'PACLIMS': A component LIM system for high-throughput functional genomic analysis

Background

Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the ~11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

Results

The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.

Conclusion

Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.     

Developmental context determines latency of MYC-induced tumorigenesis

One of the enigmas in tumor biology is that different types of cancers are prevalent in different age groups. One possible explanation is that the ability of a specific oncogene to cause tumorigenesis in a particular cell type depends on epigenetic parameters such as the developmental context. To address this hypothesis, we have used the tetracycline regulatory system to generate transgenic mice in which the expression of a c-MYC human transgene can be conditionally regulated in murine hepatocytes. MYC's ability to induce tumorigenesis was dependent upon developmental context. In embryonic and neonatal mice, MYC overexpression in the liver induced marked cell proliferation and immediate onset of neoplasia. In contrast, in adult mice MYC overexpression induced cell growth and DNA replication without mitotic cell division, and mice succumbed to neoplasia only after a prolonged latency. In adult hepatocytes, MYC activation failed to induce cell division, which was at least in part mediated through the activation of p53. Surprisingly, apoptosis is not a barrier to MYC inducing tumorigenesis. The ability of oncogenes to induce tumorigenesis may be generally restrained by developmentally specific mechanisms. Adult somatic cells have evolved mechanisms to prevent individual oncogenes from initiating cellular growth, DNA replication, and mitotic cellular division alone, thereby preventing any single genetic event from inducing tumorigenesis.     

Bph1p, the Saccharomyces cerevisiae homologue of CHS1/beige, functions in cell wall formation and protein sorting

Mutations in the Chediak-Higashi syndrome gene (CHS1) and its murine homologue Beige result in the formation of enlarged lysosomes. BPH1 (Beige Protein Homologue 1) encodes the Saccharomyces cerevisiae homologue of CHS1/Beige. BPH1 is not essential and the encoded protein was found to be both cytosolic and peripherally bound to a membrane. Neither disruption nor overexpression of BPH1 affected vacuole morphology as assessed by fluorescence microscopy. The deltabph1 strain showed an impaired growth on defined synthetic media containing potassium acetate buffered below pH 4.25, increased sensitivity to calcofluor white, and increased agglutination in response to low pH. A library screen identified VPS9, FLO1, FLO9, BTS1 and OKP1 as high copy suppressors of the growth defect of deltabph1 on both low pH potassium acetate and calcofluor white. The deltabph1 strain demonstrated a mild defect in sorting vacuolar components, including increased secretion of carboxypeptidase Y and missorting of alkaline phosphatase. Overexpression of VPS9, BTS1 and OKP1 suppressed the carboxypeptidase Y secretion defect of deltabph1. Overexpression of BPH1 was found to suppress the calcofluor white sensitivity of a class E VPS deletion strain, deltavta1. Together, these data suggest that Bph1p associates with a membrane and is involved in protein sorting and cell wall formation.     

Calcineurin activation influences muscle phenotype in a muscle-specific fashion

Background  

The calcium activated protein phosphatase 2B, also known as calcineurin, has been implicated as a cell signaling molecule involved with transduction of physiological signals (free cytosolic Ca²⁺) into molecular signals that influence the expression of phenotype-specific genes in skeletal muscle. In the present study we address the role of calcineurin in mediating adaptations in myosin heavy chain (MHC) isoform expression and muscle mass using 3-month old wild-type (WT) and transgenic mice displaying high-level expression of a constitutively active form of calcineurin (MCK-CN* mice).     

Male signalling and lek attractiveness in the Mediterranean fruit fly

I tested the null hypothesis that females of the Mediterranean fruit fly, Ceratitis capitata, were equally likely to visit leks composed of males with high versus low mating success. In laboratory trials, the observed distribution of matings among males differed significantly from that expected by chance, owing primarily to the higher than expected numbers of individuals with low (mated 0-1 days over 6 consecutive observation days) or high (mated 4 or more days) mating scores. I termed these two groups as 'low' and 'high' maters, respectively. In the field, greater numbers of female sightings were made at artificial leks of high maters than low maters. This result apparently reflected a greater calling propensity among high maters. Slopes of female sightings versus calling level did not differ significantly between leks of low and high maters, suggesting that the observed relationship between calling activity and female sightings was independent of male mating status. Following the same protocol, I conducted a second experiment to examine whether males used the signals of conspecific males to locate lek sites and, if so, whether signal attractiveness varied with male mating ability. Attraction of males to calling conspecifics was far weaker than that observed for females, and over five different trials a total of only seven male sightings were made at any of the established leks. Copyright 2000 The Association for the Study of Animal Behaviour.     

Does non-exercise activity thermogenesis contribute to non-shivering thermogenesis?

We wanted to examine if spontaneous physical activity contributes to non-shivering thermogenesis. Ten lean, healthy male subjects wore a physical activity, micro-measurement system while the room temperature was randomly altered at two hourly intervals between thermoneutral (72 °F), cool (62 °F) and warm (82 °F) temperatures. Physical activity measured during the thermoneutral, cooling and warming periods was not significantly different. Cooling increased energy expenditure above basal and thermoneutral values 2061±344 kcal/day (p<0.01). Thus, the increase in energy expenditure associated with short-term environmental cooling in lean, healthy males does not appear to be due to increased spontaneous physical activity or fidgeting.     

Sedentariness at Work: How Much Do We Really Sit?

Sedentariness is associated with obesity. We examined whether people with sedentary jobs are equally inactive during their work days and leisure days. We enrolled 21 subjects of varying weight and body fat (11 men:10 women, 38 ± 8 years, 83 ± 17 kg, BMI 28 ± 5 kg/m², 29 ± 11 fat kg, 35 ± 9% fat). All subjects continued their usual work and leisure‐time activities whilst we measured daily activity and body postures for 10 days. The data supported our hypothesis that people sit more at work compared to leisure (597 ± 122 min/day cf 484 ± 83 min/day; P < 0.0001). The mean difference was 110 ± 99 min/day. Similarly, work days were associated with less standing (341 ± 97 min/day; P = 0.002) than leisure days (417 ± 101 min/day). Although the walking bouts did not differ significantly between work and leisure (46 ± 9 vs. 42 ± 9 walking bouts/day); the mean free‐living velocity of a walk at work was 1.08 ± 0.28 mph and on leisure days was 0.94 ± 0.24 mph (P = 0.03) and the average time spent walking was 322 ± 91 min on work days and 380 ± 108 min on leisure days (P = 0.03). Estimates of the daily energetic cost of walking approximated 527 ± 220 kcal/day for work days and 586 ± 326 kcal/day for leisure days (r = 0.72, P < 0.001). Work days are associated with more sitting and less walking/standing time than leisure days. We suggest a need to develop approaches to free people from their chairs and render them more active.     

Development of Sound Localization Strategies in Children with Bilateral Cochlear Implants

Localizing sounds in our environment is one of the fundamental perceptual abilities that enable humans to communicate, and to remain safe. Because the acoustic cues necessary for computing source locations consist of differences between the two ears in signal intensity and arrival time, sound localization is fairly poor when a single ear is available. In adults who become deaf and are fitted with cochlear implants (CIs) sound localization is known to improve when bilateral CIs (BiCIs) are used compared to when a single CI is used. The aim of the present study was to investigate the emergence of spatial hearing sensitivity in children who use BiCIs, with a particular focus on the development of behavioral localization patterns when stimuli are presented in free-field horizontal acoustic space. A new analysis was implemented to quantify patterns observed in children for mapping acoustic space to a spatially relevant perceptual representation. Children with normal hearing were found to distribute their responses in a manner that demonstrated high spatial sensitivity. In contrast, children with BiCIs tended to classify sound source locations to the left and right; with increased bilateral hearing experience, they developed a perceptual map of space that was better aligned with the acoustic space. The results indicate experience-dependent refinement of spatial hearing skills in children with CIs. Localization strategies appear to undergo transitions from sound source categorization strategies to more fine-grained location identification strategies. This may provide evidence for neural plasticity, with implications for training of spatial hearing ability in CI users.