Development and cytodifferentiation of the rabbit pars intermedia

The developing pars intermedia (PI) of rabbits of between 14 days post coitum (PC) and one day post partum (PP) have been studied by light and electron microscopy. Cell division is marked until 4th week PC, after which it is reduced. The (PI) loses its homogeneity by the 5th week PC due to localisation both intrinsic and invading cells and blood vessels. Four groups of parenchyma cells are recognisable: PI-glandular cells, interstitial cells, ACT-type cells and a heterogeneous group of dark cells. The ultrastructure of the ACT-type cells in the rabbit PI are here described for the first time. The differentiation of these cell types has been traced from 14 days PC to 32 days PC, in particular ACT-type cells are shown to develop in situ and the significance of this is discussed. In the PI-glandular cells dense cored granules appear first on the 15th day PC which is one day before any nerve connection is made with the primitive neural lobe and more than a week before vascularisation. Thereafter granularity increases until parturition when there is a phase of degranulation. Relatively electron lucent, larger vesicles are not found until 4th week PC.     

Conformational studies on nucleotide-amino acid interactions leading to origin of life

Living processes may be defined as the self-sustained chemical reactions based on the special chemical machinery of nucleic acid-directed protein synthesis. Its genesis may be traced to the molecular interaction between nucleotides and amino acids leading to a primitive adaptor-mediated ordered synthesis of polypeptides. A primitive decoding system is described and its characteristics are shown to imitate, in a primitive manner, the present-day elaborate machinery of protein synthesis. This molecular interaction theory may be rightly considered as the missing link between the Protochemical and biological Evolution. The origin of chiral specificity observed in living organisms is also traced to this specific molecular interaction in the protobiological milieu.     

Personal computer-based visualization of molecular models by available ray-tracing software

Developed primarily for the graphic arts, ray-tracing algorithms offer a high level of flexibility with reference to photorealistic and surrealistic image rendering. The utility of these programs is further enhanced by portability (i.e., compatibility with a number of operating systems), accessibility through various sources, and low cost. This report documents, through the use of existing software, the application of these ray-tracing attributes to molecular graphics on a desktop computer. This application is especially pertinent in view of rapid speed enhancements in personal computers (PCs), which have enabled molecular modeling and dynamics on these systems. In this regard, ray tracing on a PC provides enhanced capabilities for molecular graphics rendering that are potentially equivalent to those achieved by workstations.     

BLMT

Statistical analysis of amino acid and nucleotide sequences, especially sequence alignment, is one of the most commonly performed tasks in modern molecular biology. However, for many tasks in bioinformatics, the requirement for the features in an alignment to be consecutive is restrictive and "n-grams" (aka k-tuples) have been used as features instead. N-grams are usually short nucleotide or amino acid sequences of length n, but the unit for a gram may be chosen arbitrarily. The n-gram concept is borrowed from language technologies where n-grams of words form the fundamental units in statistical language models. Despite the demonstrated utility of n-gram statistics for the biology domain, there is currently no publicly accessible generic tool for the efficient calculation of such statistics. Most sequence analysis tools will disregard matches because of the lack of statistical significance in finding short sequences. This article presents the integrated Biological Language Modeling Toolkit (BLMT) that allows efficient calculation of n-gram statistics for arbitrary sequence datasets. AVAILABILITY: BLMT can be downloaded from http://www.cs.cmu.edu/~blmt/source and installed for standalone use on any Unix platform or Unix shell emulation such as Cygwin on the Windows platform. Specific tools and usage details are described in a "readme" file. The n-gram computations carried out by the BLMT are part of a broader set of tools borrowed from language technologies and modified for statistical analysis of biological sequences; these are available at http://flan.blm.cs.cmu.edu/.     

Paleo-parasitology and the antiquity of human host-parasite relationships

Paleo-parasitology may be developed as a new tool to parasite evolution studies. DNA sequences dated thousand years ago, recovered from archaeological material, means the possibility to study parasite-host relationship coevolution through time. Together with tracing parasite-host dispersion throughout the continents, paleo-parasitology points to the interesting field of evolution at the molecular level. In this paper a brief history of paleo-parasitology is traced, pointing to the new perspectives opened by the recent techniques introduced.     

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells

Macromolecular crowding dramatically affects cellular processes such as protein folding and assembly, regulation of metabolic pathways, and condensation of DNA. Despite increased attention, we still lack a definition for how crowded a heterogeneous environment is at the molecular scale and how this manifests in basic physical phenomena like diffusion. Here, we show by means of fluorescence correlation spectroscopy and computer simulations that crowding manifests itself through the emergence of anomalous subdiffusion of cytoplasmic macromolecules. In other words, the mean square displacement of a protein will grow less than linear in time and the degree of this anomality depends on the size and conformation of the traced particle and on the total protein concentration of the solution. We therefore propose that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale.     

Structural characterization of proteoglycans produced by testicular peritubular cells and Sertoli cells

The structural characteristics of proteoglycans produced by seminiferous peritubular cells and by Sertoli cells are defined. Peritubular cells secrete two proteoglycans designated PC I and PC II. PC I is a high molecular mass protein containing chondroitin glycosaminoglycan (GAG) chains (maximum 70 kDa). PC II has a protein core of 45 kDa and also contains chondroitin GAG chains (maximum 70 kDa). Preliminary results imply that PC II may be a degraded or processed form of PC I. A cellular proteoglycan associated with the peritubular cells is described which has properties similar to those of PC I. Sertoli cells secrete two different proteoglycans, designated SC I and SC II. SC I is a large protein containing both chondroitin (maximum 62 kDa) and heparin (maximum 15 kDa) GAG chains. Results obtained suggest that this novel proteoglycan contains both chondroitin and heparin GAG chains bound to the same core protein. SC II has a 50-kDa protein core and contains chondroitin (maximum 25 kDa) GAG chains. A proteoglycan obtained from extracts of Sertoli cells is described which contains heparin (maximum 48 kDa) GAG chains. In addition, Sertoli cells secrete a sulfoprotein, SC III, which is not a proteoglycan. SC III has properties similar to those of a major Sertoli cell-secreted protein previously defined as a dimeric acidic glycoprotein. The stimulation by follicle-stimulating hormone of the incorporation of [35S]SO2(-4) into moieties secreted by Sertoli cells is shown to represent an increased production or sulfation of SC III (i.e. dimeric acidic glycoprotein), and not an increased production or sulfation of proteoglycans. Results are discussed in relation to the possible functions of proteoglycans in the seminiferous tubule.     

从一种富含藻胆蛋白的螺旋藻中大量提取和纯化藻蓝蛋白的研究

采用新鲜藻丝为原料和分段梯度盐析分离纯化钝顶螺旋藻Sp(NS)-90020的藻蓝蛋白（PC）,经羟基磷灰石一次层析,能使提取的PC的纯度大于普遍认可的标准,由于该工艺流程较为简单,适合藻蓝蛋白的大量生产,藻胆蛋白经Sephadex凝胶过滤后的可达电泳纯度标准,经SDS-PAE测得PC,APC的分子量分别约为38.33kD。     

Phase separation dynamics and lateral organization of two-component lipid membranes.

The non-equilibrium dynamic ordering process of coexisting phases has been studied for two-component lipid bilayers composed of saturated di-acyl phospholipids with different acyl chain lengths, such as DC14PC-DC18PC and DC12PC-DC18PC. By means of a microscopic interaction model and computer-simulation techniques the non-equilibrium properties of these two mixtures have been determined with particular attention paid to the effects of the non-equilibrium ordering process on membrane heterogeneity in terms of local and global lateral membrane organization. The results reveal that a sudden temperature change that takes the lipid mixture from the fluid one-phase region into the gel-fluid phase-coexistence region leads to the formation of a large number of small lipid domains which slowly are growing in time. The growth of the lipid domains, which is limited by long-range diffusion of the lipid molecules within the two-dimensional membrane plane, gives rise to the existence of a highly heterogeneous percolative-like structure with a network of interfacial regions that have properties different from those of the phase-separated gel and fluid bulk phases. The results, which are discussed in relation to recent experimental observations interpreted in terms of a percolative-like membrane structure within the two phase region (Almeida, P.F.F., Vaz, W.L.C., and T.E. Thompson. 1992. Biochemistry 31:7198-7210), suggest that non-equilibrium effects may influence lipid domain formation and membrane organization on various length and time scales. Such effects might be of importance in relation to membrane processes that require molecular mobility of the membrane components in restricted geometrical environments of the compartmentalized lipid membrane.     

Lipid molecular shape affects erythrocyte morphology: a study involving replacement of native phosphatidylcholine with different species followed by treatment of cells with sphingomyelinase C or phospholipase A2

In a previous report it was shown that the replacement of native erythrocyte phosphatidylcholine (PC) with different PC species which have defined acyl chain compositions can lead to morphological changes (Kuypers, F.A., W. Berendsen, B. Roelofsen, J. A. F. Op den Kamp, and L.L.M. van Deenen, 1984, J. Cell Biol., 99:2260-2267). It was proposed that differences in molecular shape between the introduced PC species and normal erythrocyte PC caused the membrane to bend outwards or inwards, depending on the shape of the PC exchanged. To support this proposal, two requirements would have to be fulfilled: the exchange reaction would take place only with the outer lipid monolayer of the erythrocyte, and the extent of lipid transbilayer movement would be restricted. If this theory is correct, any treatment causing unilateral changes in lipid molecular shape should lead to predictable morphological changes. Since this hypothesis is a refinement of the coupled bilayer hypothesis, but so far lacks experimental support, we have sought other means to change lipid molecular shape unilaterally. Shape changes of human erythrocytes were induced by the replacement of native PC by various PC species using a phosphatidylcholine-specific transfer protein: by hydrolysis of phospholipids in intact cells using sphingomyelinase C or phospholipase A2, and by the combination of both procedures. The morphological changes were predictable; additive when both treatments were applied, and explicable on the basis of the geometry of the lipid molecules involved. The results strongly support the notion that lipid molecular shape affects erythrocyte morphology.     

Current status of molecular markers for early detection of sporadic pancreatic cancer

Pancreatic cancer (PC) is a highly lethal malignancy with near 100% mortality. This is in part due to the fact that most patients present with metastatic or locally advanced disease at the time of diagnosis. Significantly, in nearly 95% of PC patients there is neither an associated family history of PC nor of diseases known to be associated with an increased risk of PC. These groups of patients who comprise the bulk of PC cases are termed as "sporadic PC" in contrast to the familial PC cases that comprise only about 5% of all PCs. Given the insidious onset of the malignancy and its extreme resistance to chemo and radiotherapy, an abundance of research in recent years has focused on identifying biomarkers for the early detection of PC, specifically aiming at the sporadic PC cohort. However, while several studies have established that asymptomatic individuals with a positive family history of PC and those with certain heritable syndromes are candidates for PC screening, the role of screening in identifying sporadic PC is still an unsettled question. The present review attempts to assess this critical question by investigating the recent advances made in molecular markers with potential use in the early diagnosis of sporadic PC - the largest cohort of PC cases worldwide. It also outlines a novel yet simple risk factor based stratification system that could be potentially employed by clinicians to identify those individuals who are at an elevated risk for the development of sporadic PC and therefore candidates for screening.     

Postconflict behaviour of wild Indian langur monkeys: avoidance of opponents but rarely affinity

Friendly postconflict (PC) interactions between former opponents have been described for a large number of primate species held in captivity. We investigated conflict management behaviour for wild Hanuman langurs, Semnopithecus (Presbytis) entellus entellus, in India, using a large sample of over 6000 agonistic and affinitive interactions recorded in one one-male/multifemale troop and three all-male bands. We compared dyadic PC affinity with the dyadic baseline affinity during the overall observation time to minimize biases of traditional matched-control samples. PC affinity was recorded during only 15% of all dyads (immature male-immature male 0%, adult male-adult male 0%, adult male-immature male 5%, adult male-adult female 0%, adult female-adult female 42%). PC affinity is probably absent amongst males because their dominance relationships are strongly asymmetrical, leaving little room for emotional insecurity. Dyads among females, on the other hand, reflect frequent rank changes and close kinship which probably corresponds to higher levels of emotional uncertainty and greater need for PC affinity. Overall, PC affinity reached only 26% of the randomly expected value. Thus, the vast majority of langur monkey opponents avoided each other after conflicts. Avoidance as a low-cost option for group-living animals to cope with conflicts is often not possible in captivity. This suggests that reports of high rates of reconciliation may be at least partly artefacts of captivity. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.     

Dextran sulfate-dependent fusion of liposomes containing cationic stearylamine.

The incorporation of the positively charged stearylamine into phosphatidylcholine liposomes was studied by measuring electrophoretic mobilities. Up to a molar ratio SA/PC = 0.5 an increase of the positive zeta potential can be observed. Addition of the negatively charged macromolecule dextran sulfate leads to a change of the sign of the surface potential of the PC/SA liposomes indicating binding of the macromolecule to the surface. This process is accompanied by an increase in turbidity, which is dependent on the molecular weight of the dextran sulfate and the SA concentration (measured by turbidimetry). Using the NBD/Rh and Pyr-PC fluorescence assays the fusion of SA containing liposomes was investigated. A strong influence of the SA content and molecular weight of dextran sulfate on the fusion extent was observed. The fusion extent is proportional to the SA content in the PC membrane and the molecular weight of dextran sulfate. PC/SA/PE liposomes exhibit a higher fusion extent after addition of dextran sulfate compared to PC/SA liposomes indicating that PE additionally destabilizes the bilayer. Freeze-fracture electron microscopy reveals that the reaction products are large complexes composed of multilamellar stacks of tightly packed, straight membranes and aggregated vesicles. The tight packing of the membranes in the stacks (and the narrow contact of the aggregated vesicles) indicates a strong adherence of opposite membrane surfaces induced by dextran sulfate.     

Binding mode of Thioflavin T and other molecular probes in the context of amyloid fibrils—current status

Because understanding amyloid fibrillation in molecular detail is essential for development of strategies to control amyloid formation and overcome neurodegenerative disorders, increased understanding of present molecular probes as well as development of new probes are of utmost importance. To date, the binding modes of these molecular probes to amyloid fibrils are by no means adequately described or understood, and the large number of studies on Thioflavin T (ThT) and Congo Red (CR) binding have resulted in models that are incomplete and conflicting. Different types of binding sites are likely to be present in amyloid fibrils with differences in binding modes. ThT may bind in channels running parallel to the long axis of the fibril. In the channels, ThT may bind in either a monomeric or dimeric form of which the molecular conformation is likely to be planar. CR may bind in grooves formed along the β-sheets as a planar molecule in either a monomeric or supramolecular form.     

Genome-tools: a flexible package for genome sequence analysis

Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools.     

Molecular weight distribution of carrageenans by size exclusion chromatography and low angle laser light scattering

A procedure to determine the absolute weight average molecular weight and molecular weight distribution of carrageenans by high pressure aqueous size exclusion chromatography coupled with low angle laser light scattering is described. Experimental parameters are successively discussed, particular attention being focused on the absence of shear degradation during elution. The distribution curves were highly reproducible in time and weight average molecular weights integrated along the chromatogram were in good agreement with static light scattering results. A large difference in the molecular weight range between native (food-grade) and acidic degraded carrageenan samples was observed. Weight average molecular weights were found to be in good correlation with viscosity values, for degraded as well as undegraded products. It is also shown that the method described can help people using carrageenans in pharmacological studies by providing information on the real molecular weight distribution of the products they are employing.     

Specificity and rate of human and mouse liver and plasma phosphatidylcholine synthesis analyzed in vivo

Phosphatidylcholine (PC) synthesis by the direct cytidine diphosphate choline (CDP-choline) pathway in rat liver generates predominantly mono- and di-unsaturated molecular species, while polyunsaturated PC species are synthesized largely by the phosphatidylethanolamine-N-methyltransferase (PEMT) pathway. Although altered PC synthesis has been suggested to contribute to development of hepatocarcinoma and nonalcoholic steatohepatitis, analysis of the specificity of hepatic PC metabolism in human patients has been limited by the lack of sensitive and safe methodologies. Here we incorporated a deuterated methyl-D(9)-labled choline chloride, to quantify biosynthesis fluxes through both of the PC synthetic pathways in vivo in human volunteers and compared these fluxes with those in mice. Rates and molecular specificities of label incorporated into mouse liver and plasma PC were very similar and strongly suggest that label incorporation into human plasma PC can provide a direct measure of hepatic PC synthesis in human subjects. Importantly, we demonstrate for the first time that the PEMT pathway in human liver is selective for polyunsaturated PC species, especially those containing docosahexaenoic acid. Finally, we present a multiple isotopomer distribution analysis approach, based on transfer of deuterated methyl groups to S-adenosylmethionine and subsequent sequential methylations of PE, to quantify absolute flux rates through the PEMT pathway that are applicable to studies of liver dysfunction in clinical studies.     

GIMSAN: a Gibbs motif finder with significance analysis

We present GIMSAN (GIbbsMarkov with Significance ANalysis): a novel tool for de novo motif finding. GIMSAN combines GibbsMarkov, our variant of the Gibbs Sampler, described here for the first time, with our recently introduced significance analysis. AVAILABILITY: GIMSAN is currently available as a web application and a stand-alone application on Unix and PBS (Portable Batch System) cluster through links from http://www.cs.cornell.edu/~keich.