Distribution Of Functional Categories Research Articles

Comparative transcriptome analysis of the venom sac and gland of social wasp Vespa tropica and solitary wasp Rhynchium brunneum

To investigate genes differentially expressed in the venom of social and solitary wasps, a comparative transcriptome analysis was conducted. Subtractive expressed sequence tag (EST) libraries specific to the venom gland and sac (gland/sac) of a social wasp species, Vespa tropica and a solitary hunting wasp species, Rhynchium brunneum, was constructed by suppression subtractive hybridization. In BLASTx analysis, 41% and 56% of the total ESTs showed statistically best-matched hits (E≤10−4) in the libraries of V. tropica and R. brunneum, respectively. Although the functional category analysis did not show remarkable differences in the distribution of functional categories between the two venom gland/sac cDNA libraries, perhaps due to the lack of functional information on many of the venom components, there were groups of genes that are specific to either V. tropica or R. brunneum. Venom allergen 5 and serine protease were found to be social wasp-specific venom transcripts. In contrast, venom peptides, metalloendopeptidases, arginine kinase and dendrotoxin were observed in solitary wasp at much higher frequencies.

Gene expression analysis in cadmium-stressed roots of a low cadmium-accumulating solanaceous plant, Solanum torvum

Solanum torvum Sw. cv. Torubamubiga (TB) is a low cadmium (Cd)-accumulating plant. To elucidate the molecular mechanisms of the Cd acclimation process in TB roots, transcriptional regulation was analysed in response to mild Cd treatment: 0.1 μM CdCl2 in hydroponic solution. A unigene set consisting of 6296 unigene sequences was constructed from 18 816 TB cDNAs. The distribution of functional categories was similar to tomato, while 330 unigenes were suggested to be TB specific. For expression profiling, the SuperSAGE method was adapted for use with Illumina sequencing technology. Expression tag libraries were constructed from Cd-treated (for 3 h, 1 d, and 3 d) and untreated roots, and 34 269 species of independent tags were collected. Moreover, 6237 tags were ascribed to the TB or eggplant (aubergine) unigene sequences. Time-course changes were examined, and 2049 up- and 2022 down-regulated tags were identified. Although no tags annotated to metal transporter genes were significantly regulated, a tag annotated to AtFRD3, a xylem-loading citrate transporter, was down-regulated. In addition to induction of heavy metal chaperone proteins, antioxidative and sulphur-assimilating enzymes were induced, confirming that oxidative stress developed even using a mild Cd concentration. Rapid repression of dehydration-related transcription factors and aquaporin isoforms suggests that dehydration stress is a potential constituent of Cd-induced biochemical impediments. These transcriptional changes were also confirmed by real-time reverse transcription-PCR. Further additions of TB unigene sequences and functional analysis of the regulated tags will reveal the molecular basis of the Cd acclimation process, including the low Cd-accumulating characteristics of TB.

Using patient-reported outcomes for technology assessment (TA) and quality improvement (QI) in prostate cancer brachytherapy

5139 Background: Despite their sensitivity, validity and increasing prominence in clinical reports, patient-reported outcomes have played little role in TA and QI. We used our validated disease-specific instrument to compare outcomes after alternative brachytherapy techniques for early prostate cancer, both experimental vs. standard technique and between implementations of the standard technique. Methods: One radiation oncologist performed experimental MRI-guided brachytherapy (MRB) on protocol and 2 performed standard ultrasound-guided brachytherapy (USB1 and USB2). We prospectively measured urinary and bowel function of 237 men before brachytherapy and at 1, 3 and 12 months after treatment. Each symptom index is scored from 0 (no dysfunction) to 100 (maximum dysfunction). We report outcomes both as mean change in scale score from baseline and as the distribution of functional categories, grouped by pretreatment functional level: normal, intermediate, and poor (severe dysfunction). Results: Among all patients, MRB caused less urinary obstruction/irritation at 3 months after treatment than ultrasound-guided brachytherapy (mean score change 9.2 vs. 23.6, p<.001). Significant differences in outcome also existed between USB1 and USB2 (19.5 vs. 29.0, p=.01). When baseline function was normal, 15% of MRB patients reported severe 3-month dysfunction, compared to 50% of USB1 and 71% of USB2 patients ( Table ). Outcomes of patients with pretreatment urinary dysfunction differed less. Preliminary results documenting inferior outcomes prompted modification of the USB2 brachytherapy technique, producing a trend toward improved outcomes in small patient numbers (mean score change: 30.4 vs. 22.8, p=.25). Bowel symptom outcomes varied less. Conclusions: Patient-reported outcomes can provide sensitive and valid indicators of TA and QI that may contribute to optimal patient-centered care. [Table: see text] No significant financial relationships to disclose.

The “Domino Theory” of Gene Death: Gradual and Mass Gene Extinction Events in Three Lineages of Obligate Symbiotic Bacterial Pathogens

During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudogenization) and deletion. Here, we examine the evolutionary sequence of gene-death events during the process of genome miniaturization in three bacterial species that have experienced extensive genome reduction: Mycobacterium leprae, Shigella flexneri, and Salmonella typhi. We infer that in all three lineages, the distribution of functional categories is similar in pseudogenes and genes but different from that of absent genes. Based on an analysis of evolutionary distances, we propose a two-step "domino effect" model for reductive genome evolution. The process starts with a gradual gene-by-gene-death sequence of events. Eventually, a crucial gene within a complex pathway or network is rendered nonfunctional triggering a "mass gene extinction" of the dependent genes. In contrast to published reports according to which genes belonging to certain functional categories are prone to nonfunctionalization more frequently and earlier than genes belonging to other functional categories, we could discern no characteristic regularity in the temporal order of function loss.