口咽腔较大,具颌齿、腭齿及犁齿;舌由基舌骨突出部分覆盖粘膜构成。食道、胃及肠均由粘膜层、粘膜下层、肌层及外膜构成。食道粘膜层绒毛分柱状上皮区及扁平上皮区,扁平上皮区表面为杯状细胞层;食道粘膜下层中有食道腺。胃呈V形,由贲门部、胃体部及幽门部组成,胃壁粘膜层上皮为单层柱状上皮,胃腺位于贲门部与胃体部的固有层中。肠细长,呈S型,由前、中、后肠构成,粘膜层向肠腔突起形成肠绒毛,粘膜上皮为单层柱状上皮,上皮游离面有微绒毛密集排列而成的纹状缘,上皮中含有杯状细胞,且杯状细胞的数量从前向后呈递减趋势;肠长/体长约为1.6。胃与小肠相接处有3对指状幽门盲囊,幽门盲囊的组织学结构与肠相同。     

野生与养殖黄鳍鲷消化道形态组织结构

采用常规石蜡组织切片的方法对野生和养殖黄鳍鲷(Sparus latus)消化道的形态组织结构进行了比较观察。结果表明,野生和养殖黄鳍鲷的消化道存在一定差异。(1)形态学研究表明,食道粗而短,胃呈V形,分为贲门部、胃体部和幽门部,胃与肠的连接处有4条幽门盲囊,肠道在体腔内迂回两个回折。野生黄鳍鲷牙齿更为坚硬锋利,体腔中脂肪较少,消化道更为粗短。野生和养殖黄鳍鲷的肠道系数分别为0.71±0.03和0.94±0.12。(2)组织学研究表明,食道黏膜上皮由扁平细胞层和杯状细胞层组成,杯状细胞发达。胃黏膜由单层柱状上皮组成,无杯状细胞,贲门部和胃体部胃腺发达。幽门盲囊组织学特征与肠相似,上皮为柱状上皮,其中的杯状细胞少于肠。肠中,前肠杯状细胞最多,中肠次之,后肠最少。直肠杯状细胞多于肠。野生与养殖黄鳍鲷组织学的区别在于,消化道相同部位养殖鱼的杯状细胞多于野生鱼,野生鱼的肌层厚度大于养殖鱼。黄鳍鲷消化道的形态组织结构与其生活环境和食物是相关的。     

川金丝猴胃的观察

本文对川金丝猴的胃进行了观察。其胃呈Ｓ形,自胃的左端至第一曲长１５ｃｍ,第一曲至第二曲长９ｃｍ,第二曲以下部长７ｃｍ。胃底包括左、右二盲囊,右盲囊可分前、中、后三部。二纵肌带沿胃的大、小弯行,纵肌带间形成两列肠袋样膨大。膨大自胃底向第二曲逐渐变小,第二曲以下为幽门部。胃管由贲门沿小弯伸至第二曲处。贲门周围为无腺区,其余部均有腺体分布。胃小凹明显。此外,对胃的分部、功能、形态成因以及一些结构术语作了     

宽体沙鳅脑组织学研究

为探究鱼类脑结构及其与生态习性的相关性, 采用HE及Nissl染色法对健康性成熟宽体沙鳅脑组织结构进行观察。结果显示: 宽体沙鳅脑由端脑、间脑、中脑、小脑、延脑五部分组成。嗅叶为典型的“鲤型”嗅叶; 大脑视前核呈索状排列, 未见视前核大、小细胞群; 间脑乳头体及副错位核清晰可见, 血管囊及下叶发达; 中脑视盖由5层构成; 小脑发达, 由3层构成; 延脑分化出面叶和发达的迷叶。这表明, 宽体沙鳅视觉稍有退化, 嗅觉、听觉、触觉、味觉及运动中枢发达, 生活中主要依靠嗅觉、听觉、触觉、味觉觅食及逃避敌害。     

银鲳消化道形态与组织学结构特征及其消化酶活性

为了解银鲳(Pampus argenteus)消化道结构特点与其功能及食性的相关性, 采用解剖、石蜡切片、AB-PAS染色及酶活性检测技术对银鲳消化道的形态、组织结构、黏液细胞分布及消化酶活性进行研究。结果显示, 银鲳的消化道由口咽腔(舌)、食道侧囊、食道、胃及肠构成, 胃肠交界处有很多幽门盲囊。食道侧囊呈椭球形, 食道粗短, 胃呈U型, 肠有多个盘曲, 肠指数为2.03。舌上皮内有少量味蕾及较多黏液细胞。食道侧囊、食道、胃及肠均由黏膜层、黏膜下层、肌层及浆膜组成。食道侧囊内皱襞较发达, 被覆复层扁平上皮, 内含较多黏液细胞, 且以Ⅳ型为主, 皱襞顶端及侧面有内含角质刺的次级突起; 黏膜下层及肌层中有固定皱襞的骨质脚根; 侧囊内胃蛋白酶活性较高。食道内皱襞较高, 被覆复层扁平上皮, 内含较多黏液细胞, 且以Ⅳ型为主。胃内皱襞发达, 被覆单层柱状上皮, 未见黏液细胞分布; 胃腺发达, 胃内蛋白酶活性较高。肠道内褶襞多, 高度呈先下降后上升趋势, 黏液细胞密度前、中肠较高, 后肠较低, 且均以Ⅰ型为主; 肠道内胰蛋白酶、脂肪酶、淀粉酶及碱性磷酸酶活性较高。幽门盲囊组织结构与肠相似。银鲳的消化道结构特点、黏液细胞分布及消化酶活性与其功能及偏肉食的杂食性相适应。     

宽体金线蛭消化道的组织学观察

运用解剖学和组织学方法对宽体金线蛭消化道的结构进行了组织学研究。结果表明,宽体金线蛭的嗉囊向两侧伸出11对侧盲囊,第6对侧盲囊狭长并延伸到直肠两侧;咽主要由黏膜层、肌层和外膜构成,外膜几乎不可见;食道、嗉囊、肠和直肠管壁由黏膜层、黏膜下层、肌层和浆膜构成;咽和直肠的上皮具纹状缘。除肠外,其他消化道的上皮细胞均无发达的纤毛,且黏膜上皮皆为单层柱状上皮;除肠和直肠外,腺体及导管较少;直肠的黏膜肌层为内环外纵两层,其他各部均为纵行肌一层;消化道各部黏膜下层较发达;外膜为浆膜,与黏膜下层分界不明显。     

石磺消化系统的组织学观察

对石磺消化系统各部分结构进行组织学观察.石磺的消化系统由消化道和消化腺两部分组成.消化道包括口、食道、贲门胃、幽门胃、中肠和后肠,不具吻;消化腺包括肝胰腺、唾液腺和肛门腺.在光学显微镜下,消化道由粘膜层、粘膜下层、肌层和外膜4层组成;肌层主要为环肌,粘膜层主要为柱状细胞.肝胰腺甚为发达,组织结构显示肝胰腺由很多分支的腺管组成,腺管由腺细胞、分泌细胞等组成.唾液腺和肛门腺发达.     

龟足消化系统形态和组织学特点

应用光学显微镜观察龟足（Capitulum mitella）消化系统的形态和组织结构。龟足的消化系统包括消化腺和消化道。消化腺一对,呈长囊状,含有分泌细胞（B细胞）、吸收细胞（R细胞）、储存细胞（F细胞）和胚细胞（E细胞）4种类型细胞。消化道呈U型,由口、食道、胃、肠、直肠和肛门组成,各部分的结构由内到外可分为黏膜层、黏膜下层、肌层和外膜4层。口器为咀嚼型,包括一片上唇、一对触须、一对大颚以及两对小颚。食道细短,具几丁质层但无基膜,管壁向腔内突起形成明显的纵褶突;食道前段的环肌特别发达,同时独有放射肌。胃略呈球袋状,肠较长;胃和肠的组织结构相似,没有几丁质层,上皮细胞都有发达的微绒毛。直肠细长,外膜分布有16组纵肌;直肠前段的组织结构与胃、肠相似,而直肠后段有几丁质层覆盖,黏膜层、黏膜下层、肌层和外膜渐退化,16组纵肌渐发达。肛门16组更加发达的纵肌挤入上皮细胞下方,在外膜外另出现一层明显的环肌。龟足消化道各部分的组织结构差异明显,反映了它们功能的差异。     

Contact patterns between helices and strands of sheet define protein folding patterns

Comparing and classifying protein folding patterns allows organizing the known structures and enumerating possible protein structural patterns including those not yet observed. We capture the essence of protein folding patterns in a concise tableau representation based on the order and contact patterns of secondary structures: helices and strands of sheet. The tableaux are intelligible to both humans and computers. They provide a database, derived from the Protein Data Bank, mineable in studies of protein architecture. Using this database, we have: (i) determined statistical properties of secondary structure contacts in an unbiased set of protein domains from ASTRAL, (ii) observed that in 98% of cases, the tableau is a faithful representation of the folding pattern as classified in SCOP, (iii) demonstrated that to a large extent the local structure of proteins indicates their complete folding topology, and (iv) studied the use of the representation for fold identification.     

Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers

Conformations of cysteine disulfides were analyzed in X-ray, nuclear magnetic resonance (NMR), and co-crystal structures of peptide toxins retrieved from Protein Data Bank. The parameters side chain torsional angles, disulfide strain energy, interatomic Cα/Cβ distances, and Ramachandran angles were used as probes to derive conformational features of cysteine disulfides. Schmidt, Ho, and Hogg (2006 Schmidt, B., Ho, L., &; Hogg, P. J. (2006). Allosteric disulfide bonds. Biochemistry, 45, 7429–7433.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) Allosteric disulfide bonds. Biochemistry, 45, 7429–7433 scheme was adapted to classify the disulfide conformations of peptide toxins. Anomalies were observed while treating “forward” and “reverse” asymmetric disulfide conformers as same disulfide conformation in peptide toxins. Thus, new scheme was proposed to classify “forward” and “reverse” asymmetric disulfide conformers separately. Total available conformers space for classification of toxins disulfides is 32. Interestingly, all 32 disulfide conformations are observed in peptide toxins. –LHSpiral is predominant disulfide conformation of peptide toxins. Significant variations were observed in population of occurrence of disulfide conformers, disulfide strain energy, and distribution of D_Cα-Cα and D_Cβ-Cβ values between X-ray, NMR, and co-crystal structures of peptide toxins. The observed differences in conformations of disulfides of same peptide toxins between different states were used as platform to demonstrate advantage of differentiating forward and reverse asymmetric disulfide conformers. Newly proposed scheme allows accurate representation of true conformational diversity of disulfides between X-ray and NMR structures of same peptide toxins. Newly proposed scheme also permits to derive additional structural information from nomenclature which was illustrated by comparing conformations of disulfides between unbound and bound form of toxin with channel/receptor. The results will be of interest for growing field of structural venomics and conformational analysis of peptide/protein disulfides.

Communicated by Ramaswamy H. Sarma     

Definition of a New Information-Based Per-Residue Quality Parameter

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.     

The cluster structure of barley amylopectins of different genetic backgrounds

The unit chains of amylopectin are organized into clusters. In this study, the cluster structure was analysed in detail in four different genotypes of barley, of which two possessed the amo1 genetic background. Amylose content of the barley starches differed from 0 to 32.6%. Isolated amylopectin was hydrolysed with α-amylase from Bacillus subtilis into domains, defined as groups of clusters, which were size-fractionated by methanol. The domain fractions were further treated with α-amylase to release single clusters. Amylopectin, domains and clusters were subsequently treated with phosphorylase and β-amylase to produce φ,β-limit dextrins and the detailed internal structures of these different structure levels were investigated. Analysis was performed with gel-permeation and anion-exchange chromatography. Equal amount of A-chains were detected in all barleys, but the distribution of B-chains differed. At least two types of domain structures were identified in all four barley varieties. Large domains were built up by large clusters and small domains by small clusters. In all four barley samples the number of long chains was small suggesting that shorter chains with a degree of polymerization of 25-35 also are involved in the interconnection of clusters. The cluster structure of the amylopectin correlated with the genetic background. The two barley samples with amo1 genetic background possessed a more dense structure. Internal chain lengths in these two barleys were shorter resulting in larger domains built up by larger clusters.     

Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments

The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is possible for many protein sequence segments to exhibit multiple 3D structures referred to as multi-structural segments. To this end, this paper presents statistical analysis of uniqueness of the 3D-structure of all possible protein sequence segments stored in the Protein Data Bank (PDB, Jan. of 2003, release 103) that occur at least twice and whose lengths are greater than 10 amino acids (AAs). We refined the set of segments by choosing only those that are not parts of longer segments, which resulted in 9297 segments called a sponge set. By adding 8197 signature segments, which occur uniquely in the PDB, into the sponge set we have generated a benchmark set. Statistical analysis of the sponge set demonstrates that rotating, missing and disarranging operations described in the text, result in the segments becoming multi-structural. It turns out that missing segments do not exhibit a change of shape in the 3D-structure of a multi-structural segment. We use the root mean square distance for unit vector sequence (URMSD) as an improved measure to describe the characteristics of hinge rotations, missing, and disarranging segments. We estimated the rate of occurrence for rotating and disarranging segments in the sponge set and divided it by the number of sequences in the benchmark set which is found to be less than 0.85%. Since two of the structure changing operations concern negligible number of segment and the third one is found not to have impact on the structure, we conclude that the 3D-structure of proteins is conserved statistically for more than 98% of the segments. At the same time, the remaining 2% of the sequences may pose problems for the sequence alignment based structure prediction methods.*Jishou Ruan research was supported by Liuhui Center for Applied Mathematics, China-Canada exchange program administered by MITACS and NSFC (10271061). ^#Ke Chen and Lukasz A. Kurgan research was partially supported by NSERC Canada. ^†Jack A. Tuszynkski research has been supported by MITACS, NSERC Canada and the Allard Foundation.     

GeneticStudio: a suite of programs for spatial analysis of genetic-marker data

The analysis of genetic marker data is increasingly being conducted in the context of the spatial arrangement of strata (e.g. populations) necessitating a more flexible set of analysis tools. GeneticStudio consists of four interacting programs: (i) Geno a spreadsheet-like interface for the analysis of spatially explicit marker-based genetic variation; (ii) Graph software for the analysis of Population Graph and network topologies, (iii) Manteller, a general purpose for matrix analysis program; and (iv) SNPFinder, a program for identifying single nucleotide polymorphisms. The GeneticStudio suite is available as source code as well as binaries for OSX and Windows and is distributed under the GNU General Public License.     

TASSER-based refinement of NMR structures

The TASSER structure prediction algorithm is employed to investigate whether NMR structures can be moved closer to their corresponding X-ray counterparts by automatic refinement procedures. The benchmark protein dataset includes 61 nonhomologous proteins whose structures have been determined by both NMR and X-ray experiments. Interestingly, by starting from NMR structures, the majority (79%) of TASSER refined models show a structural shift toward their X-ray structures. On average, the TASSER refined models have a root-mean-square-deviation (RMSD) from the X-ray structure of 1.785 A (1.556 A) over the entire chain (aligned region), while the average RMSD between NMR and X-ray structures (RMSD(NMR_X-ray)) is 2.080 A (1.731 A). For all proteins having a RMSD(NMR_X-ray) >2 A, the TASSER refined structures show consistent improvement. However, for the 34 proteins with a RMSD(NMR_X-ray) <2 A, there are only 21 cases (60%) where the TASSER model is closer to the X-ray structure than NMR, which may be due to the inherent resolution of TASSER. We also compare the TASSER models with 12 NMR models in the RECOORD database that have been recalculated recently by Nederveen et al. from original NMR restraints using the newest molecular dynamics tools. In 8 of 12 cases, TASSER models show a smaller RMSD to X-ray structures; in 3 of 12 cases, where RMSD(NMR_X-ray) <1 A, RECOORD does better than TASSER. These results suggest that TASSER can be a useful tool to improve the quality of NMR structures.     

X-ray structure of Glu 53 human lysozyme.

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.