Global mapping of the yeast genetic interaction network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.     

Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase

Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how nuclear organization contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors in yeast indicated a functional relationship between a nuclear pore subcomplex and Slx5/Slx8, a small ubiquitin-like modifier (SUMO)-dependent ubiquitin ligase, which we show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering donor sites at the nuclear periphery. This suggests that strand breaks are shunted to nuclear pores for a repair pathway controlled by a conserved SUMO-dependent E3 ligase.     

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.     

Problems in Paradise: Taiwanese Immigrants to Auckland,New Zealand

Migration from Asia to New Zealand is now a topic of heated public debate within New Zealand. This study traces the experiences of Taiwanese migrants to Auckland over the past decade and documents their adaption and revised expectations. By the end of June 1995, over 21,000 Taiwanese had been granted permanent residence in New Zealand on the basis of their skills, qualifications and work experience. Although expecting a fall in income as the necessary ‘price’ to pay for an improved quality of life, as well as some language difficulties, few immigrants were prepared for the magnitude of the drop in income, the hardship it would bring and the heavy reliance this would place on their remaining investments in Taiwan. The net result has been unemployment and underemployment of immigrants many of whom are now resigned to net gains through education coming not to them but to their children. As a result of the inability to secure adequate employment, many Taiwanese immigrants have relocated one or all of the family members back to Taiwan. The introduction in October 1995 of stricter English standards and the flatter, less academic basis to point earning qualifications, validation of job offers, recognition of New Zealand work experience together with the spouses’ human capital as well as a clearer commitment to New Zealand should all go some way to addressing many of the difficulties the history of recent Taiwanese immigration has uncovered.     

Stability of hydrolytic enzyme activity and microbial phosphorus during storage of tropical rain forest soils

Storage can markedly influence microbial and biochemical properties in soils, yet recommendations for sample storage are based on studies of temperate soils that regularly experience extended cold periods. We assessed the influence of storage conditions on microbial phosphorus and the activity of four hydrolytic enzymes (phosphomonoesterase, phosphodiesterase, β-glucosidase, and N-acetyl-β-d-glucosaminidase) in three lowland tropical forest soils from the Republic of Panama that experience a constant warm temperature. The soils spanned a strong rainfall gradient and contained contrasting physical and chemical properties (pH 3.6-5.9; total carbon 26-50 g C kg⁻¹; clay 33-62%; total phosphorus 0.30-0.60 g P kg⁻¹). Storage treatments were: (i) room temperature (22 °C in the dark), (ii) refrigerated (4 °C in the dark), (iii) air-dried (10 d, 22 °C), and (iv) frozen (−35 °C). There were significant changes in enzyme activities and microbial phosphorus during refrigerated and room temperature storage, although changes were relatively small during the first two weeks. An initial marked decline in enzyme activities for one soil analyzed within 2 h of sampling was attributed to a flush of activity caused by sampling and soil preparation (sieving, etc.). For longer-term storage (>2 weeks), ambient laboratory temperature appeared preferable to freezing and cold storage, because one month of storage caused a marked decline in enzyme activities and microbial phosphorus in one soil. Freezing preserved the activities of some enzymes in some soils at rates comparable to cold or room temperature storage, but caused a marked decline in microbial phosphorus in two soils. Air-drying caused a marked decline in microbial phosphorus and the activity of all enzymes. We therefore conclude that enzyme assays and microbial phosphorus should be determined in tropical forest soils after no more than two weeks storage in the dark at ambient laboratory temperature.     

Nematode community composition and diversity associated with a topoclimatic transect in a rain shadow desert

The effect of a topoclimatic gradient on soil nematode communities was investigated in the Israeli Judean Desert. Four locations along a 35 km gradient, from an elevation of 650 m above sea level with 620 mm rainfall to a –60 m relative to sea level with a rainfall below 110 m, were studied: Givat Yearim, Maale Adumim, Mishor Adumim and Kalia. Monthly soil samples were collected between January 1994 and December 1995. Thirteen nematode families and 17 genera were observed. Cephalobus, Heterocephalobus, Aphelenchoides, Tylenchus, Dorylaimus and Eudorylaimus were found to be the dominant genera. Ecological measurements of soil nematode community structure, diversity, and maturity indices were assessed, and comparisons between four locations and four seasons were made. Significant differences in the total numbers of nematodes were found between the locations (p < 0.01) and seasons (p < 0.05), where Givat Yearim > Maale Adumim > Mishor Adumim > Kalia, winter > spring > autumn > summer. Bacterivores were found to be the most abundant trophic group across locations and seasons, with a mean relative abundance of 55.0%. The densities of bacterivores, plant parasites and omnivores-predators during the winter season exhibited similar trends at all four locations, with Givat Yearim > Maale Adumim > Mishor Adumim > Kalia. None of the ecological indices were significantly different between locations. However, the maturity index (MI), trophic diversity (TD) and Simpson diversity (SI) exhibited significant differences between seasons.     

Bilateral phalangeal fillet technique for metacarpal pad reconstruction in a dog

Loss of the metacarpal or metatarsal pad requires reconstruction with other pad tissue to allow functional weight-bearing on the limb. This report describes the use of a bilateral phalangeal fillet technique to reconstruct a weight-bearing surface in a dog following complete excision of its right metacarpal pad for malignant melanoma. This resulted in a functional weight-bearing limb.     

Quantification of tissue shrinkage in canine small intestinal specimens after resection and fixation

The aim of this study was to quantify the longitudinal shrinkage of canine small intestinal specimens after resection and fixation in 10% formalin. Samples were obtained from 12 clinically normal dogs of medium to large breed via ventral midline coeliotomy and enterectomy. The length of each sample was measured before excision, immediately after excision, and after 24 h in 10% formalin. The results were interpreted with the use of single-sample t-tests of the average changes; P-values of less than 0.01 were considered significant. The samples indicated a significant decrease in length after resection and fixation. The mean shrinkage from the pre-excision state was 28.3% immediately after excision (P < 0.0001) and 26.3% after 24 h of fixation (P < 0.0001). There was a small but not significant increase in the length of the specimens between the 2nd and 3rd measurement points. Quantification of the longitudinal shrinkage of resected intestinal specimens may improve interpretation of the distance of surgical margins from abnormal tissue in histopathology reports and allow investigation of the margins required for the clearance of specific tumors.     

Regional scale effects of human density and forest disturbance on large-bodied vertebrates throughout the Yucatán Peninsula, Mexico

The occupancy probability of 35 large-bodied bird and mammal species was examined in relation to patch- and landscape-scale habitat and disturbance variables in 147 forest patches distributed throughout the Mexican Yucatán Peninsula. Occupancy was assessed on the basis of interviews with local informants. The most important predictors of vertebrate species richness, composition, and patch occupancy were human population density and the extent and quality of forest cover. Most forest species responded positively to forest extent, while felids in particular were sensitive to human population density. However, the effects of human density on patch occupancy operated at extremely local scales. Effects were stronger at a smaller grain size, offering optimistic prospects for conservation strategies that incorporate human population effects. Three arboreal frugivores (Ateles geoffroyi, Alouatta pigra, and Ramphastos sulfuratus) were strongly associated with total basal area of trees bearing fleshy fruits. The degree of hunting pressure was not related to human population density, and affected the occupancy probability of three game species, two of which (Mazama spp., Crax rubra) are among the most preferred prey across the Yucatán Peninsula. Levels of patch occupancy across this region varied considerably among species, and were best explained by body size and degree of forest habitat specificity, large-bodied species and habitat specialists being the most vulnerable. This study provides a quantitative assessment of the conservation potential of large vertebrates in Mesoamerica and identifies disturbance-sensitive species. This can inform regional-scale conservation planning at a time when low deforestation in parts of the Yucatán Peninsula still provides a narrow window of conservation opportunity given the rapid human population growth.