Increasing liana abundance and biomass in tropical forests: emerging patterns and putative mechanisms

Tropical forests are experiencing large-scale structural changes, the most apparent of which may be the increase in liana (woody vine) abundance and biomass. Lianas permeate most lowland tropical forests, where they can have a huge effect on tree diversity, recruitment, growth and survival, which, in turn, can alter tree community composition, carbon storage and carbon, nutrient and water fluxes. Consequently, increasing liana abundance and biomass have potentially profound ramifications for tropical forest composition and functioning. Currently, eight studies support the pattern of increasing liana abundance and biomass in American tropical and subtropical forests, whereas two studies, both from Africa, do not. The putative mechanisms to explain increasing lianas include increasing evapotranspirative demand, increasing forest disturbance and turnover, changes in land use and fragmentation and elevated atmospheric CO?. Each of these mechanisms probably contributes to the observed patterns of increasing liana abundance and biomass, and the mechanisms are likely to be interrelated and synergistic. To determine whether liana increases are occurring throughout the tropics and to determine the mechanisms responsible for the observed patterns, a widespread network of large-scale, long-term monitoring plots combined with observational and manipulative studies that more directly investigate the putative mechanisms are essential.     

青龙衣中细胞毒活性成分的研究

利用各种化学及色谱技术从青龙衣中分离得到11个化合物,通过理化性质和波谱学手段分别鉴定为2-羟基-1,4-萘醌(2-hydroxy-1,4-naphthoquinone,1)、5-羟基-1,4-萘醌(5-hydroxy-1,4-naphthoquinone,2)、2,5-二羟基-1,4-萘醌(2,5-dihydroxy-1,4-naphthoquinone,3)、3,5-二羟基-1,4-萘醌(2,5-dihydroxy-1,4-naphthoquinone,4)、5,8-二羟基-1,4-萘醌(2,5-dihydroxy-1,4-naphthoquinone,5)、5-甲氧基-1,4-萘醌(5-methoxy-1,4-naphthoquinone,6)、5,7-二羟基色原酮(5,7-dihydroxychromone,7)、异香草酸(isovanillic acid,8)、没食子酸(gallic acid,9)、β-谷甾醇(β-sitosterol,10)和β-胡萝卜苷(β-daucosterol,11)。化合物3、4、6～8为首次从该属植物中分离得到,化合物1为首次从该植物中分离得到。细胞毒活性测试结果表明,化合物3和4对HepG2细胞表现出强的抑制作用,IC50值分别为5.0±0.6μmol/L和7.0±0.5μmol/L;2和5能显著抑制HL-60细胞的增殖,IC50值分别为9.3±1.2μmol/L和2.3±0.2μmol/L。     

Microdissection of Black Widow Spider Silk-producing Glands

Modern spiders spin high-performance silk fibers with a broad range of biological functions, including locomotion, prey capture and protection of developing offspring ^1,2. Spiders accomplish these tasks by spinning several distinct fiber types that have diverse mechanical properties. Such specialization of fiber types has occurred through the evolution of different silk-producing glands, which function as small biofactories. These biofactories manufacture and store large quantities of silk proteins for fiber production. Through a complex series of biochemical events, these silk proteins are converted from a liquid into a solid material upon extrusion.Mechanical studies have demonstrated that spider silks are stronger than high-tensile steel ³. Analyses to understand the relationship between the structure and function of spider silk threads have revealed that spider silk consists largely of proteins, or fibroins, that have block repeats within their protein sequences ⁴. Common molecular signatures that contribute to the incredible tensile strength and extensibility of spider silks are being unraveled through the analyses of translated silk cDNAs. Given the extraordinary material properties of spider silks, research labs across the globe are racing to understand and mimic the spinning process to produce synthetic silk fibers for commercial, military and industrial applications. One of the main challenges to spinning artificial spider silk in the research lab involves a complete understanding of the biochemical processes that occur during extrusion of the fibers from the silk-producing glands.Here we present a method for the isolation of the seven different silk-producing glands from the cobweaving black widow spider, which includes the major and minor ampullate glands [manufactures dragline and scaffolding silk] ^5,6, tubuliform [synthesizes egg case silk] ^7,8, flagelliform [unknown function in cob-weavers], aggregate [makes glue silk], aciniform [synthesizes prey wrapping and egg case threads] ⁹ and pyriform [produces attachment disc silk] ¹⁰. This approach is based upon anesthetizing the spider with carbon dioxide gas, subsequent separation of the cephalothorax from the abdomen, and microdissection of the abdomen to obtain the silk-producing glands. Following the separation of the different silk-producing glands, these tissues can be used to retrieve different macromolecules for distinct biochemical analyses, including quantitative real-time PCR, northern- and western blotting, mass spectrometry (MS or MS/MS) analyses to identify new silk protein sequences, search for proteins that participate in the silk assembly pathway, or use the intact tissue for cell culture or histological experiments.     

The intact structural form of LLO in endosomes cannot protect against listeriosis

LLO is the major immuno-dominant antigen in listeriosis and is also required for protective immunity. Two forms of LLO can be observed in endosomal membranes, a LLO intact form and a Ctsd-processed LLO_1-491 form. Endosomes obtained from resting macrophages contained only LLO intact forms, while endosomes obtained from IFN-activated macrophages contained both forms. Both types of endosomes elicited LLO_90-91/CD8⁺ and LLO_189-201/CD4⁺ specific immune responses. However, only endosomes containing the Ctsd-processed LLO_1-491 form showed significant CD4⁺ and CD8⁺ T cell responses similar to LM infected bone marrow derived macrophages and characteristic of protective Listeria immunity. Moreover, endosomes with intact LLO could not confer protection as vaccine carriers against murine listeriosis. While endosomes with Ctsd-processed LLO_1-491 form showed a moderate ability, slightly lower than high efficiency vaccine vectors as MØ infected with LM. These studies argue that all cell-free membrane vesicles might serve as valid vaccine carriers against infectious agents. Exclusively those cell-free vesicles MIIC competent for LLO processing are protective vaccines vectors since they recruit significant numbers of mature dendritic cells to the vaccination sites and contain a LLO_1-491 form that might be accessible for MHC class I and class II antigen presentation.     

The taphonomy of colour in fossil insects and feathers

Colouration is an important multifunctional attribute of modern animals, but its evolutionary history is poorly resolved, in part because of our limited ability to recognize and interpret fossil evidence of colour. Recent studies on structural and pigmentary colours in fossil insects and feathers have illuminated important aspects of the anatomy, taphonomy, evolution and function of colour in these fossils. An understanding of the taphonomic factors that control the preservation of colour is key to assessing the fidelity with which original colours are preserved and can constrain interpretations of the visual appearance of fossil insects and theropods. Various analytical approaches can identify anatomical and chemical evidence of colour in fossils; experimental taphonomic studies inform on how colour alters during diagenesis. Preservation of colour is controlled by a suite of factors, the most important of which relate to the diagenetic history of the host sediment, that is, maximum burial temperatures and fluid flow, and subsurface weathering. Future studies focussing on key morphological and chemical aspects of colour preservation relating to cuticular pigments in insects and keratinous structures and nonmelanin pigments in feathers, for example, will resolve outstanding questions regarding the taphonomy of colour and will enhance our ability to infer original colouration and its functions in fossil insects and theropods.     

Hofmeister ions control protein dynamics

Background

Recently, we have elaborated a thermodynamic theory that could coherently interpret the diverse effects of Hofmeister ions on proteins, based on a single physical parameter, the protein–water interfacial tension (Dér et al., Journal of Physical Chemistry B. 2007, 111, 5344–5350). This theory, implying a “liquid drop model”, predicts changes in protein conformational fluctuations upon addition of Hofmeister salts (containing either kosmotropic or chaotropic anions) to the medium.

Methods

Here, we report experimental tests of this prediction using a complex approach by applying methods especially suited for the detection of protein fluctuation changes (neutron scattering, micro-calorimetry, and Fourier-transform infrared spectroscopy).

Results

It is demonstrated that Hofmeister salts, via setting the hydrophobic/hydrophilic properties of the protein–water interface, control conformational fluctuations even in the interior of the typical membrane transport protein bacteriorhodopsin, around its temperature-induced, unusual α(II) → α(I) conformational transition between 60 and 90 °C. We found that below this transition kosmotropic (COOCH₃⁻), while above it chaotropic (ClO₄⁻) anions increase structural fluctuations of bR. It was also shown that, in each case, an onset of enhanced equilibrium fluctuations presages this phase transition in the course of the thermotropic response of bR.

Conclusions

These results are in full agreement with the theory, and demonstrate that predictions based on protein–water interfacial tension changes can describe Hofmeister effects and interpret protein dynamics phenomena even in unusual cases.

General significance

This approach is expected to provide a useful guide to understand the principles governing the interplay between protein interfacial properties and conformational dynamics, in general.     

Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations

Whole chromosomal and segmental uniparental disomy (UPD) is one of the causes of imprinting disorder and other recessive disorders. Most investigations of UPD were performed only using cases with relevant phenotypic features and included few markers. However, the diagnosis of cases with segmental UPD requires a large number of molecular investigations. Currently, the accurate frequency of whole chromosomal and segmental UPD in a normal developing embryo is not well understood. Here, we present whole chromosome and segmental UPD analysis using single nucleotide polymorphism (SNP) microarray data of 173 mother-father-child trios (519 individuals) from six populations (including 170 HapMap trios). For two of these trios, we also investigated the possibility of shorter segmental UPD as a consequence of homologous recombination repair (HR) for DNA double strand breaks (DSBs) during the early developing stage using high-coverage whole-genome sequencing (WGS) data from 1000 Genomes Project. This could be overlooked by SNP microarray. We identified one obvious segmental paternal uniparental isodisomy (iUPD) (8.2 mega bases) in one HapMap sample from 173 trios using Genome-Wide Human SNP Array 6.0 (SNP6.0 array) data. However, we could not identify shorter segmental iUPD in two trios using WGS data. Finally, we estimated the rate of segmental UPD to be one per 173 births (0.578%) based on the UPD screening for 173 trios in general populations. Based on the autosomal chromosome pairs investigated, we estimate the rate of segmental UPD to be one per 3806 chromosome pairs (0.026%). These data imply the possibility of hidden segmental UPD in normal individuals.     

HSM — a hybrid system based approach for modelling intracellular networks

The paper proposes a hybrid system based approach for modelling of intracellular networks and introduces a restricted subclass of hybrid systems – HSM – with an objective of still being able to provide sufficient power for the modelling of biological systems, while imposing some restrictions that facilitate analysis of systems described by such models.     

Sequence Effects On The Propeller Twist Of Base Pairs In DNA Helices

Abstract

Molecular mechanics calculations are performed on all the ten base pair steps (duplex dimers) and also a number of trimer and tetramer duplexes comprising them, in an attempt to systematically examine the possible base sequence effects on the magnitudes of propeller twists of base pairs at a given step. The analysis reveals that though propeller twist is a base pair property, it behaves very much like other base step parameters such as slide, roll, twist etc., Hence, it may be necessary to monitor the nature and variation of magnitudes of pt at a step. Calculations performed on 45 out of the 136 unique tetramer combinations involving all the ten unique base steps show that the difference in magnitudes of propeller twists of the base pairs of a given step has been found to be either steep or moderate depending on base pairs that flank the base step. These observations compare very well with the available experimental data. Tetramer sequences, wherein abase pair of a base step repeats in the same direction, exhibit a relatively steep difference in propeller twist at the step. Tetramers other than these exhibit moderate difference in propeller twist Such sequences are broadly classified as type-I and type-II respectively. Practically all the tetrads considered in the study, excepting those with GT step and a few involving CG and GC steps, conform to the above classification.