Density functional studies on the electron affinities of DNA and RNA bases

Influence of basis sets on electron affinities (EAs) of DNA and RNA bases has been investigated using density functional method (B3LYP functional) with different basis sets (6-31G, TZVP and 6-311+ + G**). Effect of some PBE functionals namely, PBEOP, PBELYP and PBEVWN, on EA values of the nucleobases was studied using basis set which predicted the most reliable values with B3LYP functional. Observation of the trends in the values of EA and dipole moment of the molecules enable us to identify the features of a basis set that shows the presence of dipole-bound state of some of the nucleobases. The vertical electron affinities with B3LYP and PBEOP functionals are close to the experimental values. The adiabatic electron affinities of uracil and thymine were found to be positive for basis set with diffuse functions using B3LYP functional. Adenine does not have a stable covalently bound anion at all levels of basis sets and functionals. The sign of adiabatic electron affinity value of cytosine is inconsistent with that of experimental value but in agreement with previous theoretical results. For guanine the adiabatic electron affinity value with 6-311+ + G** basis set was found to be very high as comparison with other two basis sets confirming the formation of mixed covalent-dipole character.     

Stratigraphical distribution of the Ordovician graptolite Azygograptus Nicholson & Lapworth in the Central Andean Basin (northwestern Argentina and southern Bolivia)

We analyzed new occurrences of Azygograptus lapworthi from the Cordillera Oriental, Argentina. The bearer sandstones levels, corresponding to the Acoite Formation, are overlying the deposits, in which the Didymograptellus bifidus Biozone (Lower Ordovician, upper Floian, Fl3) was previously recognized, and are overlain by younger pelitic levels yielding Xiphograptus lofuensis (Middle Ordovician, early Dapingian, Dp2). Previous records from the Central Andean Basin are also reviewed in detail and accurately correlated, allowing us to conclude that the Azygograptus lapworthi Biozone corresponds to the Middle Ordovician (lower Dapingian, Dp1). This biostratigraphic framework documents that the transition between the Lower and Middle Ordovician deposits occurs in the uppermost levels of the Acoite Formation in the Argentine Cordillera Oriental. It is additionally integrated with up to date conodont records to establish a high-resolution regional correlation, with equivalent deposits from the Puna of northwestern Argentina and Cordillera Oriental of Bolivia, and to discuss new insights for global correlation.     

A bubaline-derived satellite DNA probe uncovers generic affinities of gaur with other bovids

DNA typing using genome derived cloned probes may be conducted for ascertaining genetic affinities of closely related species. We analysed gaurBos gaurus, cattleBos indicus, buffaloBubalus bubalis, sheepOvis aries and goatCapra hircus DNA using buffalo derived cloned probe pDS5 carrying an array ofBamHI satellite fraction of 1378 base residues to uncover its genomic organization. Zoo-blot analysis showed that pDS5 does not cross hybridize with non-bovid animals and surprisingly with female gaur genomic DNA. The presence of pDS5 sequences in the gaur males suggests their possible location on the Y chromosome. Genotyping of pDS5 withBamHI enzyme detected mostly monomorphic bands in the bubaline samples and polymorphic ones in cattle and gaur giving rise to clad specific pattern. Similar typing withRsaI enzyme also revealed clad specific band pattern detecting more number of bands in buffalo and fewer in sheep, goat and gaur samples. Copy number variation was found to be prominent in cattle and gaur withRsaI typing. Our data based on matched band profiles (MBP) suggest that gaur is genetically closer to cattle than buffalo contradicting the age-old notion held by some that gaur is a wild buffalo. The pDS5 clone has a potential for estimating the generic and genetic relationship amongst closely related bovid species.     

Collagen and the myocardium: fibrillar structure,biosynthesis and degradation in relation to hypertrophy and its regression

The extracellular matrix of the myocardium contains an elaborate structural matrix composed mainly of fibrillar types I and III collagen. This matrix is responsible for the support and alignment of myocytes and capillaries. Because of its alignment, location, configuration and tensile strength, relative to cardiac myocytes, the collagen matrix represents a major determinant of myocardial stiffness. Cardiac fibroblasts, not myocytes, contain the mRNA for these fibrillar collagens. In the hypertrophic remodeling of the myocardium that accompanies arterial hypertension, a progressive structural and biochemical remodeling of the matrix follows enhanced collagen gene expression. The resultant significant accumulation of collagen in the interstitium and around intramyocardial coronary arteries, or interstitial and perivascular fibrosis, represents a pathologic remodeling of the myocardium that compromises this normally efficient pump. This report reviews the structural nature, biosynthesis and degradation of collagen in the normal and hypertrophied myocardium. It suggests that interstitial heart disease, or the disproportionate growth of the extracellular matrix relative to myocyte hypertrophy, is an entity that merits greater understanding, particularly the factors regulating types I and III collagen gene expression and their degradation.     

Binding affinities of CRBPI and CRBPII for 9-cis-retinoids

Background

Cellular retinol binding-protein I (CRBPI) and cellular retinol binding-protein II (CRBPII) serve as intracellular retinoid chaperones that bind retinol and retinal with high affinity and facilitate substrate delivery to select enzymes that catalyze retinoic acid (RA) and retinyl ester biosynthesis. Recently, 9-cis-RA has been identified in vivo in the pancreas, where it contributes to regulating glucose-stimulated insulin secretion. In vitro, 9-cis-RA activates RXR (retinoid × receptors), which serve as therapeutic targets for treating cancer and metabolic diseases. Binding affinities and structure–function relationships have been well characterized for CRBPI and CRBPII with all-trans-retinoids, but not for 9-cis-retinoids. This study extended current knowledge by establishing binding affinities for CRBPI and CRBPII with 9-cis-retinoids.

Methods

We have determined apparent dissociation constants, K′_d, through monitoring binding of 9-cis-retinol, 9-cis-retinal, and 9-cis-RA with CRBPI and CRBPII by fluorescence spectroscopy, and analyzing the data with non-linear regression. We compared these data to the data we obtained for all-trans- and 13-cis-retinoids under identical conditions.

Results

CRBPI and CRBPII, respectively, bind 9-cis-retinol (K′_d, 11 nM and 68 nM) and 9-cis-retinal (K′_d, 8 nM and 5 nM) with high affinity. No significant 9-cis-RA binding was observed with CRBPI or CRBPII.

Conclusions

CRBPI and CRBPII bind 9-cis-retinol and 9-cis-retinal with high affinities, albeit with affinities somewhat lower than for all-trans-retinol and all-trans-retinal.

General significance

These data provide further insight into structure–binding relationships of cellular retinol binding-proteins and are consistent with a model of 9-cis-RA biosynthesis that involves chaperoned delivery of 9-cis-retinoids to enzymes that recognize retinoid binding-proteins.     

Collagen type I fibril packing in vivo and in vitro

Reviewed are works concerning the mechanisms of collagen (type I) fibril packing and the influence of macromolecular structure and physicochemical parameters of the medium on the process.     

胶原蛋白水解物在化妆品中的功能特性

研究了胶原蛋白经酶水解后所得产物的功能特性:吸水性、保水性、溶解性都得到提高;吸油性、起泡性和泡沫稳定性均明显下降。可根据不同分子量范围的胶原水解物的功能特性满足不同化妆品的不同需求。     

Collagen XI chain misassembly in cartilage of the chondrodysplasia (cho) mouse

Molecular mechanisms controlling the assembly of cartilage-specific types II, IX and XI collagens into a heteropolymeric network of uniformly thin, unbanded fibrils are not well understood, but collagen XI has been implicated. The present study on cartilage from the homozygous chondrodysplasia (cho/cho) mouse adds support to this concept. In the absence of alpha1(XI) collagen chains, thick, banded collagen fibrils are formed in the extracellular matrix of cho/cho cartilage. A functional knock-out of the type XI collagen molecule has been assumed. We have re-examined this at the protein level to see if, rather than a complete knock-out, alternative type XI chain assemblies were formed. Mass spectrometry of purified triple-helical collagen from the rib cartilage of cho/cho mice identified alpha1(V) and alpha2(XI) chains. These chains were recovered in roughly equal amounts based on Coomassie Blue staining of SDS-PAGE gels, in addition to alpha1(II)/alpha3(XI) collagen chains. Using telopeptide-specific antibodies and Western blot analysis, it was further shown that type V/XI trimers were present in the matrix cross-linked to each other and to type II collagen molecules to form heteropolymers. Cartilage from heterozygous (cho/+) mice contained a mix of alpha1(V) and alpha1(XI) chains and a mix of thin and thick fibrils on transmission electron microscopy. In summary, the results imply that native type XI collagen molecules containing an alpha1(XI) chain are required to form uniformly thin fibrils and support a role for type XI collagen as the template for the characteristic type II collagen fibril network of developing cartilage.     

Collagen fibre reorientation around a crack in biaxially stretched aortic media

The distribution and orientation of collagen fibres in unstretched and biaxially stretched pig aortic media have been determined by an X-ray diffraction technique in order to analyse the reorientation of collagen fibres in response to the presence of a notch in biaxially stretched samples. The results show that collagen fibres align themselves following the force trajectories. This results in preferential fibre orientation perpendicular to the advancing crack tip, in agreement with the theoretical predictions of stress concentration effect due to the presence of an elliptical notch in an elastic plate.     

Ⅰ型胶原蛋白的结构、功能及其应用研究的现状与前景

胶原蛋白是动物体中普遍存在的一种大分子蛋白,在哺乳动物中的含量是整个生物体自身总蛋白含量的1/4。胶原蛋白除了具有生物力学方面的作用以外,还具有诸如信号转导、生长因子与细胞因子的运输等功能;此外,在食品、化妆品、医药等行业中,胶原蛋白也具有很广泛的用途。随着对胶原蛋白需求的日益增加,原先从屠宰的动物体的皮革、骨骼中提取胶原的方式已经不能满足日益增长的胶原蛋白的需求,而且还可能有致病之虞,于是新的生产胶原蛋白的方法——利用生物反应器,尤其是乳腺生物反应器来生产胶原蛋白就为人们所瞩目。本文就Ⅰ型胶原蛋白的结构、功能,以及利用生物反应器研究开发Ⅰ型胶原蛋白的现状、前景进行了探讨。     

Collagen fibril morphology in developing chick metatarsal tendoms: 1. X-ray diffraction studies

The low angle equatorial X-ray diffraction ($\text{R ? 30 μ}\text{m}{}^{\mathrm{?1}}$) from hydrated embryonic chick metatarsal tendon contains minima and maxima that are not seen in mature tendons. This diffraction derives from the disordered array of parallel, cylindrical fibrils of collagen of small, uniform diameter that comprise the major part of this tissue. Comparison of the positions of the minima and maxima with those expected from an array of cylinders allows estimation of the mean diameter of the cylinders and the average centre-to-centre nearest neighbour separation. It was found that in the age range from 13 to 19 days fetal, the mean diameter increased from ～ 46 to ～ 58 nm, whereas the mean nearest neighbour separation remained constant at ～ 90 nm. Detailed analysis of the X-ray intensity profile of a 17 day fetal tendon indicated the presence of a paucidisperse distribution of fibril diameters with two or more discrete populations of preferred diameters separated by 10 to 12 nm.     

海蜇胶原蛋白肽的降血脂及抗氧化作用的研究

本研究以海蜇胶原蛋白为原料,经酶解得到海蜇胶原蛋白肽,探讨海蜇胶原蛋白肽对小鼠血脂的影响及抗氧化作用。以高脂饲料喂养ICR小鼠,建立高脂血症模型,研究胶原蛋白肽对小鼠肝系数和脂肪系数的变化情况及小鼠血脂水平、肝组织抗氧化功能的影响。结果表明海蜇胶原蛋白肽能显著降低小鼠肝系数和脂肪系数,能显著降低高脂血症小鼠血清总胆固醇(TC)、低密度脂蛋白胆固醇(LDL-C)、动脉硬化指数(LDL-C/HDL-C)水平,升高高密度脂蛋白胆固醇(HDL-C)和抗动脉粥样硬化因子(HDL-C/TC);能提高肝组织超氧化物歧化酶(SOD)谷胱甘肽过氧化物酶(GSH-Px)的活力,并能减低丙二醛(MDA)的含量。海蜇胶原蛋白肽具有辅助减低血脂水平和增强抗氧化功能的作用。     

牛蛙皮胶原蛋白酸提取条件优化及其对细胞生长和粘附性的影响

应用羟脯氨酸法测定了牛蛙皮胶原蛋白含量,通过正交实验对牛蛙皮胶原蛋白酸法提取条件进行了优化,并结合MTT法测定了胶原蛋白对细胞生长和粘附性的影响。结果显示,牛蛙皮胶原蛋白的含量约为45．1％;温度条件对提取率影响最大,其次依次为酸种、时间和浓度,最优组合为乙酸、1．5mol／L、37℃、24h;在低浓度时,牛蛙皮胶原蛋白对正常人类肝细胞的生长和粘附性无显著影响,当浓度升高到一定值时,对细胞生长和粘附性有显著促进作用。     

Collagen stability and cross-linking in normal and kyphoscoliotic mouse intervertebral discs

Intervertebral discs of the cervical-thoracic region of the spine of BDL mice which are homozygous for the ky gene mutation undergo degeneration. Discs from these mice have a normal collagen content and undergo normal collagen cross linking prior to the appearance of degenerative changes. The major reducible collagen cross-link formed in discs of these mice and in normal CBA strain mice is hydroxylysino-5-ketonorleucine. These results and other previous results indicate that the discs in the ky mouse develop degenerative disease due to an extrinsic factor rather than to an intrinsic abnormality of their extracellular matrix. The extrinsic factor has been identified as spinal muscle atrophy.     

梅花鹿茸胶原酶解物对去势大鼠骨质疏松症防治作用的实验研究(英文)

观察梅花鹿茸胶原酶解物(CSDV)对去势大鼠骨质疏松症防治作用的实验研究。通过对模型组、给药组和假手术组在形态计量学指标,生物力学指标和血清生化指标的评价,考察鹿茸胶原酶解物的作用。结果表明CSDV能够明显提高去势骨质疏松症大鼠骨密度,调节血清碱性磷酸酶水平和骨钙素水平。说明鹿茸胶原酶解物在防治去势大鼠骨质疏松症方面具有明显作用。     

乌贼皮胶原蛋白的提取及结构表征

为了充分利用乌贼加工废弃物,分析了乌贼皮的基本组成成分,优化了从乌贼皮中提取胶原蛋白的工艺条件,并利用SDS-PAGE垂直电泳、紫外扫描和傅里叶变换红外光谱对所提取的胶原蛋白进行了结构表征.结果表明,乌贼皮中含有大量胶原蛋白,可作为胶原蛋白来源的补充.采用酸酶复合提取胶原蛋白的最佳条件为:酒石酸浓度为0.1mol/L,胃蛋白酶添加量为1400U/g,料液比为1:20(m:V,原料),4℃提取18h,提取率为12.08％.SDS-PAGE垂直电泳、紫外扫描和傅里叶变换红外光谱的结果表明,采用酸酶复合法从乌贼皮中提取的胶原蛋白为I型胶原蛋白,保持了完整的三螺旋结构.     

奥尼罗非鱼胶原蛋白及其酸解液美拉德反应产物的研究

以奥尼罗非鱼鱼皮中胶原蛋白为研究对象,采用氨基酸自动分析仪和GC-MS分析了胶原蛋白的游离氨基酸组成、主要风味成分及其酸解液美拉德反应产物的风味成分.结果表明：鱼皮中胶原蛋白的提取率为6.61%,酸解后的游离氨基酸组成与一般胶原蛋白的氨基酸组成一致,其中风味氨基酸占52.57%;美拉德反应产物中含3,3-二甲基正辛烷、2,6,10-三甲基十二烷等20种风味成分.     

Isoenzyme diversity and phylogenetic affinities among thePhaseolus beans (Fabaceae)

Polyacrylamide gel electrophoretic study of 8 isoenzyme systems encoded by 16 putative gene loci in 23 species of American beans of the genusPhaseolus s. str. and in the Asian moth beanVigna aconitifolia revealed in total 98 allozymes, including 34 taxon-specific and unique, 14 rare-unique and 50 shared allozymes. —P. xanthotrichus var.xanthotrichus and var.zimapanensis differed in allozymes of AAT-A, AAT-D and ADH-C.P. xanthotrichus var.zimapanensis andP. hintonii shared same allozymes of AAT-A and AAT-D, but differed in allozymes of ADH-A and ADH-C. It is proposed to recognizeP. xanthotrichus var.zimapanensis in species rank asP. zimapanensis. — P. acutifolius var.acutifolius and var.tenuifolius, except one accession of the latter, differed in allozymes of AAT-D, ADH-C and FDH-A. — Cladistic analysis of the allozymic data as unordered absence-presence characters disclosed in the genus two major monophyletic species clusters: (1)P. polystachyus, P. ritensis, P. maculatus, P. marechalii, P. jaliscanus, P. salicifolius, P. lunatus, P. filiformis, P. angustissimus, P. acutifolius, P. coccineus, P. vulgaris, P. parvulus, P. pauciflorus, andP. pluriflorus; (2)P. grayanus, P. neglectus, P. pedicellatus, P. microcarpus, P. hintonii, andP. zimapanensis. P. xanthotrichus s. str. andP. zimapanensis are discriminated as paraphyletic, supporting their specific delimitation. — Phenetic analysis of the allozyme data with the UPGMA clustering revealed essentially the same pattern of genetic affinities between the species and additionally clarified the extent of allozymic divergence by taking into account species-specific and unique allozymes.