Geographical isolation in hot spring cyanobacteria

It has been proposed that free-living microorganisms exhibit ubiquitous dispersal, do not form geographically isolated populations and rarely (if ever) speciate via allopatry. We studied island-like hot spring cyanobacterial communities in which geographical isolation should be prominent and detectable if it influences the evolution of bacteria. The genetic diversity of cyanobacteria indigenous to North American, Japanese, New Zealand and Italian springs was surveyed by (i) amplification and cloning of 16S rRNA and 16S-23S internal transcribed spacer regions; (ii) lineage-specific oligonucleotide probing (used to verify the predominance of cloned sequences); and (iii) lineage-specific polymerase chain reaction (PCR) (used to search for possible rare genotypes). Phylogenetic and distribution patterns were found to be consistent with the occurrence of geographical isolation at both global and local spatial scales, although different cyanobacterial lineages were found to vary in their distribution. A lack of correspondence between biological patterning and the chemical character of springs sampled suggested that the geographical distribution of thermophilic cyanobacteria cannot be explained by the 20 potential niche-determining chemical parameters that we assayed. Thus, geographical isolation (i.e. genetic drift) must in part be responsible for driving the observed evolutionary divergences. Geographical isolation may be an important underestimated aspect of microbial evolution.     

Synthesis and evaluation of novel oxazoline MMP inhibitors

MMP inhibitors with novel oxazoline zinc binding groups have been synthesized and evaluated. Selectivity for the inhibition of MMP-9 over MMP-1, MMP-2, and MMP-12 has been achieved in several cases.     

Mitogen activated protein kinase at the nuclear pore complex

Mitogen activated protein (MAP) kinases control eukaryotic proliferation, and import of kinases into the nucleus through the nuclear pore complex (NPC) can influence gene expression to affect cellular growth, cell viability and homeostatic function. The NPC is a critical regulatory checkpoint for nucleocytoplasmic traffic that regulates gene expression and cell growth, and MAP kinases may be physically associated with the NPC to modulate transport. In the present study, highly enriched NPC fractions were isolated and investigated for associated kinases and/or activity. Endogenous kinase activity was identified within the NPC fraction, which phosphorylated a 30 kD nuclear pore protein. Phosphomodification of this nucleoporin, here termed Nup30, was inhibited by apigenin and PD‐98059, two MAP kinase antagonists as well as with SB‐202190, a pharmacological blocker of p38. Furthermore, high throughput profiling of enriched NPCs revealed constitutive presence of all members of the MAP kinase family, extracellular regulated kinases (ERK), p38 and Jun N‐terminal kinase. The NPC thus contains a spectrum of associated MAP kinases that suggests an intimate role for ERK and p38 in regulation of nuclear pore function.     

TGF-beta1 calcium signaling in osteoblasts

Transforming growth factor-beta1 (TGF-beta1) action is known to be initiated by its binding to multiple cell surface receptors containing serine/threonine kinase domains that act to stimulate a cascade of signaling events in a variety of cell types. We have previously shown that TGF-beta1 and BMP-2 treatment of primary human osteoblasts (HOBs) enhances cell-substrate adhesion. In this report, we demonstrate that TGF-beta1 elicits a rapid, transient, and oscillatory rise in the intracellular Ca(2+) concentration, [Ca(2+)](i), that is necessary for enhancement of cell adhesion in HOBs but does not alter the phosphorylation state of Smad proteins. This rise in [Ca(2+)](i) in HOB is not observed in the absence of extracellular calcium or when the cells are treated with the L-type Ca(2+) channel blocker, nifedipine, but is stimulated upon treatment with the L-type Ca(2+) channel agonist, Bay K 8644, or under high K(+) conditions. The rise in [Ca(2+)](i) is severely attenuated after treatment of the cells with thapsigargin, a selective endoplasmic reticulum Ca(2+) pump inhibitor. TGF-beta1 enhancement of HOB adhesion to tissue culture polystyrene is also inhibited in cells treated with nifedipine. These data suggest that intracellular Ca(2+) signaling is an important second messenger of the TGF-beta1 signal transduction pathway in osteoblast function.     

Phage evolution: new worlds of genomic diversity

A recent comparative survey of genomes of phages infecting mycobacteria reveals a vast combinatorial network of gene rearrangements and may provide general models for pattern and process in genome evolution.     

Fish Rejections in the Marine Aquarium Trade: An Initial Case Study Raises Concern for Village-Based Fisheries

A major difficulty in managing wildlife trade is the reliance on trade data (rather than capture data) to monitor exploitation of wild populations. Collected organisms that die or are rejected before a point of sale often go unreported. For the global marine aquarium trade, identifying the loss of collected fish from rejection, prior to export, is a first step in assessing true collection levels. This study takes a detailed look at fish rejections by buyers before export using the Papua New Guinea marine aquarium fishery as a case study. Utilizing collection invoices detailing the species and quantity of fish (Actinopteri and Elasmobranchii) accepted or rejected by the exporting company it was determined that, over a six month period, 24.2% of the total fish catch reported (n = 13,886) was rejected. Of the ten most collected fish families, rejection frequency was highest for the Apogonidae (54.2%), Chaetodontidae (26.3%), and Acanthuridae (18.2%) and lowest for Labridae (6.6%) and Hemiscylliidae (0.7%). The most frequently cited reasons for rejection were fin damage (45.6% of cases), undersized fish (21.8%), and fish deemed too thin (11.1%). Despite fishers receiving feedback on invoices explaining rejections, there was no improvement in rejection frequencies over time (r = -0.33, P = 0.15) with weekly rejection frequencies being highly inconsistent (range: 2.8% to 79.4%; s = 16.3%). These findings suggest that export/import statistics can greatly underestimate collection for the marine aquarium trade as additional factors such as fisher discards, escapees, post-collection mortalities, and unregulated domestic trade would further contribute to this disparity.     

Sound representation methods for spectro-temporal receptive field estimation

The spectro-temporal receptive field (STRF) of an auditory neuron describes the linear relationship between the sound stimulus in a time-frequency representation and the neural response. Time-frequency representations of a sound in turn require a nonlinear operation on the sound pressure waveform and many different forms for this non-linear transformation are possible. Here, we systematically investigated the effects of four factors in the non-linear step in the STRF model: the choice of logarithmic or linear filter frequency spacing, the time-frequency scale, stimulus amplitude compression and adaptive gain control. We quantified the goodness of fit of these different STRF models on data obtained from auditory neurons in the songbird midbrain and forebrain. We found that adaptive gain control and the correct stimulus amplitude compression scheme are paramount to correctly modelling neurons. The time-frequency scale and frequency spacing also affected the goodness of fit of the model but to a lesser extent and the optimal values were stimulus dependant. Action Editor: Israel Nelken     

Nucleoside and Oxypurine Homeostasis in Adult Rabbit Cerebrospinal Fluid and Plasma

Abstract: In adult New Zealand white rabbits, the effects of food deprivation and of massive elevations of plasma uridine or thymidine concentrations on CSF and plasma nucleoside and oxypurine concentrations were studied. Nucleoside and oxypurine levels were determined by high performance liquid chromatography using unequivocal methods of compound identification. After 48 and 96 h of food deprivation, the concentrations of uridine, cytidine, inosine, thymidine, deoxycytidine, deoxyuridine, hypoxanthine, xanthine, and uric acid in CSF and plasma were not different than in controls, except at 96 h, when the plasma uridine concentration was 35% lower (p < 0.05). After elevation of the plasma and CSF thymidine concentrations to ∼200 and 100 μM, respectively, with intravenous thymidine for 5 h, there was a large increase in CSF and plasma thymine to ∼100 μM and a smaller increase in plasma and CSF deoxyuridine concentrations. After elevation of the plasma and CSF uridine concentrations to 0.6 and 0.2 mM, respectively, there was a large increase in CSF and plasma uracil and a smaller increase in plasma and CSF deoxyuridine concentrations. Elevated plasma concentration of thymidine and uridine significantly decreased the CSF to plasma ratios of deoxyuridine and thymidine; however, only elevated plasma uridine concentrations decreased the CSF to plasma ratio of uridine. These results document the powerful homeostatic mechanisms that regulate the concentrations of the principal nucleosides and oxypurine bases in CSF.