Kinship and Deep History: Exploring Connections between Culture Areas, Genes, and Languages

Large-scale geographic variation in kinship systems may have deep roots. A number of authors now argue for an "emerging synthesis," with genetic, linguistic, and archeological findings coming together to paint a consistent picture of large-scale population spreads in prehistory. This article explores a social structural dimension of this synthesis: Major culture areas based on variation in kinship systems correspond closely—yet not perfectly—to genetic and linguistic clusters identified by other researchers. Thus it may be possible to reconstruct: (1) a set of "primary" culture areas corresponding to major population blocs and associated with ancient demic expansions and parallel transmission of genes and culture, and (2) a smaller set of overlying "secondary" culture areas of more recent origin that do not map onto genetic subdivisions and result from changes in subsistence or political economy independent of large-scale demic expansions. I also review latitudinal variation in kinship systems. [Keywords: culture areas, demic expansions, kinship (prehistory), protolanguages]     

Structural Properties of Gene Regulatory Networks: Definitions and Connections

The study of gene regulatory networks is a significant problem in systems biology. Of particular interest is the problem of determining the unknown or hidden higher level regulatory signals by using gene expression data from DNA microarray experiments. Several studies in this area have demonstrated the critical aspect of the network structure in tackling the network modelling problem. Structural analysis of systems has proved useful in a number of contexts, viz., observability, controllability, fault diagnosis, sparse matrix computations etc. In this contribution, we formally define structural properties that are relevant to Gene Regulatory Networks. We explore the structural implications of certain quantitative methods and explain completely the connections between the identifiability conditions and structural criteria of observability and distinguishability. We illustrate these concepts in case studies using representative biologically motivated network examples. The present work bridges the quantitative modelling methods with those based on the structural analysis.     

Connections between virus movement, macromolecular signaling and assimilate allocation.

Studies originating with plant viruses led to the concept that plasmodesmata potentiate the cell-to-cell trafficking of viral and endogenous proteins and nucleoprotein complexes. In this article, we develop the theme that, at the tissue/organ level, cell-to-cell trafficking of information molecules enables non-cell-autonomous control over a range of processes, whereas at the organismal level, the phloem serves as an information superhighway. The capacity to deliver proteins and nucleoprotein complexes, over long distances, allowed for the development of a viral surveillance/resistance mechanism, as well as the integration of processes at the whole-plant level.     

Structural and Dynamics Comparison of Thermostability in Ancient,Modern, and Consensus Elongation Factor Tus

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Literature Mining for the Discovery of Hidden Connections between Drugs,Genes and Diseases

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also well-suited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs.     

Clinical Profiles and Factors Associated with Death in Adults with Dengue Admitted to Intensive Care Units,Minas Gerais,Brazil

The purpose of our study was to describe the clinical profile of dengue-infected patients admitted to Brazilian intensive care units (ICU) and evaluate factors associated with death. A longitudinal, multicenter case series study was conducted with laboratory-confirmed dengue patients admitted to nine Brazilian ICUs situated in Minas Gerais state, southeastern Brazil from January 1, 2008, to December 31, 2013. Demographic, clinical and laboratory data; disease severity scores; and mortality were evaluated. A total of 97 patients were studied. The in-ICU and in-hospital mortality rates were 18.6% and 19.6%, respectively. Patients classified as having severe dengue according to current World Health Organization classifications showed an increased risk of death in a univariate analysis. Nonsurvivors were older, exhibited lower serum albumin concentrations and higher total leukocyte counts and serum creatinine levels. Other risk factors (vomiting, lethargy/restlessness, dyspnea/respiratory distress) were also associated with death in a univariate analysis. Multivariate analysis indicated that in-hospital mortality was significantly associated with Acute Physiology and Chronic Health Evaluation II and the Sequential Organ Failure Assessment score. The ICU and in-hospital mortality observed in this study were higher than values reported in similar studies. An increased frequency of ICU admission due to severe organ dysfunction, higher severity indices and scarcity of ICU beds may partially explain the higher mortality.     

Connections between ecology,biogeography, and paleobiology: Relationship between local abundance and geographic distribution in fossil and recent molluscs

Summary We used data on Contemporary and Pleistocene molluscs at one site in the Gulf of California to evaluate and extend earlier ideas about the relationship between local abundance and geographic distribution. For each species whose shells occurred in one Recent and two Pleistocene deposits, we measured its abundance in the sample and relative latitudinal position within its contemporary geographic range. Species near the edges of their ranges showed uniformly low abundances, whereas those near the centres exhibited a wide range of abundances. Species near the edges of their ranges also appear to have exhibited greater changes in abundance, including more colonization and extinction events, between the Pleistocene interglacial sample and the Recent one. The constraint of location in the geographic range on maximal local and regional abundance appears to offer an example of a connection between patterns and processes on local, regional, and geographical scales. Characteristics of community structure, such as relative abundance of individual species and frequency of local co-existence of multiple species, may be influenced by the location of the sample site with respect to the geographic ranges of the constituent species. These results demonstrate emergent, statistical features of population ecology and community organization that are manifest over geographic space and evolutionary time.     

Factors that Influence the Formation and Stability of Thin,Cryo-EM Specimens

Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surface pressure) can hardly be avoided during standard cryo-EM specimen preparation. We thus suggest that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness.     

Metabolic Profiles are Principally Different between Cancers of the Liver,Pancreas and Breast

Molecular profiling of primary tumors may facilitate the classification of patients with cancer into more homogenous biological groups to aid clinical management. Metabolomic profiling has been shown to be a powerful tool in characterizing the biological mechanisms underlying a disease but has not been evaluated for its ability to classify cancers by their tissue of origin. Thus, we assessed metabolomic profiling as a novel tool for multiclass cancer characterization. Global metabolic profiling was employed to identify metabolites in paired tumor and non-tumor liver (n=60), breast (n=130) and pancreatic (n=76) tissue specimens. Unsupervised principal component analysis showed that metabolites are principally unique to each tissue and cancer type. Such a difference can also be observed even among early stage cancers, suggesting a significant and unique alteration of global metabolic pathways associated with each cancer type. Our global high-throughput metabolomic profiling study shows that specific biochemical alterations distinguish liver, pancreatic and breast cancer and could be applied as cancer classification tools to differentiate tumors based on tissue of origin.     

Connections between sister and non-sister telomeres of segregating chromatids maintain euploidy

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Transcriptome-Wide Identification and Expression Profiles of Masson Pine WRKY Transcription Factors in Response to Low Phosphorus Stress

Plant Molecular Biology Reporter - Masson pine (Pinus massoniana Lamb.) is an economically important conifer tree that can be widely used for timber, pulp, and resin production. However, the...     

Connections between finger print patterns and the form of terminal phalanges

The present paper resumes the theme taken up by Bonnevie in her studies of the embryonic development of dermatoglyphic systems. Relicts of the embryonic finger balls remain in later life (Fleischhacker) and influence the symmetry relationships of the terminal phalanges. Attention was, therefore, focussed on the connection between the asymmetry of terminal phalanges and that of the patterns. All loops and whorls with a different ridge count on the radial and on the ulnar side are asymmetrical. In order to determine the asymmetry of the terminal phalanges, casts were made of the fingers of 200 schoolchildren. Then, contour drawings were laid into various planes using the phalangograph (constructed on the same lines as the perigraph), and the plane of intersection of the two sides of the symmetry axis was determined planimetrically. A high correlation of r = 0·954 was established between the degree of asymmetry of the patterns and that of the terminal phalanges (cf. Figure 3).     

Calcium Regulates the Activity and Structural Stability of Tpr,a Bacterial Calpain-like Peptidase

Porphyromonas gingivalis is a peptide-fermenting asaccharolytic periodontal pathogen. Its genome contains several genes encoding cysteine peptidases other than gingipains. One of these genes (PG1055) encodes a protein called Tpr (thiol protease) that has sequence similarity to cysteine peptidases of the papain and calpain families. In this study we biochemically characterize Tpr. We found that the 55-kDa Tpr inactive zymogen proteolytically processes itself into active forms of 48, 37, and 33 kDa via sequential truncations at the N terminus. These processed molecular forms of Tpr are associated with the bacterial outer membrane where they are likely responsible for the generation of metabolic peptides required for survival of the pathogen. Both autoprocessing and activity were dependent on calcium concentrations >1 mm, consistent with the protein''s activity within the intestinal and inflammatory milieus. Calcium also stabilized the Tpr structure and rendered the protein fully resistant to proteolytic degradation by gingipains. Together, our findings suggest that Tpr is an example of a bacterial calpain, a calcium-responsive peptidase that may generate substrates required for the peptide-fermenting metabolism of P. gingivalis. Aside from nutrient generation, Tpr may also be involved in evasion of host immune response through degradation of the antimicrobial peptide LL-37 and complement proteins C3, C4, and C5. Taken together, these results indicate that Tpr likely represents an important pathogenesis factor for P. gingivalis.     

Functional and Structural Comparisons between Prokaryotic and Eukaryotic aa3-Type Cytochrome c Oxidases from an Evolutionary Point of View

The specificities for cytochrome c of the aa3-type cytochromec oxidase were studied with enzymes derived from Thiobacillusnovellas, Nitrobacter agilis, Paracoccus denitrificans and thecow in reaction with the cytochromes c from 5 prokaryotes and7 eukaryotes. The T. novellus enzyme reacted most rapidly withthe cytochromes c of Candida krusei, tuna and bonito as wellas T. novellus cytochrome c; the specificity for cytochromec of the N. agilis enzyme was similar to that of the T. novellusenzyme. The bovine enzyme reacted rapidly with all the eukaryoticcytochromes c tested. The P. denitrificans enzyme showed a specificitysimilar to that of the bovine enzyme, except that it reactedrapidly with P. denitrificans cytochrome c, while the bovineenzyme reacted with it very poorly. All four kinds of enzymesshowed an extremely limited reaction with Pseudomonas aeruginosacytochrome c. The amino acid composition of subunit I of the N. agilis enzymeresembled that of the bovine enzyme, while the compositionsof their subunits II were different. On the basis of these results,an evolutionary relationship between bacterial and eukaryoticenzymes was discussed. (Received May 21, 1981; Accepted August 20, 1981)     

Lysophosphatidic Acid Alters the Expression Profiles of Angiogenic Factors,Cytokines, and Chemokines in Mouse Liver Sinusoidal Endothelial Cells

Background and Aims

Lysophosphatidic acid (LPA) is a multi-function glycerophospholipid. LPA affects the proliferation of hepatocytes and stellate cells in vitro, and in a partial hepatectomy induced liver regeneration model, the circulating LPA levels and LPA receptor (LPAR) expression levels in liver tissue are significantly changed. Liver sinusoidal endothelial cells (Lsecs) play an important role during liver regeneration. However, the effects of LPA on Lsecs are not well known. Thus, we investigated the effects of LPA on the expression profiles of angiogenic factors, cytokines, and chemokines in Lsecs.

Methods

Mouse Lsecs were isolated using CD31-coated magnetic beads. The mRNA expression levels of LPAR’s and other target genes were determined by quantitative RT-PCR. The protein levels of angiogenesis factors, cytokines, and chemokines were determined using protein arrays and enzyme immunoassay (EIA). Critical LPAR related signal transduction was verified by using an appropriate chemical inhibitor.

Results

LPAR1 and LPAR3 mRNA’s were expressed in mouse LPA-treated Lsecs. Treating Lsecs with a physiological level of LPA significantly enhanced the protein levels of angiogenesis related proteins (cyr61 and TIMP-1), cytokines (C5/C5a, M-CSF, and SDF-1), and chemokines (MCP-5, gp130, CCL28, and CXCL16). The LPAR1 and LPAR3 antagonist ki16425 significantly inhibited the LPA-enhanced expression of cyr61, TIMP-1, SDF-1, MCP-5, gp130, CCL28, and CXCL16, but not that of C5/C5a or M-CSF. LPA-induced C5/C5a and M-CSF expression may have been through an indirect regulation mechanism.

Conclusion

LPA regulated the expression profiles of angiogenic factors, cytokines, and chemokines in Lsecs that was mediated via LPAR1 and LPAR3 signaling. Most of the factors that were enhanced by LPA have been found to play critical roles during liver regeneration. Thus, these results may prove useful for manipulating LPA effects on liver regeneration.     

Attentional Blink Is Hierarchically Modulated by Phonological,Morphological, Semantic and Lexical Connections between Two Chinese Characters

The ability to identify the second of two targets (T2) is impaired if that target is presented less than ∼500 ms after the first (T1). This transient deficit is known as attentional blink (AB). Previous studies have suggested that the magnitude of the AB effect can be modulated by manipulating the allocation of attentional resources to T1 or T2. However, few experiments have used Chinese characters and words to explore this phenomenon. The existence of lexical, semantic, phonological and morphological connections between Chinese characters has been well established, and understanding these connections may improve our knowledge of reading Chinese. In this study, we employed varying connections between T1 and T2 and examined how these connections modulate the AB effect. We found that the strongest AB was observed when the two Chinese characters were completely unrelated, while the AB was reduced when T1 and T2 were phonologically, orthographically or semantically related and was almost completely eliminated when T1 and T2 were united in a lexical phrase. The order of activation between Chinese characters was identified as follows: (a) lexical phrases, (b) semantic connection, (c) morphological connection, (d) phonological connection and (e) unrelated words.     

Contribution of Structural Reversibility to the Heat Stability of the Tropomyosin Shrimp Allergen

For the purification of plant endo-β-N-acetylglucosaminidase, in this report, we introduce a new affinity chromatography using the reduced and carboxymethylated yeast invertase (cm-YI) as a ligand. Two plant endo-β-N-acetylglucosaminidases (endo-LE from tomato fruits (Kimura, Y., et al. Biochim. Biophys. Acta 1381, 27-36 (1998)) and endo-GB from Ginkgo biloba seeds (Kimura, Y., et al. Biosci. Biotechnol. Biochem., 62, 253-261 (1998)) could completely bind to the high-mannose type N-glycans linked to the immobilized yeast invertase and the activities of both enzymes could be recovered by increasing the concentration of NaCl. By using this purification procedure with some other purification procedures, endo-LE could be purified 1,700-fold and endo-GB was purified to apparent homogeneity at 63 kDa as reported previously.     

Connections between dictyosomes,ER and GERL in cotyledons of mung bean (Vigna radiata L.)

Summary The connections and structural inter-relations of dictyosomes and endoplasmic reticulum (ER) in cotyledons of germinating mung beans were studied using thick (0.3 m) sections of aldehyde fixed, zinc iodide-osmium tetroxide (ZIO) impregnated tissue. The sections were examined by conventional (100 kV), rather than high voltage, transmission electron microscopy.Continuity of cisternal ER with tubular ER was confirmed and a direct connection of tubular ER totrans dictyosome cisternae was observed as were GERL networks associated withtrans dictyosome cisternae.Dictyosomes also gave rise to an extensive system of very fine tubules (10–20 nm diam) which have not been described previously in plant tissue. These tubules, which originated at thetrans dictyosome face, extended throughout the cytoplasm and were found connected to cisternal ER and tubular ER.The implications of these observations are discussed with regard to present ideas concerning endomembrane flow and protein sorting by the Golgi apparatus.