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PubMed2006

A rapidly evolving secretome builds and patterns a sea shell.

BACKGROUND: Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. RESULTS: Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. CONCLUSION: The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.

Animal Structures↗
PubMed2006

Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection.

BACKGROUND: The mutation spectra of the TP53 gene and other tumor suppressors contain multiple hotspots, i.e., sites of non-random, frequent mutation in tumors and/or the germline. The origin of the hotspots remains unclear, the general view being that they represent highly mutable nucleotide contexts which likely reflect effects of different endogenous and exogenous factors shaping the mutation process in specific tissues. The origin of hotspots is of major importance because it has been suggested that mutable contexts could be used to infer mechanisms of mutagenesis contributing to tumorigenesis. RESULTS: Here we apply three independent tests, accounting for non-uniform base compositions in synonymous and non-synonymous sites, to test whether the hotspots emerge via selection or due to mutational bias. All three tests consistently indicate that the hotspots in the TP53 gene evolve, primarily, via positive selection. The results were robust to the elimination of the highly mutable CpG dinucleotides. By contrast, only one, the least conservative test reveals the signature of positive selection in BRCA1, BRCA2, and p16. Elucidation of the origin of the hotspots in these genes requires more data on somatic mutations in tumors. CONCLUSION: The results of this analysis seem to indicate that positive selection for gain-of-function in tumor suppressor genes is an important aspect of tumorigenesis, blurring the distinction between tumor suppressors and oncogenes. REVIEWERS: This article was reviewed by Sandor Pongor, Christopher Lee and Mikhail Blagosklonny.

Journal Article↗
PubMed2006

High-throughput genomic technology in research and clinical management of breast cancer. Evolving landscape of genetic epidemiological studies.

Candidate polymorphism-based genetic epidemiological studies have yielded little success in the search for low-penetrance breast cancer susceptibility genes. The lack of progress is partially due to insufficient coverage of genomic regions with genetic markers, as well as economic constraints, limiting both the number of genetic targets and the number of individuals being studied. Recent rapid advances in high-throughput genotyping technology and our understanding of genetic variation patterns across the human genome are now revolutionizing the way in which genetic epidemiological studies are being designed and conducted. Genetic epidemiological studies are quickly progressing from candidate gene studies to comprehensive pathway investigation and, further, to genomic epidemiological studies where the whole human genome is being interrogated to identify susceptibility alleles. This paper reviews the evolving approaches in the search for low-penetrance breast cancer susceptibility gene variants and discusses their potential promises and pitfalls.

Breast Neoplasms↗
PubMed2006

Key advances in critical care in the out-of-hospital setting: the evolving role of laypersons and technology.

During the past decade, critical care in the out-of-hospital setting has transcended the original emphasis on on-scene advanced life support interventions by doctors, paramedics, and nurses. Many of the life-saving efforts and advances in critical care situations have now begun to focus more and more on how, through evolving technology, the average person can save lives and perhaps even spare precious intensive care unit (ICU) resources. A striking example was the recent study conducted at the Chicago airports at which automated external defibrillators (AEDs) were deployed throughout the airline terminals for use by the public at large. Not only did random bystanders on the concourses save an extremely high percentage of cardiac arrest patients with the AEDs, most patients rapidly awakened, even before the arrival of professional rescuers. Thus, this technology-assisted intervention, performed by an average person, pre-empted the need for many other critical care interventions and prolonged care in the ICU. Equipped with automated prompts to improve performance, new technology also exists to help to monitor the inadequacies and too-frequent interruption of life-saving chest compressions during basic cardiopulmonary resuscitation. As a result of these technological advances, survival rates for cardiac arrest are now expected to improve significantly.

Ambulatory Care↗
PubMed2003

The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.

BACKGROUND: The rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. They are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. On the basis of experimental studies with the developmental regulator rhomboid from Drosophila and the AarA protein from the bacterium Providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose signaling function is conserved in eukaryotes and prokaryotes. RESULTS: Phylogenetic tree analysis carried out using several independent methods for tree constructions and the corresponding statistical tests suggests that, despite its broad distribution in all three superkingdoms, the rhomboid family was not present in the last universal common ancestor of extant life forms. Instead, we propose that rhomboids evolved in bacteria and have been acquired by archaea and eukaryotes through several independent horizontal gene transfers. In eukaryotes, two distinct, ancient acquisitions apparently gave rise to the two major subfamilies, typified by rhomboid and PARL (presenilins-associated rhomboid-like protein), respectively. Subsequent evolution of the rhomboid family in eukaryotes proceeded by multiple duplications and functional diversification through the addition of extra transmembrane helices and other domains in different orientations relative to the conserved core that harbors the protease activity. CONCLUSIONS: Although the near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic tree analysis indicates a likely bacterial origin with subsequent dissemination by horizontal gene transfer. This emphasizes the importance of explicit phylogenetic analysis for the reconstruction of ancestral life forms. A hypothetical scenario for the origin of intracellular membrane proteases from membrane transporters is proposed.

Amino Acid Sequence↗
PubMed2005

Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

BACKGROUND: Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellular genome ever sequenced (480 kb), has been suggested as the representative of a new phylum -- the Nanoarchaeota -- that would have diverged before the Crenarchaeota/Euryarchaeota split. Confirming the phylogenetic position of N. equitans is thus crucial for deciphering the history of the archaeal domain. RESULTS: We tested the placement of N. equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes. We indicate that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers. Indeed, we show that different subsets of ribosomal proteins harbor a conflicting phylogenetic signal for the placement of N. equitans. A BLASTP-based survey of the phylogenetic pattern of all open reading frames (ORFs) in the genome of N. equitans revealed a surprisingly high fraction of close hits with Euryarchaeota, notably Thermococcales. Strikingly, a specific affinity of N. equitans and Thermococcales was strongly supported by phylogenies based on a subset of ribosomal proteins, and on a number of unrelated molecular markers. CONCLUSION: We suggest that N. equitans may more probably be the representative of a fast-evolving euryarchaeal lineage (possibly related to Thermococcales) than the representative of a novel and early diverging archaeal phylum.

Crenarchaeota↗
PubMed2026

Enhancing detection of polygenic adaptation: a comparative study of machine learning and statistical approaches using simulated evolve-and-resequence data.

BACKGROUND: Detecting signals of polygenic adaptation remains a significant challenge in population genomics, as traditional methods often struggle to identify the associated subtle, multi-locus allele-frequency shifts. Here, we introduced and tested several novel approaches combining machine learning techniques with traditional statistical tests to detect polygenic adaptation patterns in time-series of allele frequency changes from whole genome data. We implemented a Naive Bayesian Classifier (NBC) and One-Class Support Vector Machines (OCSVM), and compared their performance against the classical Fisher's Exact Test (FET). Furthermore, we combined machine learning and statistical models (OCSVM-FET and NBC-FET), resulting in 5 competing approaches. The framework is mainly designed and validated for evolve-and-resequence (EaR) experimental designs, where defined selection pressures and temporal sampling are feasible, but might be applicable for certain natural experiments as well. RESULTS: Using a simulated dataset based on empirical C. riparius Pool-Seq data, we evaluated methods across evolutionary scenarios varying in generation, selection strength, and number of loci under selection. Our results demonstrate that the combined OCSVM-FET approach consistently outperformed competing methods, achieving the lowest false positive rate, highest area under the curve, and high accuracy. The performance peak aligned with what we term the 'late dynamic phase' of adaptation - the period after initial selection has occurred but before fixation - highlighting the method's sensitivity to ongoing selective processes. CONCLUSIONS: Furthermore, we emphasize the critical role of parameter tuning, balancing biological assumptions with methodological rigor. While broader applicability remains an important direction for future work, the present benchmarking is intentionally scoped to EaR experimental contexts.

Machine Learning↗
PubMed2004

Evolving spinal analgesia practice in palliative care.

Intraspinal analgesia can be helpful in some patients with intractable pain. Over 15 years palliative care professionals evolved their spinals policy through a repeated series of evaluations, discussions and literature reviews. One hundred intraspinal lines were then reviewed. Notable changes in policy were the switch from epidurals to intrathecals, and the insertion of lines during working hours rather than as emergencies. Our efficacy, and frequency of adverse effects, is equal or better to published studies. Key issues in reducing adverse effects were the improved care of the spinal line exit site, a change from bolus administration to continuous infusions, and modifying line insertion techniques. Current policy is to use continuous infusions of diamorphine and bupivacaine in a 1:5 ratio through externalized intrathecal lines. The lines are effective in approximately two thirds of patients and can be kept in place for up to 18 months. The policy continues to be updated and common documentation is now in place.

Adult↗
PubMed2003

Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances.

The EAV/CR framework, designed for database support of rapidly evolving scientific domains, utilizes metadata to facilitate schema maintenance and automatic generation of Web-enabled browsing interfaces to the data. EAV/CR is used in SenseLab, a neuroscience database that is part of the national Human Brain Project. This report describes various enhancements to the framework. These include (1) the ability to create "portals" that present different subsets of the schema to users with a particular research focus, (2) a generic XML-based protocol to assist data extraction and population of the database by external agents, (3) a limited form of ad hoc data query, and (4) semantic descriptors for interclass relationships and links to controlled vocabularies such as the UMLS.

Database Management Systems↗
PubMed2006

Diversity in the complementarity-determining region 3 (CDR3) of antibodies from mice with evolving anti-thyroid-stimulating hormone receptor antibody responses.

In a mouse model of autoimmune Graves' disease, stimulatory anti-TSH receptor (TSHR) antibodies (TSAbs) slowly evolve upon repeated immunization with TSHR and lead to hyperthyroidism. Although all immunized mice developed high levels of TSH-binding inhibitory Ig (TBII), only a subset of these mice become hyperthyroid, suggesting that the generation of pathogenic antibodies (Abs) may require affinity maturation. We analyzed the complementarity-determining region 3 (CDR3) of IGHV1 and IGHV5 heavy chains from mice at different stages of disease development. Subcloned CDR3 PCR products were amplified from RNA isolated from enriched splenic B/plasma cells of a control mouse, and mice with low TBII and normal T(4) levels (LTNT(4)), high TBII and normal T(4) levels (HTNT(4)), and high TBII and high T(4) levels (HTHT(4)). Using statistical analyses, we correlated usage of D and J genes and the amino acid composition and length of and mutations within the CDR3 with different outcomes after TSHR immunization. CDR3 sequences from TSHR-immunized mice contained a higher frequency of D gene SP2.9 relative to control, whereas sequences from HTHT(4) contained a higher frequency of D gene Q52 compared with sequences from LTNT(4). Furthermore, HTHT(4) sequences also contained higher CDR3 replacement mutations, relative to LTNT(4) and HTNT(4) mice, that are indicative of somatic hypermutation. Collectively, our results suggest that higher somatic mutations within the CDR3 may correlate with pathogenic antibodies against the TSHR.

Animals↗
PubMed2005

Isolated autosomal dominant growth hormone deficiency: an evolving pituitary deficit? A multicenter follow-up study.

Four distinct familial types of isolated GH deficiency have been described so far, of which type II is the autosomal dominant inherited form. It is mainly caused by mutations within the first 6 bp of intervening sequence 3. However, other splice site and missense mutations have been reported. Based on in vitro experiments and transgenic animal data, there is strong evidence that there is a wide variability in phenotype in terms of the severity of GH deficiency. Therefore, we studied a total of 57 subjects belonging to 19 families suffering from different splice site as well as missense mutations within the GH-1 gene. The subjects presenting with a splice site mutation within the first 2 bp of intervening sequence 3 (5'IVS +1/+2 bp) leading to a skipping of exon 3 were found to be more likely to present in the follow-up with other pituitary hormone deficiencies. In addition, although the patients with missense mutations have previously been reported to be less affected, a number of patients presenting with the P89L missense GH form, showed some pituitary hormone impairment. The development of multiple hormonal deficiencies is not age dependent, and there is a clear variability in onset, severity, and progression, even within the same families. The message of clinical importance from these studies is that the pituitary endocrine status of all such patients should continue to be monitored closely over the years because further hormonal deficiencies may evolve with time.

Adolescent↗
PubMed2001

Glatiramer acetate reduces the proportion of new MS lesions evolving into "black holes".

The authors evaluated whether glatiramer acetate (GA) modifies the severity of tissue damage in 1,722 new lesions from 239 patients with MS enrolled in a placebo-controlled trial monitored with monthly cerebral MRI. The percentage of new lesions that evolved into "black holes" was lower in GA-treated than in placebo patients on scans at 7 (18.9 and 26.3%; p = 0.04) and 8 (15.6 and 31.4%; p = 0.002) months after lesion appearance. GA has a favorable effect on tissue disruption in MS lesions once they are formed.

Adolescent↗
PubMed2002

The evolving place of vagus nerve stimulation therapy.

Approximately 40% of patients with epilepsy have seizures that do not adequately respond to medical therapy. Vagus nerve stimulation (VNS) therapy, approved 5 years ago by the Food and Drug Administration, offers a therapeutic option for patients with pharmacoresistant seizures. This supplement updates developments with VNS therapy since its approval and suggests future directions for this still-evolving treatment.

Electric Stimulation Therapy↗
PubMed2005

The evolving and important role of anesthesiology in palliative care.

A small but clinically significant proportion of dying patients experience severe physically or psychologically distressing symptoms that are refractory to the usual first-line therapies. Anesthesiologists, currently poorly represented in the rapidly evolving specialties of hospice and palliative medicine, are uniquely qualified to contribute to the comprehensive care of patients who are in this category. Anesthesiologists' interpersonal capabilities in the management of patients and families under duress, their knowledge and comfort level with the application of potent analgesic and consciousness-altering pharmacology, and their titrating and monitoring skills would add a valuable dimension to palliative care teams. This article summarizes the state of the art and means by which anesthesiologists might contribute to improvements in the important end-of-life outcome of safe and comfortable dying.

Adenocarcinoma↗
PubMed2006

A reaction-diffusion analysis of energetics in large muscle fibers secondarily evolved for aerobic locomotor function.

The muscles that power swimming in the blue crab, Callinectes sapidus, grow hypertrophically, such that in juvenile crabs the cell diameters are <60 microm, whereas fibers of the adult crabs often exceed 600 microm. Thus, as these animals grow, their muscle fibers greatly exceed the surface area to volume ratio and intracellular diffusion distance limits of most cells. Previous studies have shown that arginine phosphate (AP) recovery in the anaerobic (light) fibers, which demonstrate a fiber size dependence on anaerobic processes following contraction, is too slow to be restricted by intracellular metabolite diffusive flux, in spite of the fiber's large size. By contrast, the aerobic (dark) fibers have evolved an intricate network of intracellular subdivisions that maintain an effectively small ;metabolic diameter' throughout development. In the present study, we examined the impact of intracellular metabolite diffusive flux on the rate of post-contractile AP resynthesis in the dark muscle, which has a much higher aerobic capacity than the light muscle. AP recovery was measured for 60 min in adults and 15 min in juveniles following burst contractile activity in dark fibers, and a mathematical reaction-diffusion model was used to test whether the observed aerobic rates of AP resynthesis were fast enough to be limited by intracellular metabolite diffusion. Despite the short diffusion distances and high mitochondrial density, the AP recovery rates were relatively slow and we found no evidence of diffusion limitation. However, during simulation of steady-state contraction, which is an activity more typical of the dark fibers, there were substantial intracellular metabolite gradients, indicative of diffusion limitation. This suggests that high ATP turnover rates may lead to diffusion limitation in muscle even when diffusion distances are short, as in the subdivided dark fibers.

Adenosine Triphosphate↗
PubMed1988

Effects of mannitol in the prevention of evolving myocardial infarction.

The ability of hyperosmolar mannitol to salvage evolving myocardial infarction was studied in 50 open-chest dogs subjected to 3 hours occlusion of the left anterior descending coronary artery. In 28 dogs, 20% hyperosmolar mannitol was infused into the distal half of the infarcted portion after commencement of reperfusion, leaving the proximal half mannitol free. In the other 22 dogs, physiological saline was infused instead of mannitol. The wall thickness at the distal half of the infarcted portion was increased 2 hours after reperfusion in both the saline and the mannitol groups. After 2 hours reperfusion the chest was closed. Thirteen out of 28 dogs in the mannitol group and 12 out of 22 dogs in the saline group died over one week. Seven days later, myocardial samples were measured for myocardial water content and creatine phosphokinase activity (CPK). Myocardial water content was increased in the infarcted portion in both the saline and the mannitol groups. In the saline group, myocardial CPK was reduced markedly in the proximal half (54.8 +/- 7.8% at the inner layer and 53.1 +/- 4.7% at the outer layer). These depletions were even more marked in the distal half (47.9 +/- 5.8 and 48.3 +/- 3.3%). In the mannitol groups, although the CPK was similarly depressed in the proximal half (44.8 +/- 5.8 and 41.1 +/- 5.4%), the CPK depletion in the distal half was less (48.1 +/- 6.1 and 58.1 +/- 6.7%) than the proximal half, suggesting mannitol preserved CPK depletion in the infarcted portion. It was concluded that intracoronary infusion of mannitol after reperfusion may salvage the infarcted myocardium.

Animals↗
PubMed1989

Role of PMN elastase on ischemic myocardial injury in evolving myocardial infarction: correlation with clinical parameters and intervention by protease inhibitor ulinastatin.

The purposes of this study were to investigate the sequential changes of PMN elastase during evolving myocardial infarction, and also to ascertain whether or not ulinastatin (UL), a clinically useful protease inhibitor, would affect the extent of ischemic myocardial injury. The levels of plasma PMN elastase (as alpha 1-proteinase inhibitor-elastase complex) were measured once in 13 normal controls, and at intervals in 30 acute myocardial infarction (AMI) patients given UL and 30 AMI controls on conventional therapy, and compared between the groups. The levels in control group on conventional therapy were significantly higher from 6 to 72 hours after the onset than those in normal controls. Maximum PMN elastase levels in non-survivors (n = 7) were significantly higher than in survivors (n = 23) at the 6-month follow-up (288.7 +/- 75.8 vs. 188.1 +/- 56.9 micrograms/l, p less than 0.01). The maximum level of PMN elastase in patients given UL was significantly lower than that in the control group (162.2 +/- 96.2 vs 207.3 +/- 70.1 micrograms/l, p less than 0.05), and the peak CK-MB in patients given UL was significantly lower than that in controls (252.3 +/- 150.9 vs 360.1 +/- 239.6 IU/l, p less than 0.05). Early mortality (seen at 6-month follow-up) in patients administered UL was significantly lower than that of the treated controls (3.3% vs 23.3%, p less than 0.05). Analysis of changes in PMN elastase levels suggested that UL would be clinically beneficial for reduction of ischemic myocardial injury.

Aged↗
PubMed1991

Intravenous recombinant tissue-type plasminogen activator (rt-PA) and urokinase (UK) in patients with evolving myocardial infarction--a multicenter double-blind, randomized trial in Japan.

Intravenous administrations of 2000 x 10(4)IU (33 mg) (rt-PA2) and 3000 x 10(4)IU (50 mg) (rt-PA3) of a new recombinant tissue plasminogen activator (rt-PA:TD-2061) derived from uterine endothelial cells and urokinase (UK) 96 x 10(4)IU were compared in a double blind, randomized trial of 198 patients with evolving myocardial infarction. All patients entered the trial within 6 h of the onset of symptoms and underwent baseline coronary angiography of the infarct-related coronary artery before thrombolytic therapy was instituted. Sixty minutes following thrombolytic therapy occluded infarct-related arteries were successfully reperfused in 41.5% of 66 patients in the UK, 76.4% of 72 patients in the rt-PA2, and 74.6% of 59 patients in the rt-PA3 group. Statistically significant differences were observed between the UK and rt-PA groups (p less than 0.01). Serum fibrinogen levels declined in all 3 groups at 60 min post-therapy by averages of 35.9 +/- 3.1% in the UK, 16.8 +/- 4.8% in the rt-PA2 and 17.5 +/- 4.5% in the rt-PA3 group. The difference between the UK and the rt-PA groups was statistically significant (p less than 0.01). Plasma plasminogen and alpha 2-plasmin inhibitor levels showed the same tendencies. Bleeding was the most commonly observed complication and was most commonly seen at the catheterization site. There was no difference in the incidence among the 3 groups. Hospital deaths occurred in 5.3%, 6.3%, and 4.7% of the cases in the UK, rt-PA2 and rt-PA3 groups, respectively. We conclude, therefore, that rt-PA achieves a significantly higher rate of recanalization with less extensive systemic fibrinogenolysis at the dose employed than does UK. The optimum intravenous dose of rt-PA for Japanese patients is considered to be 2000 x 10(4)IU (33 mg).

Blood Coagulation↗