Macrophytes and diatoms – major results and conclusions from the STAR project

The interactions between sensitivity and variability of macrophyte and diatom communities were evaluated as a research support of methodologies required by the Water Framework Directive. Slope and shading were identified as additional typological parameters improving links between unimpacted macrophyte communities and running water types. Two other studies demonstrated indication value of macrophytes for assessment of nutrient enrichment and hydromorphological degradation. The special exercises were realized within the STAR project to evaluate sources of variability/uncertainty in assessment methods based on macrophytes and diatoms. Sampling period and shading of the site were found as major factors affecting variability in macrophyte assessment results. Uncertainty of diatom assessment is predominantly associated with selection of site, substrate type and taxonomic identification. Further extension of indication systems and definition of macrophyte/diatom-specific typology of running waters are considered as the main aims of subsequent investigations.     

Separation and properties of α-mannosidase and mannanase from the basidiomycetePhellinus abietis

Proteins of a crude enzyme preparation obtained from the cultivation medium of the basidiomycetePhellinus abietis were separated by gel filtration and ion-exchange chromatography. The preparation contained a minimum of three enzymes capable of splitting α-d-mannosidic bonds: α-mannosidase, exomannanase, and endomannanase, which were separated. Some properties of the mannanase complex of the crude enzyme preparation, and of a partially purified α-mannosidase were examined. The mannanase complex exhibited two pH optima, its temperature optimum being at 46 °C The pH optimum of purified α-mannosidase was at pH 5.0, the temperature optimum was at 60 °C; the enzyme had a relatively high heat stability. The K_m of α-mannosidase forp-nitrophenyl α-d-mannopyranoside was 1.5 x 10⁻⁵ M. Pure α-mannosidase did not split mannan.     

Genomic insights on the ethno-history of the Maya and the ‘Ladinos’ from Guatemala

Background

Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs).

Results

Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America.

Conclusions

The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.     

Decaf and the Steeplechase Towards Decaffito—the Coffee from Caffeine-Free Arabica Plants

Unquestionably, the popularity of the coffee beverage relies on its alerting attribute caffeine. However, susceptibilities to this purine alkaloid, quite frequently associated with health concerns, encouraged a significant market for decaffeinated coffee. The beans of Coffea arabica render the best beverage and a decaffeinated coffee has to preserve the desired organoleptic characteristics of this species. Consequently, besides technical removal of caffeine, the endeavors to attain a decaffeinated Arabica coffee range from traditional studies on genetic variability to advanced techniques to produce genetic modified coffee. The aim of this review is to recover part of this subject focusing mainly on the natural genetic variation for caffeine content in Arabica. We also present historical information about caffeine discovery and briefly discuss molecular approaches to reduce caffeine. We introduce here the term decaffito for coffee derived from Arabica plants with beans naturally low in or almost devoid of caffeine. In the near future, coffee drinkers avoiding caffeine will have the choice between basically three Arabica coffees, namely decaffeinated by (a) selection and breeding, (b) genetic modification and (c) industrial extraction. Although only the last decaf coffee is available for the consumers, we believe that the size of the market of each type will occupy in the future depend on the price and health aspects related to the way the decaffeinated coffee beans are obtained.     

Hydromorphology – major results and conclusions from the STAR project

The major results and conclusions of the two papers in the hydromorphology section of the Hydrobiologia special issue on the EU STAR project are summarised. Several key findings have emerged from this research. Firstly, the hydromorphological characteristics of rivers between different geographical regions of Europe were found to vary considerably with rivers in each region possessing distinctive hydromorphological characteristics. Secondly, the hydromorphological attributes that most strongly influence two existing hydromorphological indices (the Habitat Quality Assessment and the Habitat Modification Score) were identified and attention was drawn to the accurate definition and recording of these attributes in field surveys and training courses. Thirdly, links between hydromorphological characteristics and macroinvertebrate quality indices were investigated. Two types of bank modification (resectioning and reinforcement) were significantly correlated with two biotic indices (EPT taxa and MTS), while channel modifications were negatively correlated with ASPT. While biotic indices were often strongly correlated with Habitat Quality Assessment they were less strongly related to Habitat Modification Score suggesting that physical habitat diversity may be more important in determining macroinvertebrate community structure than morphological alteration. The papers in this section provide important underpinning research for the implementation of the European Water Framework Directive. In both papers suggestions are made for further research on the hydromorphology of European rivers.     

Production and localization of cellulases and β-glucosidase from the thermophilic fungusThielavia terrestris

Summary The enzyme production and localization ofThielavia terrestris strains C464 and NRRL 8126 were compared to determine their optimum temperature and pH for cellulase activity. High levels of intracellular -glucosidase activity were detected in the former strain. The intracellular -glucosidase of both strains were more thermostable than the extracellular enzyme; the half life ofT.terrestris (C464) endoglucanase activity at 60°C was greater than 96 hrs.     

Lessons from the past—human and animal thermal physiology

(1) Primordial lesioning and stimulation experiments established a thermoregulatory centre in the rostral brain stem at the end of the 19th century. (2) A major landmark in understanding how deep-body temperature (T_c) is sensed, came in 1912 when Barbour found that changing rostral brain stem temperature inversely raised or lowered T_c, ultimately leading to a mono-centric concept of hypothalamic thermoregulation, prevailing for about 50 years. (3) The discovery of extrahypothalamic sites of temperature signal generation in the 1960s led to the multiple-input, multiple-controller concept of thermoregulation. (4) During the last 40 years, concepts concerning thermosensory specificity have radically changed from viewing bimodal peripheral thermoreceptors and hypothalamic thermoreceptors as the only relevant signal generators towards a complex picture including monomodality of peripheral warm and cold thermoreceptors and multimodality of deep-body thermosensors.     

Where will the wood come from? Plantation forests and the role of biotechnology

Wood is almost as important to humanity as food, and the natural forests from which most of it is harvested from are of enormous environmental value. However, these slow-growing forests are unable to meet current demand, resulting in the loss and degradation of forest. Plantation forests have the potential to supply the bulk of humanity's wood needs on a long-term basis, and so reduce to acceptable limits the harvest pressures on natural forests. However, if they are to be successful, plantation forests must have a far higher yield of timber than their natural counterparts, on much shorter rotation times. To achieve this in reasonable time, biotechnology must be applied to the tree-improvement process, for which large increases in public and private capital investment are needed. However, additional obstacles exist in the form of opposition to plantations, some forest ecocertification schemes, and concerns about aspects of forest biotechnology, especially genetic engineering. It is the intention of this article to explain, in detail, why plantation forests are needed to sustainably meet the world's demand for wood, why they are not being developed fast enough, and why the application of biotechnology to tree improvement is essential to speeding up this process.     

Multispecies biofilms and host responses: “Discriminating the Trees from the Forest”

Periodontal diseases reflect a tissue destructive process of the hard and soft tissues of the periodontium that are initiated by the accumulation of multispecies bacterial biofilms in the subgingival sulcus. This accumulation, in both quantity and quality of bacteria, results in a chronic immunoinflammatory response of the host to control this noxious challenge, leading to collateral damage of the tissues. As knowledge of the characteristics of the host-bacterial interactions in the oral cavity has expanded, new knowledge has become available on the complexity of the microbial challenge and the repertoire of host responses to this challenge. Recent results from the Human Microbiome Project continue to extend the array of taxa, genera, and species of bacteria that inhabit the multiple niches in the oral cavity; however, there is rather sparse information regarding variations in how host cells discriminate commensal from pathogenic species, as well as how the host response is affected by the three-dimensional architecture and interbacterial interactions that occur in the oral biofilms. This review provides some insights into these processes by including existing literature on the biology of nonoral bacterial biofilms, and the more recent literature just beginning to document how the oral cavity responds to multispecies biofilms.     

Mitochondrial and cytosolic hexokinase from rat brain: one and the same enzyme?

Rat brain mitochondrial hexokinase (ATP: D-hexose 6-phosphotransferase, EC 2.7.1.1) was solubilized by treatment of the mitochondria with glucose 6-phosphate and partly purified. The solubilized enzyme was compared with the cytosolic enzyme fraction. The solubilized and cytosolic enzymes were also compared with the enzyme bound to the mitochondrial membrane. The following observations were made. 1. There is no difference in electrophoretic mobility on cellulose-acetate between the cytosolic and the solubilized enzyme. Both fractions are hexokinase isoenzyme I. 2. There is no difference in kinetic parameters between the cytosolic or solubilized enzymes (P less than 0.001). For the cytosolic enzyme Km for glucose was 0.067 mM (S.E. = 0.024, n = 7); Km for MgATP2- was 0.42 mM (S.E. = 0.13, n = 7) and Ki,app for glucose 1,6-diphosphate was 0.084 mM (S.E. = 0.011, n = 5). For the solubilized enzyme Km for glucose was 0.071 mM (S.E. = 0.021, n = 6); Km for MgATP2- was 0.38 mM (S.E. = 0.11, n = 6) and Ki,app for glucose 1,6-diphosphate was 0.074 mM (S.E. = 0.010, n = 5). However when bound to the mitochondrial membrane, the enzyme has higher affinities for its substrates and a lower affinity for the inhibitor glucose 1,6-diphosphate. For the mitochondrial fraction Km for glucose was 0.045 mM (S.E. = 0.013, n = 7); Km for MgATP2- was 0.13 mM (S.E. = 0.02, n = 7) and Ki,app for glucose 1,6-diphosphate was 0.33 mM (S.E. = 0.03, n = 5). 3. The cytosolic and solubilized enzyme could be (re)-bound to depleted mitochondria to the same extent and with the same affinity. Limited proteolysis fully destroyed the enzyme's ability to bind to depleted mitochondria. 4. Our data support the hypothesis that soluble- and solubilizable enzyme from rat brain are one and the same enzyme, and that there is a simple equilibrium between the enzyme in these two pools.     

Purification and separation of the 20S immunoproteasome from the constitutive proteasome and identification of the subunits by LC–MS

The proteasome is a multicatalytic protease complex present in all eukaryotic cells, which plays a critical role in regulating essential cellular processes. During the immune response to pathogens, stimulation by γ interferon induces the production of a special form of proteasome, the immunoproteasome. Inappropriate increase of proteosomal activity has been linked to inflammatory and autoimmune diseases. Selective inhibition of the immunoproteasome specific LMP7 subunit was shown to block inflammatory cytokine secretion in human PBMC, thus making the immunoproteasome an interesting target to fight autoimmune diseases. This paper describes a method for purification and separation of the 20S immunoproteasomes from the constitutive proteasome, which is ubiquitously present in all cells, based on hydrophobic interaction chromatography. The purified immunoproteasome showed several bands, between 20–30 kDa, when subjected to polyacrylamide gel electrophoresis under denaturing conditions. The purified proteasome complexes had a molecular mass of approximately 700 kDa as estimated by gel filtration. Identification of the catalytic subunits in the immunoproteasomes was performed in Western blot with antibodies directed specifically against either the constitutive or the immunoproteasome subunits. The purified immunoproteasome possessed all three protease activities associated with the proteasome complex. LC/MS analysis confirmed the presence of the three immunoproteasome catalytic subunits in the purified immunoproteasome.     

Notes on the Diatomaceae from Ahmedabad and its environs — II

Synopsis In these notes the Diatom community of fountain-reservoirs of the Victoria garden is systematically examined and some remarks on their ecology, occurrence and distribution are given. From the observations and the halobion data available, due to extensive and valuable researches done by Hustedt, Petersen, Foged and others, it is concluded here from the occurrence of Diatom-floral types that the water of these reservoirs have a high chloride-contents. This fact is also corroborated from the water-analysis-data available from the Asstt. Officer-in-charge Public Health Laboratory, Municipal Corporation, Ahmedabad.     

Conceptualization and Measurement of Habitat Fragmentation from the Primates’ Perspective

Habitat fragmentation is one of the principal threats to primates. Studies of primates in fragments usually conclude that fragmentation negatively affects some aspect of their biology or ecology. Nevertheless, the definition and quantification of fragmentation vary considerably among studies, resulting in contradictions and results that are difficult to interpret. We here 1) discuss the problems associated with the definition of habitat fragmentation and the ways of measuring it, 2) emphasize the importance of the concepts and methods from landscape ecology and metapopulation theory for the study of primates in fragmented landscapes, and 3) offer recommendations for more precise use of concepts associated with habitat fragmentation from the primates’ perspective. When specific knowledge of the study species/population is available, we suggest that the definition of the variables to be measured should be functional from the primates’ perspective, based, e.g., on their habitat requirements and dispersal capacity. The distance to the nearest fragment may not be the best way to measure the isolation between populations. Fragmentation per se is a landscape scale process and, hence, landscape scale studies are required to understand how species are distributed across heterogeneous landscapes. Finally, it is important to consider that what happens at the fragment scale could be the consequence of processes that interact at various spatial and temporal scales.     

Hepatic stem cells: from inside and outside the liver?

The liver is normally proliferatively quiescent, but hepatocyte loss through partial hepatectomy, uncomplicated by virus infection or inflammation, invokes a rapid regenerative response from all cell types in the liver to perfectly restore liver mass. Moreover, hepatocyte transplants in animals have shown that a certain proportion of hepatocytes in foetal and adult liver can clonally expand, suggesting that hepatoblasts/hepatocytes are themselves the functional stem cells of the liver. More severe liver injury can activate a potential stem cell compartment located within the intrahepatic biliary tree, giving rise to cords of bipotential transit amplifying cells (oval cells), that can ultimately differentiate into hepatocytes and biliary epithelial cells. A third population of stem cells with hepatic potential resides in the bone marrow; these haematopoietic stem cells may contribute to the albeit low renewal rate of hepatocytes, but can make a more significant contribution to regeneration under a very strong positive selection pressure. In such instances, cell fusion rather than transdifferentiation appears to be the underlying mechanism by which the haematopoietic genome becomes reprogrammed.     

γ-N-Methylasparagine in phycobiliproteins from the cyanobacteria Mastigocladus laminosus and Calothrix

Reinvestigation of the amino acid sequences of all phycobiliproteins from Mastigocladus laminosus showed that there is a post-translationally modified asparagine residue at position 72 of the phycobiliprotein subunits β^PC, β^AP and β^16.2. This residue was identified as γ-N-methylasparagine and it was also found in β^PE of Calothrix. This study also revealed some differences in the amino acid sequences β^AP and β^PC compared to the published data.     

Message from the Editor-in-Chief

The current issue of Acta Biochimica et Biophysica Sinica (ABBS) has turned a new page of this journal since its publication forty five years ago. It is perhaps an appropriate time to share with our readers about the evolution of this journal, the changes that have taken place, and the future that we are looking forward to. ABBS was first established in 1958 with Professor Ying-Lai WANG as the founding Editor-in-Chief and has been ever since an