Extragenic Suppressors of Mutations in the Cytoplasmic C Terminus of Sec63 Define Five Genes in Saccharomyces Cerevisae

Mutations in the SEC63 gene of Saccharomyces cerevisiae affect both nuclear protein localization and translocation of proteins into the endoplasmic reticulum. We now report the isolation of suppressors of sec63-101 (formerly npl1-1), a temperature-sensitive allele of SEC63. Five complementation groups of extragenic mutations, son1-son5 (suppressor of npl1-1), were identified among the recessive suppressors. The son mutations are specific to SEC63, are not bypass suppressors, and are not new alleles of previously identified secretory (SEC61, SEC62, KAR2) or nuclear protein localization genes (NPL3, NPL4, NPL6). son1 mutations show regional specificity of suppression of sec63 alleles. At low temperatures, son1 mutants grow slowly and show partial mislocalization of nuclear antigens. The SON1 gene maps to chromosome IV and encodes a nuclear protein of 531 amino acids that contains two acidic stretches and a putative nuclear localization sequence. We show that son1 mutations suppress sec63-101 by elimination of Son1p function.     

Strategies for selecting mutation sites for methionine enhancement in the bean seed storage protein phaseolin

The complete three-dimensional structure of the bean seed storage protein phaseolin was generated from -carbon coordinates by using molecular mechanic calculations. This structure was used as a template to simulate modifications aimed at increasing the methionine content of phaseolin. A hydrophilic, methionine-rich looping insert sequence was designed. Simulated mutagenesis shows that the insert might be accommodated in turn and loop regions of the protein, but not within an -helix. Methionine content was also increased by the replacement of hydrophobic amino acids with methionine in the central core -barrels of the phaseolin protein. Calculations indicated that methionine can effectively replace conserved or variant leucine, isolecuine, and valine residues. However, alanine residues were much more sensitive to substitution, and demonstrated high variability in the effects of methionine replacement. Introduction of multiple substitutions in the barrel interior demonstrated that the replaced residues could interact favorably to relieve local perturbations caused by individual substitutions. Molecular dynamics simulations were also utilized to study the structural organization of phaseolin. The calculations indicate that there are extensive packing interactions between the major domains of phaseolin, which have important implications for protein folding and stability. Since the proposed mutant proteins can be produced and studied, the results presented here provide an ideal test to determine if there is a correlation between the effects obtained by computer simulation and the effects of the mutations on the protein structure expressedin vivo.     

Joyful by nature: approaches to investigate the evolution and function of joy in non-human animals

The nature and evolution of positive emotion is a major question remaining unanswered in science and philosophy. The study of feelings and emotions in humans and animals is dominated by discussion of affective states that have negative valence. Given the clinical and social significance of negative affect, such as depression, it is unsurprising that these emotions have received more attention from scientists. Compared to negative emotions, such as fear that leads to fleeing or avoidance, positive emotions are less likely to result in specific, identifiable, behaviours being expressed by an animal. This makes it particularly challenging to quantify and study positive affect. However, bursts of intense positive emotion (joy) are more likely to be accompanied by externally visible markers, like vocalisations or movement patterns, which make it more amenable to scientific study and more resilient to concerns about anthropomorphism. We define joy as intense, brief, and event-driven (i.e. a response to something), which permits investigation into how animals react to a variety of situations that would provoke joy in humans. This means that behavioural correlates of joy are measurable, either through newly discovered ‘laughter’ vocalisations, increases in play behaviour, or reactions to cognitive bias tests that can be used across species. There are a range of potential situations that cause joy in humans that have not been studied in other animals, such as whether animals feel joy on sunny days, when they accomplish a difficult feat, or when they are reunited with a familiar companion after a prolonged absence. Observations of species-specific calls and play behaviour can be combined with biometric markers and reactions to ambiguous stimuli in order to enable comparisons of affect between phylogenetically distant taxonomic groups. Identifying positive affect is also important for animal welfare because knowledge of positive emotional states would allow us to monitor animal well-being better. Additionally, measuring if phylogenetically and ecologically distant animals play more, laugh more, or act more optimistically after certain kinds of experiences will also provide insight into the mechanisms underlying the evolution of joy and other positive emotions, and potentially even into the evolution of consciousness.     

Gravitational sedimentation can solve the problem of cellular récycling of yeast in continuous alcoholic fermentation

Adjustments in the geometry of the separation zone of an inclined parallel plate sedimenter, previously developed, permitted an extensive increase in the volumetric clarification rate of broth containing yeast (S. cerevisiae). The prototype, having an internal capacity of 1340 ml, was fed with fermentation broth containing 18.8% v/v cells, while 16.4 ml/min of clarified broth containing 0.3% v/v cells was removed in the overflow. The underflow, containing 23.8% v/v cells, was recycled to the fermenter at a rate of 60.6 ml/min. These results demonstrated the viability of using exclusively gravitational sedimentation for cellular recycling in continuous alcoholic fermentation. Without a doubt, this system represents the simplest technological alternative among those thus far proposed for continuous alcoholic fermentation. The low cost of installation, maintenance and operation permitted projection of its application for any scale of production.List of Symbols A Cross sectional area of the sedimentation zone - b Distance between two parallel plates, height of the triangle or diameter of the circle (for rectangular, triangular or circular cross sections of the sedimentation zone, respectively) - b Mean distance travelled by the cells during sedimentation within the sedimentation zone with each cross sectional geometry - B _f Biomass content of the fermentation broth - B _o Biomass content of the overflow - B _u Biomass content of the underflow - Eff. Sedimentation efficiency - f Factor corresponding to the clarification velocity obtained with a certain cross sectional geometry relative to that obtained with the rectangular sedimentation zone geometry - g Gravitational acceleration - H Length of the plates - Q _a Clarification rate - Q _f Feed rate - Q _o Overflow rate - Q _u Underflow rate - rect Indicates a rectangular cross section - S Total sedimentation area (horizontal projection of the internal contour of the sedimentation zone - tr Indicates a triangular cross section - _s Linear settling velocity of one cell in the broth - _v Linear clarification velocity of the broth in a vertical sedimenter = _s - Linear clarification velocity of the broth in an inclined sedimenter of slope - Slope of the sedimentation zone relative to the horizontal - Porosity factor = 1 — (volume fraction of cells) - _cell Cell density - _m Density of the medium - _broth Broth viscosity     

Cavity-nesting birds are limited by nesting habitat in Neotropical agricultural landscapes

Most studies comparing biodiversity between natural and human-modified landscapes focus on patterns in species occurrence or abundance, but do not consider how different habitat types meet species' breeding requirements. Organisms that use or nest in tree cavities may be especially threatened by habitat conversion due to the loss of their nesting sites. Although cavity-nesting bird diversity is highest in the tropics, little is known about how tropical birds use cavities, how agriculture affects their reproductive biology, and how effective nest boxes could be as a conservation strategy in tropical agriculture. Here, we explored how habitat conversion from tropical forests to pasture affects the abundance, nesting habitat availability, and nest success of cavity-nesting birds in Northwest Ecuador. We conducted bird surveys and measured natural cavity availability and use in forest and agriculture. We also added artificial nest boxes to forest and agriculture to see whether cavity limitation in agriculture would elicit higher use of artificial nest boxes. We found evidence of cavity limitation in agriculture—there were many more natural cavities in forest than in agriculture, as well as more avian use of nest boxes placed in agriculture as compared to forest. Our results suggest that it is important to retain remnant trees in tropical agriculture to provide critical nesting habitat for birds. In addition, adding nest boxes to tropical agricultural systems could be a good conservation strategy for certain species, including insectivores that could provide pest-control services to farmers. Abstract in Spanish is available with online material.     

Mitochondrial DNA polymorphisms in subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel, and its peripheral isolates

Patterns of mitochondrial DNA (mtDNA) variation were examined in 133 mole-rats constituting all four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of the Spalax ehrenbergi superspecies in Israel, as well as the peripheral isolates of 2n = 60. In the main range of the complex, a total of 28 mtDNA haplotypes were found in 64 mole-rats, with most haplotypes being unique to either a single chromosomal species or population. mtDNA divergence increased from low to high diploid number in a north-to-south direction in Israel. Overall levels of mtDNA diversity were unexpectedly the highest in the 2n = 60, the youngest species of the complex. The mtDNA haplotypes can be separated into two major groups, 2n = 52-54 and 2n = 58-60, and a phylogenetic analysis for each group revealed evidence of a few haplotypes not sorted by diploid number. The overall patterns of mtDNA divergence seen within and among the four chromosomal species are consistent with the parapatric mode of speciation as suggested from previous studies of allozyme and DNA hybridization. In a separate data set the patterns of mtDNA variation were examined across the main geographic range and across peripheral semi-isolates and isolates of the 2n = 60 chromosomal species. Fifteen haplotypes were found in 69 mole-rats. High levels of mtDNA diversity characterized the main range, semi-isolated, and even some desert isolated populations. The peripheral isolates contain much mtDNA diversity, including novel haplotypes.      

A SURVEY OF SIZES AND WEIGHTS OF BEMISIA TABACI (HOMOPTERA:ALEYRODIDAE)B BIOTYPE LIFE STAGES FROM FIELD GROWN COTTON AND CANTALOUPES

Abstract Size and weight measurements were made for all the life stages of Bemisia tabaci (Gennadius) B biotype from field grown cotton ( Gossypium hirsutum L.) and cantaloupe ( Cucumis melo L., var. cantalupensis ) in Phoenix, AZ and Fargo, ND, USA in 2000 and 2001. Nymphal volumes were derived from the measurements. The average nymphal volume increase for settled 1 st to the late 4th instar was exponential. The greatest increase in body volume occurred during development from the 3rd to early 4th instar. Nymphs on cotton leaves were wider, but not longer compared with those on cantaloupe. Ventral and dorsal depth ratios of nymphal bodies from 1 st to late 4th instars from cantaloupe leaves were significantly greater compared with those from cotton leaves. During nymphal development from 1st to 4th instar, the average (from the two host species) ventral body half volume increased by nearly 51 times compared with an increase of 28 times for the dorsal body half volume. Adult female and male average lengths, from heads to wing tips, were 1 126 μm and 953 μm, respectively. Average adult female and male weights were 39 and 17 μg, respectively. Average widths, lengths, and weights of eggs from cotton and cantaloupe were, 99 μm, 197 μm, and 0.8 μg, respectively. Average widths, lengths, and weights for exuviae of non-parasitized nymphs from both cotton and cantaloupe were 492 μm, 673 μm, and 1.20 μg, respectively; and widths, lengths, and weights of parasitized nymph exuviae were 452 μm, 665 μm, and 3.62 μg, respectively. Both exuviae from non-parasitized and parasitized nymphs from cotton leaves were wider, longer, and heavier than those from cantaloupe leaves.