Chromosome-associated paracrystalline nuclear inclusions in the spermatocytes of a pulmonate snail,Planorbarius corneus L.

Chromosome-associated paraorystalloids are regularly found in the spermatocytes of snails which were reared in the laboratory. They seem to be largely specific for the male gametocytes as they have been observed only in few cases in the oocytes. It is likely that paracrystalloids are formed during pachytene at the site of large heterochromatic knobs which originate by fusion of heterochromatic terminal segments of some bivalents. During diplotene they are always connected with the telomeres of three or four bivalents, thus forming a large trefoil-like structure. During metaphase I paracrystalloids are shed off from the chromosomes and transferred to the cytoplasm. In early spermatids they are found again in the nuclei, where they fade away during spermiogenesis. Histochemically they consist of basic proteins, which are probably crystallized in the cubic system. Radioactive labeling of the structure could not be achieved, neither by ³H-uridine or thymidine, nor by amino acids. The functional significance of this peculiar structure is unknown. Certain features justify a comparison with synaptonemal polycomplexDedicated to Professor B. Rensch on the occasion of his 75th birthday     

Modeling the effect of the layer thickness and tissue conductivities of the head and the brain on the EEG potentials using finite element method

The influence of the thickness and specific resistance of the brain tissues and its surrounding coverings, brain sulci and anisotropy of white matter electric conductivity on the EEG potentials were modeled. The finite element method was used for simulation, which is realized in the Femlab module. During the comparison of two models with different thickness of the layers was shown the change of potentials by 40% for scull, which thickness varied by 9 mm, and for the gray matter and spinal fluid the change of potentials amounted to 15% by 3 mm variable thickness. The change of conductivity by 25% resulted in the difference of potentials amounted to 15% for the white matter and 1.5% for the cortex of the brain. During the assignment of the anisotropy in the model, by the whole volume of the white matter, sixfold difference of the potentials in comparison with application of isotropic parameters was discovered. The difference of the potentials for single heterogeneity, simulated the sulci of the brain, amounted to 10% in the heterogeneity projection point and increased during the drawing near to the "referent electrode". The model complex of the "sulci of cerebrum" gave significant contribution to the difference of the potentials and depended on the depth of dipole occurrence and nearness of the sulci complex. Significant influence of brain sulci on the EEG-potentials distribution, which can give rise to great artifacts, was discovered.     

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89

Computational expression deconvolution aims to estimate the contribution of individual cell populations to expression profiles measured in samples of heterogeneous composition. Zhong et al. recently proposed Digital Sorting Algorithm (BMC Bioinformatics 2013 Mar 7;14:89) and showed that they could accurately estimate population-specific expression levels and expression differences between two populations. They compared DSA with Population-Specific Expression Analysis (PSEA), a previous deconvolution method that we developed to detect expression changes occurring within the same population between two conditions (e.g. disease versus non-disease). However, Zhong et al. compared PSEA-derived specific expression levels across different cell populations. Specific expression levels obtained with PSEA cannot be directly compared across different populations as they are on a relative scale. They are accurate as we demonstrate by deconvolving the same dataset used by Zhong et al. and, importantly, allow for comparison of population-specific expression across conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0347-5) contains supplementary material, which is available to authorized users.     

Polyribosomal structures inactive for protein synthesis present in erythroid cells during terminal stages of differentiation.

During the terminal stages of differentiation nucleated erythroid cells from the fetal mouse synthesize hemoglobin at a lower rate because after the last cycle of cell division about half of their polyribosomal structures are rendered inactive for protien synthesis though they maintain their aggregated shape. Partially inactive polyribosomes are tested in comparison with normal polyribosomes for the capacity to support polypeptide chain synthesis in cell-free conditions. The following observations are made: a) no difference is found for the profile on sucrose density gradients; b) partially inactive polyribosomes carry growing polypeptide chains in reduced amounts in comparison with active polyribosomes; c) partially inactive polyribosomes are not capable to release "run off" 80 S ribosomal monomers and to dissociate to active ribosomal subunits. These data are interpreted as the evidence for a block of chain termination producing inactivation of polyribosomes during the late maturation of nucleated erythroid cells.     

系统发育和被子植物“多系-多期-多域”系统——兼答傅德志的评论

历史地回顾了谱系、系统发育、单系、多系概念的由来和发展。详细讨论了单系(monophyly )和多系(polyphyly)在叙述分类群起源和描述分类群内部系统发育线多样性的不同含义。以此为基础,说明在“多系_多2_多域”的八纲系统中“多系”和“单系”是指自然分类群内系统发育线的多样性,不等同于“多源”和“单源”。通过与近年来所发表的被子植物分类系统的比较,认为基于化石、形态、分子和地理分布证据提出的八纲系统所显示的预言性,必将在今后的科学实践中经受检验。     

A method for comparing DNA replication programmes at the level of the chromosome bands

During DNA synthesis, each pair of homologous chromosomes replicates its bands in a precise order and at a specific time. When using asynchronous cell populations, this replication programme has to be reconstructed from a series of "stills"--serial samples taken at intervals through S-transit. Obviously, the result obtained is dependent upon the kinetic progression of cells through the cycle, and any perturbation of the cycle. A difficulty arises when we wish to compare the replication programme of a chromosome in two different cultures (e.g. cells from different origins, or after different treatments). Kinetic differences between cultures make it almost impossible to obtain two samples for analysis containing the same "mixture" of cells. Thus, a false programme difference could be introduced, or a real one masked. In this paper, we present a method of comparison that overcomes this problem. It is based upon the observation that with serial sampling of steady-state cell populations through S-phase, band appearance curves are sigmoidal and are very well approximated by cumulative Normal distributions with very similar standard deviations. If a family of such curves, closely spaced in time, is sampled twice, the two observed frequencies for each curve are related, their probits all lying on a single straight line. This line has a slope of 45 degrees and its displacement from the origin is a function of the time interval between the two samples. Given two identical families of such curves, exactly the same relationship will hold if one sample is drawn from each. If, however, the two families differ (in order, spacing, standard deviation etc.), the probit/probit plot will deviate in various ways from a straight line with 45 degrees slope. Any two subsets of chromosome replication-band frequencies can be regarded as derived from a family of cumulative Normal curves and probit/probit comparisons used to test the similarity of their replication programmes.     

FishNet: an online database of zebrafish anatomy

Background

Embryos of taxonomically different vertebrates are thought to pass through a stage in which they resemble one another morphologically. This "vertebrate phylotypic stage" may represent the basic vertebrate body plan that was established in the common ancestor of vertebrates. However, much controversy remains about when the phylotypic stage appears, and whether it even exists. To overcome the limitations of studies based on morphological comparison, we explored a comprehensive quantitative method for defining the constrained stage using expressed sequence tag (EST) data, gene ontologies (GO), and available genomes of various animals. If strong developmental constraints occur during the phylotypic stage of vertebrate embryos, then genes conserved among vertebrates would be highly expressed at this stage.

Results

We established a novel method for evaluating the ancestral nature of mouse embryonic stages that does not depend on comparative morphology. The numerical "ancestor index" revealed that the mouse indeed has a highly conserved embryonic period at embryonic day 8.0–8.5, the time of appearance of the pharyngeal arch and somites. During this period, the mouse prominently expresses GO-determined developmental genes shared among vertebrates. Similar analyses revealed the existence of a bilaterian-related period, during which GO-determined developmental genes shared among bilaterians are markedly expressed at the cleavage-to-gastrulation period. The genes associated with the phylotypic stage identified by our method are essential in embryogenesis.

Conclusion

Our results demonstrate that the mid-embryonic stage of the mouse is indeed highly constrained, supporting the existence of the phylotypic stage. Furthermore, this candidate stage is preceded by a putative bilaterian ancestor-related period. These results not only support the developmental hourglass model, but also highlight the hierarchical aspect of embryogenesis proposed by von Baer. Identification of conserved stages and tissues by this method in various animals would be a powerful tool to examine the phylotypic stage hypothesis, and to understand which kinds of developmental events and gene sets are evolutionarily constrained and how they limit the possible variations of animal basic body plans.     

Crystallographic analysis of synechocystis cyanoglobin reveals the structural changes accompanying ligand binding in a hexacoordinate hemoglobin

The crystal structures of cyanide and azide-bound forms of the truncated hemoglobin from Synechocystis are presented at 1.8 angstroms resolution. A comparison with the structure of the endogenously liganded protein reveals a conformational shift unprecedented in hemoglobins, and provides the first picture of a hexacoordinate hemoglobin in both the bis-histidyl and the exogenously coordinated states. The structural changes between the different conformations are confined to two regions of the protein; the B helix, and the E helix, including the EF loop. A molecular "hinge" controlling movement of the E helix is observed in the EF loop, which is composed of three principal structural elements: Arg64, the heme-d-propionate, and a three-residue extension of the F helix. Additional features of the structural transition between the two protein conformations are discussed as they relate to the complex ligand-binding behavior observed in hexacoordinate hemoglobins, and the potential physiological function of this class of proteins.     

Alignment of non-covalent interactions at protein-protein interfaces

Background

The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces.

Methodology/Principal Findings

Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions.

Conclusions/Significance

The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.     

Comparison of Three Different LCIA Methods: EDIP97, CML2001 and Eco-indicator 99

Goal, Scope and Background

A number of impact assessment methodologies are available to the LCA practitioner. They differ, and often there is not one obvious choice among them. The question therefore naturally arises: ‘Does it make any difference to my conclusions which method I choose?’ To investigate this issue, a comparison is performed of three frequently applied life cycle impact assessment methods.

Methods

The three life cycle impact assessment methods EDIP97 [1], CML2001 [2] and Eco-indicator 99 [3] are compared on their performance through application to the same life cycle inventory from a study of a water-based UV-lacquer. EDIP97 and CML2001 are both midpoint approaches and hence quite similar in their scope and structure, and this allows a comparison during both characterisation and normalisation. The third impact assessment method Eco-indicator 99 is an endpoint method and different in scope and structure from the other two. A detailed comparison can not be done but a comparative analysis of the main contributors to the Eco-indicator 99 results and the weighted and aggregated EDIP97 results is performed.

Results and Discussion

Following a translation into common units of the EDIP97 and CML2001 output, differences up to two orders of magnitude are found for some of the indicator results for the impact categories describing toxicity to humans and ecosystems, and there is little similarity in the patterns of major contributors among the two methods. For human toxicity the CML2001 score is dominated by contribution from metals while the EDIP97 score is caused by a solvent and nitrogen oxides. For aquatic ecotoxicity, metals are the main contributors for both methods but while it is vanadium for CML2001, it is strontium for EDIP97. After normalisation, the differences are reduced but still considerable. For the other impact categories, the two methods show only minor differences. The comparison of the main contributors to the Eco-indicator 99 results and the weighted and aggregated EDIP97 results identifies nitrogen oxides as the main contributor for both methods. It is, however, much more dominant for Eco-indicator 99 while the EDIP97 score represents important contributions from a number of different substances, and furthermore, the analysis reveals that the aggregated scores for the two methods come from different impacts. It is thus difficult to extend the findings for these two methods to other inventories.

Conclusion

For EDIP97 and CML2001, it mainly matters which method is used if the chemical impacts on human health and ecosystem health are important for the study. For the other impact categories, the differences are minor for these two methodologies. For EDIP97 and Eco-indicator 99, the patterns of most important contributors to the weighted and aggregated impact scores are rather different, and considering the known differences in the underlying framework and models, the results of the two methods may well go in opposite directions for some inventories even if the conclusion is the same for the inventory studied in this paper.

Recommendations and Oudook

Particularly for the impact categories representing toxic impacts from chemicals, the study demonstrates the need for more a detailed analysis of the causes underlying the big differences revealed between the methods.

     

生态系统服务的物质量与价值量评价方法的比较分析

对生态系统服务的物质量评价和价值量评价这两类评价方法进行比较,分析了这两类评价方法的优点和缺点,结果表明,采用物质量和价值量两种不同的方法对同一生态系统进行服务评价,往往会得出不同甚至相反的结论：对于不同的评价目的和不同的评价空间尺度,这两类评价方法的作用是有较大区别的,同时这两类评价方法在一定意义上又是相互促进和互为补充的。     

High-performance size-exclusion chromatography (HPSEC) and fluorophore-assisted carbohydrate electrophoresis (FACE) to describe the chain-length distribution of debranched starch

Chain-length (CL) distribution is an important feature of the "fine structure" of starch molecules, which are comprised of amylose and amylopectin. The objective of the present work was to combine data for two methods to achieve a more comprehensive data set that would allow a fuller comparison of the CL distribution for different starches. Both high-performance size-exclusion chromatography (HPSEC) and fluorophore-assisted carbohydrate electrophoresis (FACE) were carried out on endosperm starch isolated from five maize genotypes. For the CL distribution in the range DP50, data in the HPSEC chromatogram were transformed to the form of a FACE electrophoregram, in which the x-axis is DP and the y-axis is the number of chains. The two sets of data in this region were shown to be similar. We conclude that the data sets from HPSEC and FACE may be considered together to describe the CL distribution more completely than for either method alone. We further note that for DP 6-50, data from HPSEC may be transformed to allow a similar presentation as for that obtained by FACE, such that FACE analysis might not be required for comparison of CL distribution of different starches.     

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns

Background

During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earliest events in the development of the vertebrate embryo is the establishment of three germ layers, consisting of the ectoderm, mesoderm and endoderm. Attempts to measure gene expression in vivo in different germ layers and cell types are typically complicated by the heterogeneity of cell types within biological samples (i.e., embryos), as the responses of individual cell types are intermingled into an aggregate observation of heterogeneous cell types. Here, we propose a novel method to elucidate gene regulatory circuits from these aggregate measurements in embryos of the frog Xenopus tropicalis using gene network inference algorithms and then test the ability of the inferred networks to predict spatial gene expression patterns.

Results

We use two inference models with different underlying assumptions that incorporate existing network information, an ODE model for steady-state data and a Markov model for time series data, and contrast the performance of the two models. We apply our method to both control and knockdown embryos at multiple time points to reconstruct the core mesoderm and endoderm regulatory circuits. Those inferred networks are then used in combination with known dorsal-ventral spatial expression patterns of a subset of genes to predict spatial expression patterns for other genes. Both models are able to predict spatial expression patterns for some of the core mesoderm and endoderm genes, but interestingly of different gene subsets, suggesting that neither model is sufficient to recapitulate all of the spatial patterns, yet they are complementary for the patterns that they do capture.

Conclusion

The presented methodology of gene network inference combined with spatial pattern prediction provides an additional layer of validation to elucidate the regulatory circuits controlling the spatial-temporal dynamics in embryonic development.     

THE POWER OF THE " A" -" NOT A" METHOD

The " A" - " Not A" method is a rating method with two categories. It is often treated as a discrimination method. Unlike forced choice procedures, the Thurstonian model for this method involves a choice criterion. In statistical tests, it is treated as a comparison of two proportions. In this paper, the power for hypothesis tests involving the monadic and replicated monadic " A" - " Not A" method is discussed. The power functions and the sample sizes needed for 80% power are given based on Thurstone's δ. Designs with equal and unequal allocations for A and A (Not A) samples are considered. The power of the method is also compared with that of four forced choice methods under the assumption that the perceptual variance is identical among methods. The comparison shows that, in general, the power for the five methods ranks from high to low: the 3-AFC, 2-AFC, " A" - " Not A", triangular and duo-trio. The comparison also shows that, based on the same number of panelists and/or the same sample size for the A and A⁻ samples for the methods, if the panelists are not too discrepant and the choice criterion in the " A" - " Not A" method is not too strict or too lax, the power of the " A" - " Not A" method is very close to that of the 2-AFC method.     

QTL analysis: further uses of ‘marker regression’

A variety of approaches are available for identifying the location and effect of QTL in segregating populations using molecular markers. However, these have problems in distinguishing two linked QTL, particularly in relation to the size of the test statistic when many independent tests are performed. An empirical method for obtaining the distribution of the test statistic for specific datasets is described, and its power for demonstrating the inadequacy of a single-QTL model is explored through computer simulation. The method is an extension of the previously described technique of marker regression, and it is applied here to demonstrate two situations in which it may be useful. Firstly, we examine the power of the technique to distinguish two, linked QTL from one and compare this ability with that of two contemporary methods, Mapmaker/QTL and regression mapping. Secondly, we show how to combine information from two, or more, populations that may be segregating for different marker loci in a given linkage group. This is illustrated for two populations having in common just two linked marker loci although the sharing of loci is not a pre-requisite. Empirical tests are used to determine whether the same or different QTL are segregating and, if they are the same QTL, whether they are the same alleles. Evidence is discussed which suggests that the upper limit to the number of QTL that can be located for any single quantitative trait in a segregating populations is 12.     

Environmental influences on the sensitization by drugs measured in peripheral blood lymphocyte chromatin

An "allergo-kinetic" method was introduced, which measures early changes of nuclear chromatin structure of lymphocyte subpopulations. The method is used as an in vitro test for drug allergy. The comparison of data from two sampling places (Budapest-Esztergom) shows the following results: The drug allergy scores (obtained from T-cells) may reflect environmental influences on the population under study. During the 13 months period after Atomic Reactor accident in Chernobyl, both the frequency of severe skin manifestations and that of organ manifestations (without skin lesions) increased. The ratio of negative test results decreased in both of drug allergic patient groups (small town = Esztergom, large city = Budapest)--tendency to polysensibilization. The scores obtained in drug related groups of generalized urticaria and Quincke's oedema increased significantly within 13 months after accident followed by a normalization in the subsequent year.     

The memory of water: Archaeobotanical evidence of wetland plants from Modena (Emilia-Romagna,northern Italy) and palaeoecological remarks

Modena, founded by the Romans (183 BC), has always been conditioned by water in all its urban history. In the city, numerous archaeobotanical investigations have been carried out in order to reconstruct the natural landscape and human–environment interactions over time. During these investigations, four archaeological sites (two Roman and two medieval) have revealed deposits with a marked character of palaeobiocoenosis, largely resulting from the natural environment surrounding the sites, due to natural “seed rain”. These deposits are characterized by widespread evidence of plants related to water, constituting a valuable archive to investigate habitats which currently have become very rare and threatened, if they have not completely disappeared. The present paper aims to reveal the peculiarities of the Roman/medieval archaeocarpological floristic lists (through a comparison with the flora over the last two centuries in the area of Modena) and highlight the possible causes explaining the presence or the demise of several taxa, considering also the palaeoecological reconstruction of the environment in which they have been found.