Genome plasticity in Paramecium bursaria revealed by population genomics.

BACKGROUND: Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. RESULTS: We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. CONCLUSIONS: We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

Multiple intermolecular interactions facilitate rapid evolution of essential genes.

Essential genes are commonly assumed to function in basic cellular processes and to change slowly. However, it remains unclear whether all essential genes are similarly conserved or if their evolutionary rates can be accelerated by specific factors. To address these questions, we replaced 86 essential genes of Saccharomyces cerevisiae with orthologues from four other species that diverged from S. cerevisiae about 50, 100, 270 and 420 Myr ago. We identify a group of fast-evolving genes that often encode subunits of large protein complexes, including anaphase-promoting complex/cyclosome (APC/C). Incompatibility of fast-evolving genes is rescued by simultaneously replacing interacting components, suggesting it is caused by protein co-evolution. Detailed investigation of APC/C further revealed that co-evolution involves not only primary interacting proteins but also secondary ones, suggesting the evolutionary impact of epistasis. Multiple intermolecular interactions in protein complexes may provide a microenvironment facilitating rapid evolution of their subunits.

Mutation at a distance caused by homopolymeric guanine repeats in Saccharomyces cerevisiae.

Mutation provides the raw material from which natural selection shapes adaptations. The rate at which new mutations arise is therefore a key factor that determines the tempo and mode of evolution. However, an accurate assessment of the mutation rate of a given organism is difficult because mutation rate varies on a fine scale within a genome. A central challenge of evolutionary genetics is to determine the underlying causes of this variation. In earlier work, we had shown that repeat sequences not only are prone to a high rate of expansion and contraction but also can cause an increase in mutation rate (on the order of kilobases) of the sequence surrounding the repeat. We perform experiments that show that simple guanine repeats 13 bp (base pairs) in length or longer (G 13+ ) increase the substitution rate 4- to 18-fold in the downstream DNA sequence, and this correlates with DNA replication timing (R = 0.89). We show that G 13+ mutagenicity results from the interplay of both error-prone translesion synthesis and homologous recombination repair pathways. The mutagenic repeats that we study have the potential to be exploited for the artificial elevation of mutation rate in systems biology and synthetic biology applications.

Association of the PPAR-γ Gene with Altered Glucose Levels and Psychosis Profile in Schizophrenia Patients Exposed to Antipsychotics.

OBJECTIVE: Metabolic abnormalities, e.g., diabetes, are common among schizophrenia patients. Peroxisome proliferator activated receptor-γ (PPAR-γ) regulates glucose/lipid metabolisms, and schizophrenia like syndrome may be induced by actions involving retinoid X receptor-α/PPAR-γ heterodimers. We examined a possible role of the PPAR-γ gene in metabolic traits and psychosis profile in schizophrenia patients exposed to antipsychotics. METHODS: Single nucleotide polymorphisms (SNPs) of the PPAR-γ gene and a serial of metabolic traits were determined in 394 schizophrenia patients, among which 372 were rated with Positive and Negative Syndrome Scale (PANSS). RESULTS: SNP-10, -12, -18, -19, -20 and -26 were associated with glycated hemoglobin (HbA1c) whereas SNP-18, -19, -20 and -26 were associated with fasting plasma glucose (FPG). While SNP-23 was associated with triglycerides, no associations were identified between the other SNPs and lipids. Further haplotype analysis demonstrated an association between the PPAR-γ gene and psychosis profile. CONCLUSION: Our study suggests a role of the PPAR-γ gene in altered glucose levels and psychosis profile in schizophrenia patients exposed to antipsychotics. Although the Pro12Ala at exon B has been concerned an essential variant in the development of obesity, the lack of association of the variant with metabolic traits in this study should not be treated as impossibility or a proof of error because other factors, e.g., genes regulated by PPAR-γ, may have complicated the development of metabolic abnormalities. Whether the PPAR-γ gene modifies the risk of metabolic abnormalities or psychosis, or causes metabolic abnormalities that lead to psychosis, remains to be examined.

The evolution of low mutation rates in experimental mutator populations of Saccharomyces cerevisiae.

Mutation is the source of both beneficial adaptive variation and deleterious genetic load, fueling the opposing selective forces than shape mutation rate evolution. This dichotomy is well illustrated by the evolution of the mutator phenotype, a genome-wide 10- to 100-fold increase in mutation rate. This phenotype has often been observed in clonally expanding populations exposed to novel or frequently changing conditions. Although studies of both experimental and natural populations have shed light on the evolutionary forces that lead to the spread of the mutator allele through a population, significant gaps in our understanding of mutator evolution remain. Here we use an experimental evolution approach to investigate the conditions required for the evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ∼6,700 generations, four out of eight experimental mutator lines had evolved a decreased mutation rate. We provide evidence that the accumulation of deleterious mutations leads to selection for reduced mutation rate clones in populations of mutators. Finally, we test the long-term consequences of the mutator phenotype, finding that mutator lines follow different evolutionary trajectories, some of which lead to drug resistance.

The quantitative detection of aripiprazole and its main metabolite by using capillary-electrophoresis.

BACKGROUND: We aimed to establish a feasible and reliable method to measure the level of aripiprazole and its main metabolite, dehydroaripiprazole, using a capillary-electrophoresis (CE) machine. METHODS: Two blood samples were obtained from psychiatric patients hospitalized in Yu-Li Hospital who had been treated with aripiprazole for more than 4 weeks, at least 10 mg/d. Conditions for voltage, temperature and buffer concentration was optimized on a CE machine. RESULTS: The most optimal conditions for CE were 80 mM 2-3% DMSO-phosphate as a buffer under pH = 3.0, 15 KV, 20°C and a detection wavelength of 214 nm. The linear ranges of aripiprazole and dehydroaripiprazole concentration were from 0.5 to 50 ng/mL. CONCLUSION: CE method is a feasible method to measure aripiprazole level with relatively low price compared with other analytical techniques for clinical use.

Significance of morphological features in schizophrenia of a Chinese population.

Neuro-developmental hypothesis suggests that schizophrenia is originated from aberrant brain development during first and/or early trimester of gestation. Accordingly, when a schizophrenia gene is involved in the regulation of embryonic development and continues to play a role in the later life, it may result in the co-occurrence of defective organ systems and/or physiological functions with schizophrenia. We proposed a checklist with 13 morphological features and examine their prevalence rates in 151 schizophrenic patients and 151 controls. Statistical analyses showed that single transverse palmar crease, head circumference, covered epicanthus, finger length difference, and inner canthus distance, made significant contributions to schizophrenia. To rule out the age confounding effects on morphological features, we dropped older schizophrenic subjects and younger controls in further regression analysis. The regression model correctly classified 82.8% of control subjects (specificity) and 86.4% of schizophrenic patients (sensitivity), and provided an overall successful classification rate of 84.5%, with single transverse palmar crease on the first rank. The association of morphological features and schizophrenia is probably genetic in origin, as specific morphological features were more frequent in non-affected parents with higher genetic loading of schizophrenia. In addition, the association of finger length difference in schizophrenia found in this study has never been reported elsewhere. Our study showed that five out of 13 morphological features in the propose checklist may be used as biomarkers for schizophrenia, either for clinical practice or research purposes.

Pulsed electromagnetic field stimulation of bone marrow cells derived from ovariectomized rats affects osteoclast formation and local factor production.

This study examined the effects of a specific pulsed electromagnetic field (PEMF) stimulation on osteoclast formation in bone marrow cells from ovariectomized rats and to determine if the signal modulates the production of cytokines associated with osteoclast formation. Adult female Wistar rats were subjected to bilateral or sham ovariectomy, and primary bone marrow cells were harvested at 4 days (Subgroup I) and 7 days (Subgroup II) after surgery. Primary bone marrow cells were subsequently placed in chamber slides and set inside solenoids powered by a pulse generator (300 micros, 7.5 Hz) for 1 h per day for 9 days (OVX + PEMF group). Others (INT, SHAM, and OVX groups) were cultured under identical conditions, but no signal was applied. Recruitment and authentication of osteoclast-like cells were evaluated by determining multinuclear, tartrate-resistant acid phosphatase (TRAP) positive cells on day 10 of culture and by pit formation assay, respectively. The PEMF signal caused significant reductions in osteoclast formation in both Subgroups I (-55%) and II (-43%). Tumor necrosis factor-alpha (TNF-alpha), interleukin 1beta (IL-1beta), and interleukin 6 (IL-6) in OVX + PEMF group of Subgroup I were significantly reduced at 5, 7, and 9 days as compared to OVX group. The results found in this study suggest that osteoclastogenesis can be inhibited by PEMF stimulation, putatively due to a concomitant decrease in local factor production. Bioelectromagnetics 25:134-141, 2004.