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PubMed2026

A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia.

As the largest group of vertebrates, fish exhibit frequent turnover of sex-determining (SD) genes. Here, we assemble a chromosome-level YY red tilapia genome and identify figla-like (figlal) as the SD gene on tilapia linkage group (LG) 1. Integrative phylogenetic and genomic evidence suggests that figlal originated from a tilapia-specific duplication and transposition of the ancestral bHLH family gene figla from LG12 to LG1. Fluorescence in situ hybridization reveals expression divergence between figla and figlal, with figla expressed in female oocytes and figlal expressed in male gonadal somatic cells during early gonadal differentiation. The shift in expression after duplication might be driven by the insertion of cis-regulatory elements mediated by transposable elements. Knockout of figlal in XY fish results in male-to-female sex reversal as indicated by ovarian morphology, down-regulation of the male pathway gene dmrt1, and up-regulation of the female pathway gene cyp19a1a in the gonads. In contrast, overexpression of figlal in XX fish induces female-to-male sex reversal. These findings implicate figlal as an SD gene on tilapia LG1 and reveal the history of a unique evolutionary innovation in which a female oocyte gene evolved into a male SD gene via duplication, transposition, and cis-regulatory rewiring.

Animals↗
PubMed2006

Characterization of synthetic oxomanganese complexes and the inorganic core of the O2-evolving complex in photosystem II: evaluation of the DFT/B3LYP level of theory.

The capabilities and limitations of the Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional are investigated as applied to studies of mixed-valent multinuclear oxomanganese complexes. Benchmark calculations involve the analysis of structural, electronic and magnetic properties of di-, tri- and tetra-nuclear Mn complexes, previously characterized both chemically and spectroscopically, including the di-mu-oxo bridged dimers [Mn(III)Mn(IV)(mu-O)(2)(H(2)O)(2)(terpy)(2)](3+) (terpy=2,2':6,2''-terpyridine) and [Mn(III)Mn(IV)(mu-O)(2)(phen)(4)](3+) (phen=1,10-phenanthroline), the Mn trimer [Mn(3)O(4)(bpy)(4)(H(2)O)(2)](4+) (bpy=2,2'-bipyridine), and the tetramer [Mn(4)O(4)L(6)](+) with L=Ph(2)PO(2)(-). Furthermore, the density functional theory (DFT) B3LYP level is applied to analyze the hydrated Mn(3)O(4)CaMn cluster completely ligated by water, OH(-), Cl(-), carboxylate and imidazole ligands, analogous to the '3+1 Mn tetramer' of the oxygen-evolving complex of photosystem II. It is found that DFT/B3LYP predicts structural and electronic properties of oxomanganese complexes in pre-selected spin-electronic states in very good agreement with X-ray and magnetic experimental data, even when applied in conjunction with rather modest basis sets. However, it is conjectured that the energetics of low-lying spin-states is beyond the capabilities of the DFT/B3LYP level, constituting a limitation to mechanistic studies of multinuclear oxomanganese complexes where until now the performance of DFT/B3LYP has raised little concern.

Biomimetics↗
PubMed2005

Directed evolution, phage display and combination of evolved mutants: a strategy to recover the neutralization properties of the scFv version of BCF2 a neutralizing monoclonal antibody specific to scorpion toxin Cn2.

BCF2, a monoclonal antibody raised against scorpion toxin Cn2, is capable of neutralizing both, the toxin and the whole venom of the Mexican scorpion Centruroides noxius Hoffmann. The single chain antibody fragment (scFv) of BCF2 was constructed and expressed in Escherichia coli. Although its affinity for the Cn2 toxin was shown to be in the nanomolar range, it was non-neutralizing in vivo due to a low stability. In order to recover the neutralizing capacity, the scFv of BCF2 was evolved by error-prone PCR and the variants were panned by phage display. Seven improved mutants were isolated from three different libraries. One of these mutants, called G5 with one mutation at CDR1 and another at CDR2 of the light chain, showed an increased affinity to Cn2, as compared to the parental scFv. A second mutant, called B7 with a single change at framework 2 of heavy chain, also had a higher affinity. Mutants G5 and B7 were also improved in their stability but they were unable to neutralize the toxin. Finally, we constructed a variant containing the changes present in G5 and B7. The purpose of this construction was to combine the increments in affinity and stability borne by these mutants. The result was a triple mutant capable of neutralizing the Cn2 toxin. This variant showed the best affinity constant (KD=7.5x10(-11) M), as determined by surface plasmon resonance (BIAcore). The k(on) and k(off) were improved threefold and fivefold, respectively, leading to 15-fold affinity improvement. Functional stability determinations by ELISA in the presence of different concentrations of guanidinium hydrochloride (Gdn-HCl) revealed that the triple mutant is significantly more stable than the parental scFv. These results suggest that not only improving the affinity but also the stability of our scFv were important for recovering its neutralization capacity. These findings pave the way for the generation of recombinant neutralizing antisera against scorpion stings based on scFvs.

Amino Acid Sequence↗
PubMed2005

Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?

Statistical analysis of the functional constraints acting on eukaryotic protein kinases (EPKs) and on distantly related kinases suggests that EPK regulatory mechanisms evolved around an ancient structural component whose most distinctive features include the HxD-motif adjoining the catalytic loop, the F-helix, an F-helix aspartate, and the DFG-motif adjoined to the activation loop. The HxD-histidine constitutes a convergence point for signal integration, as conserved interactions link it to key catalytic residues, to the F-helix aspartate, and to both ends of the DFG-motif. These and other conserved features appear to be associated with DFG conformational changes and with coordinated movements possibly associated with phosphate transfer and ADP release. The EPKs have acquired structural features that link this core component to likely substrate-interacting regions at either end of the F-helix (most notably involving an F-helix tryptophan) and to three regions undergoing conformational changes upon kinase activation: the activation segment, the C-helix, and the nucleotide-binding pocket.

Adenosine Diphosphate↗
PubMed2006

Structures of in vitro evolved binding sites on neocarzinostatin scaffold reveal unanticipated evolutionary pathways.

We have recently applied in vitro evolution methods to create in Neocarzinostatin a new binding site for a target molecule unrelated to its natural ligand. The main objective of this work was to solve the structure of some of the selected binders in complex with the target molecule: testosterone. Three proteins (1a.15, 3.24 and 4.1) were chosen as representative members of sequence families that came out of the selection process within different randomization schemes. In order to evaluate ligand-induced conformational adaptation, we also determined the structure of one of the proteins (3.24) in the free and complexed forms. Surprisingly, all these mutants bind not one but two molecules of testosterone in two very different ways. The 3.24 structure revealed that the protein spontaneously evolved in the system to bind two ligand molecules in one single binding crevice. These two binding sites are formed by substituted as well as by non-variable side-chains. The comparison with the free structure shows that only limited structural changes are observed upon ligand binding. The X-ray structures of the complex formed by 1a.15 and 4.1 Neocarzinostatin mutants revealed that the two variants form very similar dimers. These dimers were observed neither for the uncomplexed variants nor for wild-type Neocarzinostatin but were shown here to be induced by ligand binding. Comparison of the three complexed forms clearly suggests that these unanticipated structural responses resulted from the molecular arrangement used for the selection experiments.

Binding Sites↗
PubMed2005

Substrate utilization and kinetics of surfactant metabolism in evolving bronchopulmonary dysplasia.

OBJECTIVES: To use stable isotopically labeled precursors of pulmonary surfactant phospholipids to measure precursor utilization and surfactant turnover in premature infants who required mechanical ventilation at birth, 2 weeks, and >4 weeks of age. STUDY DESIGN: Infants of < or =28 weeks' gestation received simultaneous 24-hour intravenous infusions of [1,2,3,4-13C4] palmitate and [1-13C1] acetate at birth, 2 weeks, and > or =4 weeks of life. Disaturated phospholipids were extracted from sequential tracheal aspirate samples obtained over a period of 2 weeks. Fractional catabolic rate (a measure of total turnover) and the fractional synthetic rates from plasma palmitate and de novo synthesis (acetate) were measured. RESULTS: The fractional catabolic rate increased from 25.3% +/- 7.0% per day at birth to 53.8% +/- 14.4% per day at 4 weeks (P=.001). The combined contribution from plasma palmitate and de novo synthesis to total synthesis increased from 44.2% +/- 19.8% at birth to 85.2% +/- 32.8% at 4 weeks (P=.03). CONCLUSIONS: Total surfactant turnover increased in premature infants with evolving bronchopulmonary dysplasia. The increasing contributions from acetate and plasma palmitate suggest a decrease in surfactant phospholipid recycling.

Acetic Acid↗
PubMed2005

Charting epilepsy by searching for intelligence in network space with the help of evolving autonomous agents.

The problem of demarcating neural network space is formidable. A simple fully connected recurrent network of five units (binary activations, synaptic weight resolution of 10) has 3.2 *10(26) possible initial states. The problem increases drastically with scaling. Here we consider three complementary approaches to help direct the exploration to distinguish epileptic from healthy networks. [1] First, we perform a gross mapping of the space of five-unit continuous recurrent networks using randomized weights and initial activations. The majority of weight patterns (>70%) were found to result in neural assemblies exhibiting periodic limit-cycle oscillatory behavior. [2] Next we examine the activation space of non-periodic networks demonstrating that the emergence of paroxysmal activity does not require changes in connectivity. [3] The next challenge is to focus the search of network space to identify networks with more complex dynamics. Here we rely on a major available indicator critical to clinical assessment but largely ignored by epilepsy modelers, namely: behavioral states. To this end, we connected the above network layout to an external robot in which interactive states were evolved. The first random generation showed a distribution in line with approach [1]. That is, the predominate phenotypes were fixed-point or oscillatory with seizure-like motor output. As evolution progressed the profile changed markedly. Within 20 generations the entire population was able to navigate a simple environment with all individuals exhibiting multiply-stable behaviors with no cases of default locked limit-cycle oscillatory motor behavior. The resultant population may thus afford us a view of the architectural principles demarcating healthy biological networks from the pathological. The approach has an advantage over other epilepsy modeling techniques in providing a way to clarify whether observed dynamics or suggested therapies are pointing to computational viability or dead space.

Action Potentials↗
PubMed2006

Contemporary management of right atrial isomerism: effect of evolving therapeutic strategies.

OBJECTIVES: Infants with right atrial isomerism have poor outcomes because of a complex combination of cardiac anomalies. Aggressive management of total anomalous pulmonary venous drainage might have a positive effect on the prognosis. METHODS: Outcomes of all children with right atrial isomerism from 1994 to the present were reviewed. Management of total anomalous pulmonary venous drainage evolved from no repair or conventional surgical technique to primary sutureless repair on initial palliation. Cox survival models were used to identify variables associated with reduced survival. RESULTS: There were 55 children enrolled in the study. The median age at the initial visit was 2 days. Fifty-one patients had total anomalous pulmonary venous drainage (obstructive in 22 patients). Withdrawal of treatment occurred in 11 (20%) of 55 patients during an interval of institutional bias toward no treatment. Thirteen (24%) of 55 patients had palliations without total anomalous pulmonary venous drainage repair, and 3 (23%) of 13 survived. Thirty-one (56%) of 55 patients had operations that included total anomalous pulmonary venous drainage repair, of whom 13 (42%) of 31 underwent primary sutureless repair for total anomalous pulmonary venous drainage. Sixteen (52%) of 31 survived, and their current status 1 to 10 years (median, 5.8 years) after repair is post-Fontan (7/16 [44%]), postbidirectional Glenn (6/16 [38%]), and others (3 [20%]). In patients who underwent total anomalous pulmonary venous drainage repair (n = 31), 2 risk factors of decreased survival were identified: drainage site obstruction and infracardiac or mixed-type total anomalous pulmonary venous drainage. After adjustment, sutureless repair appeared to be associated with improved survival (hazard ratio, 0.43), but this beneficial effect did not reach significance (P = .19). CONCLUSIONS: Mortality continues to be high; however, aggressive total anomalous pulmonary venous drainage repair for right atrial isomerism has resulted in improved survival. The role of primary sutureless repair for total anomalous pulmonary venous drainage remains to be defined.

Anastomosis, Surgical↗
PubMed2006

Cytokinesis-block micronucleus assay evolves into a "cytome" assay of chromosomal instability, mitotic dysfunction and cell death.

The cytokinesis-block micronucleus (CBMN) assay was originally developed as an ideal system for measuring micronuclei (MNi) however it can also be used to measure nucleoplasmic bridges (NPBs), nuclear buds (NBUDs), cell death (necrosis or apoptosis) and nuclear division rate. Current evidence suggests that (a) NPBs originate from dicentric chromosomes in which the centromeres have been pulled to the opposite poles of the cell at anaphase and are therefore indicative of DNA mis-repair, chromosome rearrangement or telomere end-fusions, (b) NPBs may break to form MNi, (c) the nuclear budding process is the mechanism by which cells remove amplified and/or excess DNA and is therefore a marker of gene amplification and/or altered gene dosage, (d) cell cycle checkpoint defects result in micronucleus formation and (e) hypomethylation of DNA, induced nutritionally or by inhibition of DNA methyl transferase can lead to micronucleus formation either via chromosome loss or chromosome breakage. The strong correlation between micronucleus formation, nuclear budding and NPBs (r=0.75-0.77, P<0.001) induced by either folic acid deficiency or exposure to ionising radiation is supportive of the hypothesis that folic acid deficiency and/or ionising radiation cause genomic instability and gene amplification by the initiation of breakage-fusion-bridge cycles. In its comprehensive mode, the CBMN assay measures all cells including necrotic and apoptotic cells as well as number of nuclei per cell to provide a measure of cytotoxicity and mitotic activity. The CBMN assay has in fact evolved into a "cytome" method for measuring comprehensively chromosomal instability phenotype and altered cellular viability caused by genetic defects and/or nutrional deficiencies and/or exogenous genotoxins thus opening up an exciting future for the use of this methodology in the emerging fields of nutrigenomics and toxicogenomics and their combinations.

Animals↗
PubMed2006

Differential sensitivity of in vivo and ex vivo diffusion tensor imaging to evolving optic nerve injury in mice with retinal ischemia.

Decreased axial (lambda(||)) and increased radial (lambda( perpendicular)) diffusivity have been shown to reflect axonal and myelin injury respectively. In the present study, evolving white matter injury within the optic nerves of mice with retinal ischemia was examined by in vivo and ex vivo measurements of lambda(||) and lambda( perpendicular). The results show that at 3 days after retinal ischemia, a 33% decrease in vivo and a 38% decrease ex vivo in lambda(||) without change in lambda( perpendicular) was observed in the injured optic nerve compared to the control, suggestive of axonal damage without myelin injury. At 14 days, both in vivo and ex vivo measured lambda( perpendicular) increased significantly to 220-240% of the control level in the injured optic nerve suggestive of myelin damage. In contrast, the axonal injury that was clearly detected in vivo as a significantly decreased lambda(||) (33% decrease) was not as clearly detected by ex vivo lambda(||) (17% decrease). The current findings suggest that ex vivo lambda( perpendicular) is comparable to in vivo lambda( perpendicular) in detecting myelin injury. However, the structural changes resulting from axonal damage causing the decreased in vivo lambda(||) may not be preserved ex vivo in the fixed tissues. Despite the accurate depiction of the pathology using lambda(||) and lambda( perpendicular) in vivo, the use of ex vivo lambda(||) to extrapolate the status of axonal injury in vivo would require further investigation.

Algorithms↗
PubMed2004

Generalised myoclonus evolving into epilepsia partialis continua due to a cingulate gyrus lesion: case report and review of the literature.

A young Chinese male was admitted for a generalised tonic-clonic seizure preceded by a week-long history of fever. Subsequently, he developed continuous myoclonic jerks in all four limbs, with clear left sided predominance, and no accompanying clouding of consciousness. Contrast MRI of the brain demonstrated a venous angioma in the right cingulate gyrus. Over the next few days, the clinical picture evolved, with focal motor status involving primarily the left lower limb and the abdomen. These movements resolved with anticonvulsant therapy. This case illustrates generalised myoclonus arising from a focal brain abnormality. The epileptiform aetiology became obvious only after evolution into the typical features of a focal motor seizure and supportive neuroimaging. This demonstrates the protean manifestations of epileptic seizures which have been ascribed to the cingulate gyrus. The lack of clear declarative clinical and EEG features highlights the melding of the fields of epileptology and movement disorders.

Adult↗
PubMed2004

The rapidly evolving field of plant centromeres.

Meiotic and mitotic chromosome segregation are highly conserved in eukaryotic organisms, yet centromeres--the chromosomal sites that mediate segregation--evolve extremely rapidly. Plant centromeres have DNA elements that are shared across species, yet they diverge rapidly through large- and small-scale changes. Over evolutionary time-scales, centromeres migrate to non-centromeric regions and, in plants, heterochromatic knobs can acquire centromere activity. Discerning the functional significance of these changes will require comparative analyses of closely related species. Combined with functional assays, continued efforts in plant genomics will uncover key DNA elements that allow centromeres to retain their role in chromosome segregation while allowing rapid evolution.

Centromere↗
PubMed2005

Otitis media: re-evaluation of diagnosis and treatment in the era of antimicrobial resistance, pneumococcal conjugate vaccine, and evolving morbidity.

The changing susceptibility of bacterial otopathogens is only one aspect of the evolving concepts regarding pathogenesis, immunoprophylaxis, pharmacodynamics, and sequelae of acute otitis media that mandates new insights for achieving a successful outcome. 2004 guidelines by the American Academy of Pediatrics for the treatment of acute otitis media provide one perspective that proposes a rethinking of the routine use of antimicrobial therapy with the hope of preventing further increases in bacterial resistance among otopathogens. The goals of this article are to incorporate the advances in diagnosis, treatment, prevention, and management of sequelae into strategies that optimize the outcome of acute otitis media and limit further emergence of resistant otopathogens.

Acute Disease↗
PubMed2004

The evolving role of postoperative adjuvant radiation therapy for pancreatic cancer.

The benefit of postoperative adjuvant chemoradiation in the treatment of resected pancreatic cancers was first established by a randomized trial conducted by the Gastrointestinal Tumor Study Group in 1974. During the past 3 decades, treatment has evolved toward more dose-intensive regimens of chemoradiation. Historical split-course conventional radiation therapy has been replaced by continuous-course radiotherapy to higher doses, and gemcitabine is being actively investigated as a potentially more effective agent than 5-fluorouracil. This article critically examines the results of important randomized multi-institutional trials and reviews the evolution toward dose-intensive adjuvant treatment regimens. Implications of the recently completed intergroup study are discussed, modern radiation therapy delivery techniques are reviewed, and suggestions for future trials are made.

Adenocarcinoma↗
PubMed2006

Prevalence of aspirin resistance in patients with an evolving acute myocardial infarction.

OBJECTIVE: To study the prevalence and importance of aspirin resistance in patients with an evolving acute myocardial infarction (AMI) by use of the Platelet Function Analyzer-100. INTRODUCTION: Previous studies have demonstrated the existence of aspirin resistance, but the clinical relevance of the phenomenon remains to be clarified. If aspirin resistant patients comprise a high-risk subgroup, it might be expected that the prevalence of aspirin resistance in patients with AMI would be higher than in patients without AMI. We hypothesized that the prevalence of aspirin resistance in patients with AMI was twice the prevalence in patients without AMI. METHODS: We included 298 consecutive patients with known cardiovascular disease who were admitted to hospital with symptoms suggestive of an AMI. All had been taking aspirin 150 mg/day for at least 7 days prior to hospital admission. Platelet function was measured immediately at admission, and aspirin resistance was defined as a collagen/epinephrine Closure Time (CT(CEPI))<165 s. RESULTS: We found that 70 (23.5%) patients were aspirin resistant, and 70 (23.5%) patients ended up with the diagnosis of an AMI. The prevalence of aspirin resistance was significantly higher in patients with AMI as compared to patients without (36% versus 20%, OR 2.26, CI 95% 1.19-4.22, p=0.0058). The CT(CEPI) measured at admission was an independent factor associated with an AMI. CONCLUSIONS: Aspirin resistance is present in almost one fourth of patients admitted to hospital with symptoms suggestive of an AMI, and aspirin resistance is significantly associated with the diagnosis of a definite AMI.

Aged↗
PubMed2004

Synthetic biology evolves.

Synthetic biology is advancing rapidly as biologists, physicists and engineers are combining their efforts to understand and program cell function. By characterizing isolated genetic components or modules, experimentalists have paved the way for more quantitative analyses of genetic networks. A recent paper presents a method of computational, or in silico, evolution in which a set of components can evolve into networks that display desired behaviors. An integrated approach that includes a strategy of in silico design by evolution, together with efforts exploiting directed evolution in vivo, is likely to be the next step in the evolution of synthetic biology.

Algorithms↗
PubMed2004

Evolving practice patterns in heart transplantation: a single-center experience over 15 years.

This analysis is a retrospective characterization of evolving patterns in donor and recipient risk factors for early and late outcomes (survival and freedom from rejection) along with determinants of hospital and 1-year mortality after heart transplantation over a 15-year experience in a single center. Profiles and outcomes were evaluated for procedures performed between 1988 and 1995 (group A, n = 105) versus 1996 and 2003 (group B, n = 218). The following parameters were considered: pretransplant diagnosis, recipient age UNOS status, donor age, total postretrieval ischemic time, donor/recipient size match, and degree of myocardial necrosis at biopsy. Recipients in group B were significantly more compromised as demonstrated by UNOS status (11.4% vs 19.3%; P =.05) and pretransplant pulmonary vascular resistance (2.3 +/- 1.5 vs 3.1 +/- 1.5; P =.04). Marginal donors were more frequently used for group B procedures (21.9% vs 47.7%; P <.0001). Outcomes were significantly more favorable among group B patients in terms of hospital mortality (18.1% vs 10.6%; P =.046), and 1- and 5-year actuarial survival (72.4% vs 83.4%, 60% vs 73.3%, respectively; P =.006). Analysis of the causes of death disclosed a significant reduction in fatal events due to graft failure and acute rejection in group B. No difference emerged with regard to actual freedom from acute rejection. Determinants of hospital mortality were pretransplant diagnosis, UNOS status, donor age, and cardioplegic solution. Transplant era, recipient age, infectious episodes, and ischemic necrosis at biopsy were risk factors for 1-year mortality. We conclude that despite extensive usage of marginal donors and selection of worse candidates, significantly better outcomes were achieved due to improvements in global management strategies.

Cause of Death↗
PubMedDate not supplied

Evolving techniques and perspectives in lung transplantation.

Lung transplantation is currently a suitable option for patients with end-stage lung disease. Since the early 1980s the surgical technique and immunosuppressive protocols have been progressively modified to improve results and favor long-term survival. The original heart-lung transplantation under cardiopulmonary bypass is now rarely performed and single or bilateral lung transplantation is the procedure of choice. Bilateral transplantation is performed with two single lung transplants performed in sequence. Extracorporeal support is rarely employed and in most cases it is instituted through the femoral approach. Also, the surgical approach has been modified and the original clam shell incision has been replaced by two small anterior thoracotomies. The use of marginal donors has been increasingly proposed to enlarge the number of organs potentially available for transplantation. Immunosuppressive protocols have evolved to patient-specific regimens that can be quickly modified if required by the clinical status. Induction is now more aggressive and also rescue protocols for obliterative bronchiolitis can contribute to improved outcomes. Overall, lung transplantation is now performed with encouraging long-term results.

Humans↗