Deep homology in the age of next-generation sequencing

The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'

Influence of thoracic epidural analgesia on cardiovascular autonomic control after thoracic surgery

Background. Thoracic epidural analgesia (TEA) is effective in alleviating pain after major thoracoabdominal surgery and may also reduce postoperative mortality and morbidity. This study investigated cardiovascular autonomic control in patients undergoing elective thoracic surgery and its modulation by continuous TEA. Methods. Thirty‐eight patients were randomly assigned to receive patient‐controlled analgesia (PCA group) or thoracic epidural analgesia (TEA group) with doses of bupivacaine (0.25% during operation, 0.125% after operation) and fentanyl (2 µgml-1). Heart rate variability (HRV), baroreflex function and pressure response to nitroglycerine and phenylephrine were assessed before operation, 4 h after the end of surgery (POD 0) and on the first and second postoperative days (POD1 and POD2). Results. Early after surgery, all HRV variables and baroreflex sensitivities were markedly decreased in both groups. In the TEA group, total HRV and its high‐frequency components (HF) increased towards preoperative values at POD1 and POD2, whereas the ratio of low to high frequencies (LF/HF) was significantly reduced (mean (sd), -44 (15)% at POD 0, -38 (17)% at POD1, -37 (18%) at POD2) and associated with blunting of the postoperative increase in heart rate and blood pressure. In the PCA group, the ratio of LF/HF remained unchanged and the decrements in HRV variables persisted until POD2. In the two groups, baroreflex sensitivities and pressure responses recovered preoperative values at POD2. Conclusions. In contrast with PCA management, TEA using low concentrations of bupivacaine and fentanyl blunted cardiac sympathetic neural drive, resulting in vagal predominance, while HRV variables were better restored after surgery. Br J Anaesth 2003; 91: 525-3

Cysteine 230 is essential for the structure and activity of the cytotoxic ligand TRAIL.

Unlike other tumor necrosis factor family members, the cytotoxic ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)/Apo-2L contains an unpaired cysteine residue (Cys(230)) in its receptor-binding domain. Here we show that the biological activity of both soluble recombinant TRAIL and cell-associated, full-length TRAIL is critically dependent on the presence of Cys(230). Mutation of Cys(230) to alanine or serine strongly affected its ability to kill target cells. Binding to its receptors was decreased by at least 200-fold, and the stability of its trimeric structure was reduced. In recombinant TRAIL, Cys(230) was found engaged either in interchain disulfide bridge formation, resulting in poorly active TRAIL, or in the chelation of one zinc atom per TRAIL trimer in the active, pro-apoptotic form of TRAIL

Structural, elastic and thermal properties of cementite (Fe3_3C) calculated using Modified Embedded Atom Method

Structural, elastic and thermal properties of cementite (Fe$_3$C) were studied using a Modified Embedded Atom Method (MEAM) potential for iron-carbon (Fe-C) alloys. Previously developed Fe and C single element potentials were used to develop an Fe-C alloy MEAM potential, using a statistically-based optimization scheme to reproduce structural and elastic properties of cementite, the interstitial energies of C in bcc Fe as well as heat of formation of Fe-C alloys in L$_{12}$ and B$_1$ structures. The stability of cementite was investigated by molecular dynamics simulations at high temperatures. The nine single crystal elastic constants for cementite were obtained by computing total energies for strained cells. Polycrystalline elastic moduli for cementite were calculated from the single crystal elastic constants of cementite. The formation energies of (001), (010), and (100) surfaces of cementite were also calculated. The melting temperature and the variation of specific heat and volume with respect to temperature were investigated by performing a two-phase (solid/liquid) molecular dynamics simulation of cementite. The predictions of the potential are in good agreement with first-principles calculations and experiments.Comment: 12 pages, 9 figure

Perioperative mortality and major cardio-pulmonary complications after lung surgery for non-small cell carcinoma

Objectives: A database of patients operated of lung cancer was analyzed to evaluate the predictive risk factors of operative deaths and life-threatening cardiopulmonary complications. Methods: From 1990 to 1997, data were collected concerning 634 consecutive patients undergoing lung resection for non-small cell carcinoma in an academic medical centre and a regional hospital. Operations were managed by a team of experienced surgeons, anaesthesiologists and chest physicians. Operative mortality was defined as death within 30 days of operation and/or intra-hospital death. Respiratory failure, myocardial infarct, heart failure, pulmonary embolism and stroke were considered as major non-fatal complications. Preoperative risk factors, extent of surgery, pTNM staging, perioperative mortality and major cardiopulmonary complications were recorded and evaluated using chi-square statistics and multivariate logistic regression. Results: Complete data were obtained in 621 cases. The overall operative mortality was 3.2% (n=19). Cardiovascular complications (n=10), haemorrhage (n=4) and sepsis or acute lung injury (n=5) were incriminated as the main causative factors. In addition, there were 13 life-threatening complications (2.1%) consisting in strokes (n=4), myocardial infarcts (n=5), pulmonary embolisms (n=1), acute lung injury (n=1) and respiratory failure (n=2). Four independent predictors of operative death were identified: pneumonectomy, evidence of coronary artery disease (CAD), ASA class 3 or 4 and period 1990-93. In addition, the risk of major complications was increased in hypertensive patients and in those belonging to ASA class 3 or 4. A trend towards improved outcome was observed during the second period, from 1994 to 97. Conclusion: Our data demonstrate that perioperative mortality is mainly dependent on the extent of surgery, the presence of CAD and provision of adequate medical and nursing care. Preoperative testing and interventions to reduce the cardiovascular risk factors may help to further improve perioperative outcom

Quantifying the Energetics and Length Scales of Carbon Segregation to Fe Symmetric Tilt Grain Boundaries Using Atomistic Simulations

Segregation of impurities to grain boundaries plays an important role in both the stability and macroscopic behavior of polycrystalline materials. The research objective in this work is to better characterize the energetics and length scales involved with the process of solute and impurity segregation to grain boundaries. Molecular dynamics simulations are used to calculate the segregation energies for carbon within multiple grain boundary sites over a database of 125 symmetric tilt grain boundaries in Fe. The simulation results show that the majority of atomic sites near the grain boundary have segregation energies lower than in the bulk. Moreover, depending on the boundary, the segregation energies approach the bulk value approximately 5-12 \AA\ away from the center of the grain boundary, providing an energetic length scale for carbon segregation. A subsequent data reduction and statistical representation of this dataset provides critical information such as about the mean segregation energy and the associated energy distributions for carbon atoms as a function of distance from the grain boundary, which quantitatively informs higher scale models with energetics and length scales necessary for capturing the segregation behavior of impurities in Fe. The significance of this research is the development of a methodology capable of ascertaining segregation energies over a wide range of grain boundary character (typical of that observed in polycrystalline materials), which herein has been applied to carbon segregation in a specific class of grain boundaries in iron

Influenza Virus Infection in Travelers to Tropical and Subtropical Countries

Background. Influenza outbreaks have been reported among travelers, but attack rates and incidence are unknown. Methods. A cohort study was conducted. Travelers to subtropical and tropical countries recruited at the University of Zurich Travel Clinic (Switzerland), January 1998 to March 2000, were investigated with pre- and posttravel assessment of hemagglutination inhibition and by questionnaire. Results. Among 1450 travelers recruited who completed questionnaires and provided serum samples before departure, 289 (19.9%) reported febrile illness during or after traveling abroad; of these, 211 (73.0%) provided paired serum samples. Additionally, paired serum samples were collected from 321 frequency-matched afebrile control subjects among the remaining 1161 subjects of the study population. Seroconversion for influenza virus infection was demonstrated in 40 (2.8%) of all travelers; 18 participants (1.2%) had a ⩾4-fold increase in antibody titers. This corresponds to an incidence of 1.0 influenza-associated events per 100 person-months abroad. Among the 211 febrile participants, 27 (12.8%) had seroconversion, 13 (6.2%) with a ⩾4-fold increase; among the 321 afebrile control subjects, 13 (4.0%) had seroconversion, 5 (1.6%) with a ⩾4-fold increase. Twenty-five seroconverters (62.5%; P = .747) acquired influenza outside of the European epidemic season. Sixteen patients (40.0%) sought medical attention either abroad or at home, and 32 (80.0%) were asymptomatic at the time of completion of the survey. Conclusions. This survey indicates that influenza is the most frequent vaccine-preventable infection among travelers to subtropical and tropical countries. Infections occur mainly outside the domestic epidemic season, and they have a considerable impact. Pretravel vaccination should be considered for travelers to subtropical and tropical countrie