Identification of the ubiquitin interfacial residues in a ubiquitin-E2 covalent complex

One of the key intermediates formed during the protein ubiquitination cycle is a covalent complex between ubiquitin (Ub) and the conjugation enzyme, UBC1. In order to probe the interface between these two proteins we have formed the covalent complex in situ (in the NMR tube) using Ub, the catalytic domain of UBC1, UBC1450, an activation enzyme, E1, and Mg²⁺-ATP. The size of the Ub-UBC1450 complex (25 kDa) and its relatively short lifetime ( 4 h) makes assignment of the backbone resonances in the covalent species difficult. In order to monitor the formation and identify the interface in the complex we have used fast ¹H-¹⁵N HSQC spectra to monitor the decay of ¹H-¹⁵N correlations as a function of time until the complex formed reached about 90%. The residual peak intensities were used to probe the surface of interaction between Ub and UBC1450 and provided a clear surface of interaction on Ub.     

The assembly of an H2A2,H2B2,H3,H4 hexamer onto DNA under conditions of physiological ionic strength

A novel nucleohistone particle is generated in high yield when a complex of DNA with the four core histones formed under conditions that are close to physiological (0.15 M NaCl, pH 8) is treated with micrococcal nuclease. The particle was found to contain 102 base pairs of DNA in association with six molecules of histones in the ratio 2H2A:2H2B:1H3:1H4 after relatively brief nuclease treatment. Prolonged nuclease digestion resulted in a reduction in the DNA length to a sharply defined 92-base pair fragment that was resistant to further degradation. Apparently normal nucleosome core particles containing two molecules each of the four core histones in association with 145 base pairs of DNA and a particle containing one molecule each of histones H2A and H2B in association with approximately 40 base pairs of DNA were also generated during nuclease treatment of the histone-DNA complexes formed under physiological ionic strength conditions. Kinetic studies have shown that the hexamer particle is not a subnucleosomal fragment produced by the degradation of nucleosome core particles. Furthermore, the hexamer particle was not found among the products of nuclease digestion when histones and DNA were previously assembled in 0.6 M NaCl. The high sedimentation coefficient of the hexameric complex (8 S) suggests that the DNA component of the particle has a folded conformation.     

A scientific basis for restoring fish spawning habitat in the St. Clair and Detroit Rivers of the Laurentian Great Lakes

Loss of functional habitat in riverine systems is a global fisheries issue. Few studies, however, describe the decision‐making approach taken to abate loss of fish spawning habitat. Numerous habitat restoration efforts are underway and documentation of successful restoration techniques for spawning habitat of desirable fish species in large rivers connecting the Laurentian Great Lakes are reported here. In 2003, to compensate for the loss of fish spawning habitat in the St. Clair and Detroit Rivers that connect the Great Lakes Huron and Erie, an international partnership of state, federal, and academic scientists began restoring fish spawning habitat in both of these rivers. Using an adaptive management approach, we created 1,100 m² of productive fish spawning habitat near Belle Isle in the Detroit River in 2004; 3,300 m² of fish spawning habitat near Fighting Island in the Detroit River in 2008; and 4,000 m² of fish spawning habitat in the Middle Channel of the St. Clair River in 2012. Here, we describe the adaptive‐feedback management approach that we used to guide our decision making during all phases of spawning habitat restoration, including problem identification, team building, hypothesis development, strategy development, prioritization of physical and biological imperatives, project implementation, habitat construction, monitoring of fish use of the constructed spawning habitats, and communication of research results. Numerous scientific and economic lessons learned from 10 years of planning, building, and assessing fish use of these three fish spawning habitat restoration projects are summarized in this article.     

Genetic isolation between two recently diverged populations of a symbiotic fungus

Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind‐dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na⁺/H⁺ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.     

Cloning and tissue expression of the mouse ortholog of AIM1, a βγ-crystallin superfamily member

We report the isolation of the murine ortholog of AIM1, a human gene whose expression is associated with the reversal of tumorigenicity in an experimental model of melanoma. Mouse and human AIM1 are more than 90% identical in amino acid sequence in the βγ-crystallin repeats and the C-terminal domain, and more than 75% identical in the extended N-terminal domain. Consistent with the isolated cDNA representing the authentic AIM1 ortholog, linkage analysis localized mouse Aim1 to proximal mouse Chromosome (Chr) 10 in a conserved linkage group with genes localized to human Chr band 6q21. Searches of EST databases identified a second AIM1-like gene in both mouse and human, suggesting the existence of a gene family. Northern analysis demonstrates Aim1 is expressed most abundantly in adult skin, lung, heart, liver, and kidney and is temporally regulated during embryogenesis. Aim1 is expressed highly in the shaft region of the hair follicles and the presumptive ectoderm, but not at detectable levels in melanocytes or melanocyte precursor cells. Received: 18 February 1998 / Accepted: 8 May 1998     

Physical mapping of three fruit ripening genes：Endopolygalacturonase,ACC oxidase and ACC synthase from apple（Malus x domestica） in an apple rootstock A106（Malus sieboldii

The apple rootstock,A106(Malus sieboldii),had 17 bivalents in pollen mother cells at meiotic metaphase 1,and 17 chromosomes in a haploid pollen cell.Karyotypes were prepared from root-tip cells with 2n=34 chromosomes,Seven out of 82 karyotypes(8.5%) showed one pari of satellites at the end of the short arm of chromosome 3.C-bands were shown on 6 pairs of chromosomes 2,4,6,8,14,and 16 near the telomeric regions of short arms.Probes for three ripening-related genes from Malus x domestica:endopolygalacturonase(EPG,0.6kb),ACC oxidase(1.2kb),and ACC synthase(2kb)were hybridized in situ to metaphase chromosomes of A106.Hybridization sites for the EPG gene were observed on the long arm of chromosome 14 in 15 out of 16 replicate spreads and proximal to the centromere of chromosomes 6 and 11.For the ACC oxidase gene,hylridization sites were observed in the telomeric region of the short arm of chromosomes 5 and 11 in 87% and 81% of 16 spreads respectively,proxiaml to the centromere of chromosome 1 in 81% of the spreads,and on the long arm of chromosome 13 in 50% of the spreads. Physical mapping of three fruit ripening genes in an apple rootstock A106.Twenty five spreads were studied for the ACC synthase gene and hybridization sites were observed in the telomeric region of the short arm of chromosome 12 in 96% of the spreads.chromosomes 9 and 10 in 76% of the spreads,and chromosome 17 in 56% of the spreads.     

Foraminifera and meiofauna on an intertidal mudflat,Cornwall, England: Populations; respiration and secondary production; and energy budget

A rich and varied meiofauna inhabits a Cornish mudflat near the mouth of the Tamar River in southwestern England. Population densities range from 117 to 943 individuals · g^–1 (wet) sediment (1.4–11.4 × 10⁶ individuals · m^–2), with foraminifera, harpacticoid copepods and nematodes appearing in nearly equal numbers and comprising most of the meiofauna. Seasonally, meiofaunal numbers rise and fall with solar radiation and vary inversely with river discharge. Two species, the atestate allogromiid A and the calcareous Haynesina germanica (Ehrenberg), far outnumber other foraminifera; their population densities and growth rates reach maxima in spring and summer.Monthly rates of sediment respiration are locally variable, but clearly increase from winter (4.13 ml O₂ · m^–2 · h^–1 in December) to spring (38.87 ml O₂ · m^–2 · h^–1 in April). Experiments and calculations ascribe approximately 30% of this total to the meiofauna (including microfauna and microflora), 50% to bacteria and less than 20% to chemical oxidation. A tentative energy budget for the mudflat suggests that secondary production by meiofauna is small as compared with coastal environments elsewhere, and that meiofaunal production (426 Kcal · m^–2 · y^–1) is nearly twice meiofaunal respiration (252 Kcal · m^–2 · yr^–1).     

A chimeric ubiquitin conjugating enzyme that combines the cell cycle properties of CDC34 (UBC3) and the DNA repair properties of RAD6 (UBC2): implications for the structure, function and evolution of the E2s.

The CDC34 (UBC3) protein from Saccharomyces cerevisiae has a 125 residue tail that contains a polyacidic region flanked on either side by sequences of mixed composition. We show that although a catalytic domain is essential for CDC34 activity, a major cell cycle determinant of this enzyme is found within a 74 residue segment of the tail that does not include the polyacidic stretch or downstream sequences. Transposition of the CDC34 tail onto the catalytic domain of a functionally unrelated E2 such as RAD6 (UBC2) results in a chimeric E2 that combines RAD6 and CDC34 activities within the same polypeptide. In addition to the tail, the cell cycle function exhibited by the chimera and CDC34 is probably dependent on a conserved region of the catalytic domain that is shared by both RAD6 and CDC34. Despite this similarity, the CDC34 catalytic domain cannot substitute for the DNA repair and growth functions of the RAD6 catalytic domain, indicating that although these domains are structurally related, sufficient differences exist to maintain their functional individuality. Expression of the CDC34 catalytic domain and tail as separate polypeptides are capable of only partial function; thus, while the tail displays autonomous structural characteristics, there is considerable advantage gained when both domains coexist within the same polypeptide. The ability of these and other derivatives to restore partial function to a cdc34 temperature-sensitive mutant but not to a disruption mutant suggests that interaction between two CDC34 polypeptides is a requirement of CDC34 activity. Based on this idea we propose a model that accounts for the initiating steps leading to multi-ubiquitin chain synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)     

Radiolabeled octreotide. What lessons for antibody-mediated targeting?

Octreotide is a synthetic analog of the peptide hormone somatostatin (SMS). A wide variety of tumors express enhanced numbers of SMS receptors, notably neuroendocrine tumors and lymphomas, but also some of the more common adenocarcinomas. Octreotide contains only eight amino acids, some of which are in the (D) configuration in order to enhance the stability of the molecule in vivo. Tyrosine and DTPA-containing analogs of octreotide have been synthesized and labeled with iodine-123 and indium-111, respectively, with the intention of targeting SMS receptor-containing tumors for diagnostic purposes. Both radiopharmaceuticals demonstrate a high sensitivity and specificity for these tumors, indicating a clinical role for these agents in management of these diseases. Lessons can be learned from the success of these agents when designing improved antibody-based molecules. Tumor uptake of radiolabeled octreotide is very rapid, occurring within minutes of administration. Blood clearance is also rapid, such that tumors are soon visible even in areas of high blood background. An interesting finding has been the differences between the pharmacokinetics of the iodinated and indium-labeled species. Although the majority of 123I-Tyr3-octreotide undergoes hepatobiliary excretion, 111In-DTPAPhe1-octreotide is eliminated predominantly by the kidneys. These results suggest that the smallest possible antibody-like tracers are likely to have advantages over native immunoglobulins and conventional Fab-like fragments.