The possible role of soluble salts in chemical evolution

Summary A model is proposed for a prebiotic environment in which concentration, condensation, and chemical evolution of biomolecules could have taken place. The main reactions expected of proteins, nucleic acids, lipids, and some of their precursors in this environment are examined.The model is based on our previously developed concept of a fluctuating system in which hydration and dehydration processes take place in a cyclic manner. In the present model, however, high concentrations of soluble salts, such as chlorides and sulfates, are taken into account, whereas previously a more or less salt-free system had been assumed. Thus the preponderance of surfaces of soluble salts is implied, even though sparingly soluble minerals, such as clay minerals or quartz, are also present.During the dehydration stage biomolecules tend to leave the solution and concentrate at certain microenvironments, such as in micelles and aggregates, at the liquid-gas surface and, possibly, at the emerging solid surfaces. Moreover, in these brines, and especially during the last stages of dehydration, high temperatures are attainable, which may enhance certain reactions between the organic molecules, and result in a net increase of condensation over degradation.In the dehydrated state, solid-state condensation and synthesis reactions are possible in which the surface of soluble salts may serve as a catalyst. Several reports in the literature support this hypothesis. Hydration brings about dissolution of the minerals and redistribution of the biomolecules. In such a system, evolutionary processes like those postulated by White (1980) and by Lahav and White (1980) are possible. Moreover, since several soluble salts of known geological occurrence are optically active in their crystalline state, the involvement of the model system in the selection and evolution of chiral organic compounds should also be considered. In addition, organic molecules in the above microenvironments are also expected to undergo selective interactions based on factors such as molecular pattern and chiral recognition and hydrophobicity. The proposed system emphasizes the need to develop the theoretical background and experimental methods for the study of interactions among biomolecules in the presence of high salt concentrations and solid surfaces of soluble salts, as well as interactions between the biomolecules and these surfaces.     

Can we predict butterfly diversity along an elevation gradient from space?

An important challenge in ecology is to predict patterns of biodiversity across eco‐geographical gradients. This is particularly relevant in areas that are inaccessible, but are of high research and conservation value, such as mountains. Potentially, remotely‐sensed vegetation indices derived from satellite images can help in predicting species diversity in vast and remote areas via their relationship with two of the major factors that are known to affect biodiversity: productivity and spatial heterogeneity in productivity. Here, we examined whether the Normalized Difference Vegetation Index (NDVI) can be used effectively to predict changes in butterfly richness, range size rarity and beta diversity along an elevation gradient. We examined the relationship between butterfly diversity and both the mean NDVI within elevation belts (a surrogate of productivity) and the variability in NDVI within and among elevation belts (surrogates for spatial heterogeneity in productivity). We calculated NDVI at three spatial extents, using a high spatial resolution QuickBird satellite image. We obtained data on butterfly richness, rarity and beta diversity by field sampling 100 m quadrats and transects between 500 and 2200 m in Mt Hermon, Israel. We found that the variability in NDVI, as measured both within and among adjacent elevation belts, was strongly and significantly correlated with butterfly richness. Butterfly range size rarity was strongly correlated with the mean and the standard deviation of NDVI within belts. In our system it appears that it is spatial heterogeneity in productivity rather than productivity per se that explained butterfly richness. These results suggest that remotely‐sensed data can provide a useful tool for assessing spatial patterns of butterfly richness in inaccessible areas. The results further indicate the importance of considering spatial heterogeneity in productivity along elevation gradients, which has no lesser importance than productivity in shaping richness and rarity, especially at the local scale.     

Crystallization of dimers of the manganese-stabilizing protein of Photosystem II

The manganese-stabilizing protein (MSP) of Photosystem II was purified from spinach photosynthetic membranes. The MSP was crystallized in the presence of calcium. Despite the apparent purity of the isolated protein, the crystals grew to only about 0.05 mm in their largest dimension. The MSP was analyzed to identify possible sources of protein heterogeneity that could hinder crystal growth. Tandem reverse-phase HPLC/ electronspray ionization mass spectrometry analysis of the MSP showed a major peak and four smaller peaks. All five peaks had molecular masses of 26 535, as expected for mature MSP, indicating the absence of heterogeneities due to covalent modifications. MALDI mass spectroscopy was utilized to identify heterogeneities in the MSP oligomeric state. These measurements showed that purified MSP in solution is a mixture of monomers and dimers, while solubilized MSP crystals contained only dimers. Size-exclusion chromatography and dynamic light scattering were used to probe the effect of the crystallization conditions on the MSP. Size-exclusion chromatography of concentrated MSP showed the presence of aggregates and monomers, while dilute MSP contained monomers. Dynamic light scattering experiments in the absence, or in the presence of 10–50 mM or 100 mM calcium, yielded calculated molecular mass values of 34 kDa, 48 kDa and 68 kDa, respectively. These changes in the observed molecular mass of the MSP could have been caused by the formation of dimers and higher oligomers and/or significant conformational changes. Based on the results reported in this study, a model is presented which details the effect of oligomeric heterogeneity on the inhibition of MSP crystal growth. This revised version was published online in June 2006 with corrections to the Cover Date.     

From Schooling to Shoaling: Patterns of Collective Motion in Zebrafish (Danio rerio)

Animal groups on the move can take different configurations. For example, groups of fish can either be ‘shoals’ or ‘schools’: shoals are simply aggregations of individuals; schools are shoals exhibiting polarized, synchronized motion. Here we demonstrate that polarization distributions of groups of zebrafish (Danio rerio) are bimodal, showing two distinct modes of collective motion corresponding to the definitions of shoaling and schooling. Other features of the group''s motion also vary consistently between the two modes: zebrafish schools are faster and less dense than zebrafish shoals. Habituation to an environment can also alter the proportion of time zebrafish groups spend schooling or shoaling. Models of collective motion suggest that the degree and stability of group polarization increases with the group''s density. Examining zebrafish groups of different sizes from 5 to 50, we show that larger groups are less polarized than smaller groups. Decreased fearfulness in larger groups may function similarly to habituation, causing them to spend more time shoaling than schooling, contrary to most models'' predictions.     

2-Aminoethoxydiphenyl-borate (2-APB) increases excitability in pyramidal neurons

Calcium ions (Ca²⁺) released from inositol trisphosphate (IP₃)-sensitive intracellular stores may participate in both the transient and extended regulation of neuronal excitability in neocortical and hippocampal pyramidal neurons. IP₃ receptor (IP₃R) antagonists represent an important tool for dissociating these consequences of IP₃ generation and IP₃R-dependent internal Ca²⁺ release from the effects of other, concurrently stimulated second messenger signaling cascades and Ca²⁺ sources. In this study, we have described the actions of the IP₃R and store-operated Ca²⁺ channel antagonist, 2-aminoethoxydiphenyl-borate (2-APB), on internal Ca²⁺ release and plasma membrane excitability in neocortical and hippocampal pyramidal neurons. Specifically, we found that a dose of 2-APB (100 μM) sufficient for attenuating or blocking IP₃-mediated internal Ca²⁺ release also raised pyramidal neuron excitability. The 2-APB-dependent increase in excitability reversed upon washout and was characterized by an increase in input resistance, a decrease in the delay to action potential onset, an increase in the width of action potentials, a decrease in the magnitude of afterhyperpolarizations (AHPs), and an increase in the magnitude of post-spike afterdepolarizations (ADPs). From these observations, we conclude that 2-APB potently and reversibly increases neuronal excitability, likely via the inhibition of voltage- and Ca²⁺-dependent potassium (K⁺) conductances.     

Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus

Precursor-mRNA splicing removes the introns and ligates the exons to form a mature mRNA. This process is carried out in a spliceosomal complex containing >150 proteins and five small nuclear ribonucleoproteins. Splicing protein hSlu7 is required for correct selection of the 3' splice site. Here, we identify by bioinformatics and mutational analyses three functional domains of the hSlu7 protein that have distinct roles in its subcellular localization: a nuclear localization signal, a zinc-knuckle motif, and a lysine-rich region. The zinc-knuckle motif is embedded within the nuclear localization signal in a unique functional structure that is not required for hSlu7's entrance into the nucleus but rather to maintain hSlu7 inside it, preventing its shuttle back to the cytoplasm via the chromosomal region maintenance 1 pathway. Thus, the zinc-knuckle motif of hSlu7 determines the cellular localization of the protein through a nucleocytoplasmic-sensitive shuttling balance. Altogether, this indicates that zinc-dependent nucleocytoplasmic shuttling might be the possible molecular basis by which hSlu7 protein levels are regulated within the nucleus.     

HIV-specific CD8+ T cell function in children with vertically acquired HIV-1 infection is critically influenced by age and the state of the CD4+ T cell compartment

The immunology of vertical HIV transmission differs from that of adult infection in that the immune system of the infant is not fully matured, and the factors that influence the functionality of CD8(+) T cell responses against HIV in children remain largely undefined. We have investigated CD8(+) T cell responses in 65 pediatric subjects with vertically acquired HIV-1 infection. Vigorous, broad, and Ag dose-driven CD8(+) T cell responses against HIV Ags were frequently observed in children who were older than 3 years of age and maintained CD4(+) T cell counts >400 cells/ micro l. In contrast, younger age or a CD4(+) T cell count <400 cells/ micro l was associated with poor CD8(+) T cell responses and high HIV loads. Furthermore, subjects with a severely depleted and phenotypically altered CD4(+) T cell compartment had circulating Gag-specific CD8(+) T cells with impaired IFN-gamma production. When viral load was not suppressed by antiviral treatment, subjects that fell below the putative age and CD4(+) T cell count thresholds had significantly reduced CD8(+) T cell responses and significantly higher viral loads. Thus, the data suggest that fully effective HIV-specific CD8(+) T cell responses take years to develop despite an abundance of Ag in early life, and responses are further severely impaired, independent of age, in children who have a depleted or skewed CD4(+) T cell compartment. The results are discussed in relation to differences between the neonatal and adult immune systems in the ability to respond to HIV infection.     

PANDORA: keyword-based analysis of protein sets by integration of annotation sources

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.     

miR-192 Directly Binds and Regulates Dicer1 Expression in Neuroblastoma

Neuroblastoma (NB) arises from the embryonic neural crest and is the most common extracranial solid tumor in children under 5 years of age. Reduced expression of Dicer1 has recently been shown to be in correlation with poor prognosis in NB patients. This study aimed to investigate the mechanisms that could lead to the down-regulation of Dicer1 in neuroblastoma. We used computational prediction to identify potential miRs down-regulating Dicer1 in neuroblastoma. One of the miRs that were predicted to target Dicer1 was miR-192. We measured the levels of miR-192 in 43 primary tumors using real time PCR. Following the silencing of miR-192, the levels of dicer1 cell viability, cell proliferation and migration capability were analyzed. Multivariate analysis identified miR-192 as an independent prognostic marker for relapse in neuroblastoma patients (p=0.04). We were able to show through a dual luciferase assay and side-directed mutational analysis that miR-192 directly binds the 3'' UTR of Dicer1 on positions 1232-1238 and 2282-2288. An increase in cell viability, proliferation and migration rates were evident in NB cells transfected with miR-192-mimic. Yet, there was a significant decrease in proliferation when NB cells were transfected with an miR-192-inhibitor We suggest that miR-192 might be a key player in NB by regulating Dicer1 expression.