Localization of human cardiac beta-myosin heavy chain gene (MYH7) to chromosome 14q12 by in situ hybridization

The genes coding for each human cardiac myosin heavy chain (alpha-MHC and beta-MHC, MYH6 and MYH7, respectively) are tightly linked and the alpha-MHC gene has been assigned to chromosome 14. In order to provide a more precise regional localization, in situ hybridization experiments were carried out using a 3H-labeled probe derived from a beta-MHC genomic clone. The results demonstrated that the human cardiac MHC genes are located within the q12 band of chromosome 14.     

Mapping and sequence-specific identification of phosphopeptides in unfractionated protein digest mixtures by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

We have demonstrated a procedure for the rapid (minutes), sensitive (less than pmol), and sequence-specific identification of phosphopeptides in unfractionated digests of phosphoproteins using matrix-assisted UV laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. The mass-dependent identification of one specific 13-residue phosphopeptide (S105-K117), observed among the 153 possible trypsin digest fragments of human beta-casein (211 residues), was confirmed by amino acid sequence analysis of the 33P-labeled peptide after isolation by reverse-phase HPLC. MALDI-TOF was also used to monitor the rate and extent to which an 18-residue N-terminal beta-casein peptide (R1-K18) was phosphorylated in vitro. These results demonstrate that MALDI-TOF may be used (i) to facilitate the identification of sequence-specific sites of protein phosphorylation and dephosphorylation, (ii) to monitor protein and peptide phosphorylation and dephosphorylation reaction rates, even in complex unfractionated mixtures, (iii) to determine the minimum primary structure necessary for the phosphorylation of specific protein surface domains, and (iv) to evaluate the effects of intact protein phosphorylation and dephosphorylation on susceptibility to subsequent proteolytic events.     

The minimum capture proportion for reliable estimation in capture-recapture models.

We derive estimates of the minimum capture proportion required to obtain a reliable estimate of the population size for several continuous and discrete-time capture-recapture models. The models considered are M(0), M(t), M(b), M(h), M(ht), and M(tb) in the notation of Otis et al., (1978, Wildlife Monograph62, 1-135). Numerical results with simulation studies are given, and two real examples for the model M(h) are also considered. Potential applications of these results are suggested.     

Fatty acid as markers to demonstrating trophic relationships among diatoms, rotifers and green-lipped mussels

Green-lipped mussels Perna viridis, collected from Peng Chau, Hong Kong were allotted into two treatment groups, each containing three experimental tanks. The first treatment group comprised of mussels fed with the diatom Thalassiosira pseudonana only, whereas the second treatment group contained mussels fed with the marine rotifer Brachionus plicatilis, which was in turn fed with diatom T. pseudonana. The mussels were fed two times each day over the experimental period of 14 days. On Days 4, 7 and 14, three mussels were collected from each tank of each treatment group and treated as a single replicate. Fatty acid profiles of diatoms, marine rotifers and the three organs (digestive gland, mantle margin and adductor muscle) of the two mussel groups were analyzed. Results showed that monosaturated fatty acid (MUFA) 16:1n7 was conserved along the food chain among diatoms, marine rotifers and green-lipped mussels. This suggested that 16:1n7 or the ratio of 16:1n7 to saturated fatty acid (SFA) 16:0 can be a trophic marker for diatom T. pseudonana and elevated amounts of 16:1n7 in mussels can reflect the dominance of diatoms in its diet. The present results also showed that rotifers could accumulate MUFA 18:1n7 and PUFA 20:4n6 which were transferred up to mussels, especially 18:1n7, as zooplankton have the ability to synthesize or actively accumulate certain fatty acids that they need for growth or reproduction. There was an increase in the amount of 18:1n7 in the digestive gland of mussels fed with rotifers but the level of this fatty acid remained unchanged in those fed with diatoms, further confirming that 18:1n7 can be used as a marker for the presence of rotifers in trophic relationship studies. The relatively faster responses in the digestive gland of mussels to acquire the fatty acid signatures from their food suggested that the fatty acid profiles in the digestive gland can be a good marker to show a short-term fluctuation of food conditions in the marine environment.     

Protein interactions with immobilized transition metal ions: quantitative evaluations of variations in affinity and binding capacity

The interaction of proteins with immobilized transition-metal ions proceeds via mechanisms influenced by metal type and degree of coordination, variations in mobile phase constituents, and protein surface architecture at or near the metal binding site(s). The contributions each of these variables make toward the affinity of protein surfaces for immobilized metal ions remain empirical. We have used equilibrium binding analyses to evaluate the influence of pH and competitive binding reagents on the apparent equilibrium dissociation constant (Kd) and binding capacity of immobilized Cu(II) and Ni(II) ions for several model proteins of known three-dimensional structure. Linear Scatchard plots suggested that 8/13 of the proteins evaluated interacted with immobilized metal ions via a single class of operational (Kd = 10-700 microM) binding sites. Those proteins with the highest affinities for the immobilized Cu(II) ions (5/13) showed evidence of multiple, non-identical or nonindependent binding sites. The effects of altered metal type, pH, and concentration of competitive affinity reagents (e.g., imidazole, free metal ions) on the apparent Kd and binding capacity varied in magnitude for individual proteins. The presence of free Cu(II) ions did not detectably alter either the affinity or binding capacity of the proteins for immobilized Cu(II) ions. The expected relationship between the relative chromatographic elution sequence and calculated affinity constants was not entirely evident by evaluation under only one set of conditions. Our results demonstrate the utility of nonchromatographic equilibrium binding analyses for the quantitative evaluation of experimental variables affecting the relative affinity and capacity of immobilized metal ions for proteins. This approach affords the opportunity to improve understanding and to vary the contribution of interaction mechanisms involved.     

Assessment of the safety of the cationic arginine-rich peptides (CARPs) poly-arginine-18 (R18 and R18D) in ex vivo models of mast cell degranulation and red blood cell hemolysis

Our laboratory focuses on the development of novel neuroprotective cationic peptides, such poly-arginine-18 (R18: 18-mer of l-arginine; net charge +18) and its d-enantiomer R18D in stroke and other brain injuries. In the clinical development of R18/R18D, their cationic property raises potential safety concerns on their non-specific effects to induce mast cell degranulation and hemolysis. To address this, we first utilised primary human cultured mast cells (HCMCs) to examine anaphylactoid effects. We also included as controls, the well-characterised neuroprotective TAT-NR2B9c peptide and the widely used heparin reversal peptide, protamine. Degranulation assay based on β-hexosaminidase release demonstrated that R18 and R18D did not induce significant mast cell degranulation in both untreated (naïve) and IgE-sensitised HCMCs in a dose-response study to a maximum peptide concentration of 16 μM. Similarly, TAT-NR2B9c and protamine did not induce significant mast cell degranulation. To examine hemolytic effects, red blood cells (RBCs), were incubated with the peptides at a concentration range of 1–16 μM in the absence or presence of 2% plasma. Measurement of hemoglobin absorbance revealed that only R18 induced a modest, but significant degree of hemolysis at the 16 μM concentration, and only in the absence of plasma. This study addressed the potential safety concern of the application of the cationic neuroprotective peptides, especially, R18D, on anaphylactoid responses and hemolysis. The findings indicate that R18, R18D, TAT-NR2B9c and protamine are unlikely to induce histamine mediated anaphylactoid reactions or RBC hemolysis when administered intravenously to patients.     

Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic,oligotrophic, low‐pH geothermal ecosystem

Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near‐surface temperatures at sub‐meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50–52 °C, but temperatures reach 93 °C locally. We extracted DNA from water and sediments collected from warm (52 °C) and hot (73–83 °C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5‐year time span, indicating a stable community with little inter‐annual variation, despite the documented seasonal temperature cycle. BSL water‐derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle.