What Is the Tree of Life?

A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” [1]. Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain [2–4].     

Perfusion-CT - Can We Predict Acute Pancreatitis Outcome within the First 24 Hours from the Onset of Symptoms?

Purpose

Severe acute pancreatitis (AP) is still a significant clinical problem which is associated with a highly mortality. The aim of this study was the evaluation of prognostic value of CT regional perfusion measurement performed on the first day of onset of symptoms of AP, in assessing the risk of developing severe form of acute pancreatitis.

Material and Methods

79 patients with clinical symptoms and biochemical criteria indicative of acute pancreatitis (acute upper abdominal pain, elevated levels of serum amylase and lipase) underwent perfusion CT within 24 hours after onset of symptoms. The follow-up examinations were performed after 4–6 days to detect progression of the disease. Perfusion parameters were compared in 41 people who developed severe form of AP (pancreatic and/or peripancreatic tissue necrosis) with parameters in 38 consecutive patients in whom course of AP was mild. Blood flow, blood volume, mean transit time and permeability surface area product were calculated in the three anatomic pancreatic subdivisions (head, body and tail). At the same time the patient''s clinical status was assessed by APACHE II score and laboratory parameters such as CRP, serum lipase and amylase, AST, ALT, GGT, ALP and bilirubin were compared.

Results

Statistical differences in the perfusion parameters between the group of patients with mild and severe AP were shown. Blood flow, blood volume and mean transit time were significantly lower and permeability surface area product was significantly higher in patients who develop severe acute pancreatitis and presence of pancreatic and/or peripancreatic necrosis due to pancreatic ischemia. There were no statistically significant differences between the two groups in terms of evaluated on admission severity of pancreatitis assessed using APACHE II score and laboratory tests.

Conclusions

CT perfusion is a very useful indicator for prediction and selection patients in early stages of acute pancreatitis who are at risk of developing pancreatic and/or peripancreatic necrosis already on the first day of the onset of symptoms and can be used for treatment planning and monitoring of therapy of acute pancreatitis. Early suspicion of possible pancreatic necrosis both on the basis of scores based on clinical status and laboratory tests have low predictive value.     

What is Life? Defining Life in the Context of Emergent Complexity

Erwin Schrödinger defined life not only as a “self-reproducing” aperiodic crystal of DNA coding for proteins but within the context of living entities increasing their order by dissipating matter/energy gradients to maintain themselves away from equilibirium. Since then most definitions of life have focused on the former. But living cells do more than replicate their DNA. Cells also have membrane barriers across which metabolites must move, via which energy transduction as well as information processing occurs, and within which metabolic transformation occurs. An approach of complex systems dynamics, including nonequilibrium thermodynamics, may provide a more robust approach for defining life than a “naked replicator” at the origin of life. The crucial issue becomes the process of emergence of life from pre-biotic chemistry, concomitant with the emergence of function, information, and semiosis. Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution. Understanding how life might have emerged should sharpen our definition of what life is.     

Is the behaviour of the leg during oscillation linear?

The linear behaviour of the human leg was studied using a free oscillation method. The lower leg is represented by a simple mass, spring and dashpot model. Forty-five subjects underwent free vibration tests on their right legs. The force amplitude and the time period, for successive oscillations enabled calculation of the stiffness to mass ratio values. It was found that the time period of the second oscillation cycle was significantly lower than that of the first, implying a corresponding increase in stiffness. The experimental data consistently exhibits these non-linear characteristics, indicating that the use of non-linear models could be of benefit for future free oscillation studies.     

Nursing Home Admission during the First Year after Hospitalization – The Contribution of Cognitive Impairment

Objective

The importance of cognitive and physical functioning for nursing home admission among medically hospitalized older patients is rarely studied in a one-year follow-up perspective. This study aims to explore the association between patient characteristics and nursing home admission within one year after hospitalization in persons 65 years or more.

Design

A one-year longitudinal study.

Methods

We included 463 (234 women) persons aged 65 years or more from internal medical wards in a rural area of Norway. Cognitive function was assessed using the Mini Mental State Examination; physical and instrumental functional status was assessed using the physical self-maintenance scale and instrumental activities of daily living scale of Lawton and Brody. Comorbidity was measured with the Charlson index. Admission to nursing home within one year (yes versus no) was analyzed using logistic regression analysis and Cox proportional hazard regression analysis.

Results

The mean age of the sample was 80.5 (SD 7.4) years, mean Mini Mental State Examination score was 24.1 (SD 3.8) (maximum score is 30). In adjusted analysis participants with cognitive impairment (a Mini Mental State Examination score <25) or impaired physical functioning at baseline had higher risk of admission to nursing home within one year (OR 3.0, 95%CI 1.5–6.2 and OR 3.5, 95%CI 1.8–9.6, respectively). The time before admission was also associated with cognitive impairment and impaired physical functioning in the adjusted analysis (HR 2.6 95%CI 1.4–4.8 and HR 3.7, 95%CI 1.5–8.9, respectively).

Conclusion

Impaired cognitive and physical functioning increased the risk for nursing home admission within one year after hospitalization. However, putative regressors, such as education and social network were not included in the analysis.     

Quantifying Landscape Spatial Pattern: What Is the State of the Art?

Landscape ecology is based on the premise that there are strong links between ecological pattern and ecological function and process. Ecological systems are spatially heterogeneous, exhibiting considerable complexity and variability in time and space. This variability is typically represented by categorical maps or by a collection of samples taken at specific spatial locations (point data). Categorical maps quantize variability by identifying patches that are relatively homogeneous and that exhibit a relatively abrupt transition to adjacent areas. Alternatively, point-data analysis (geostatistics) assumes that the system property is spatially continuous, making fewer assumptions about the nature of spatial structure. Each data model provides capabilities that the other does not, and they should be considered complementary. Although the concept of patches is intuitive and consistent with much of ecological theory, point-data analysis can answer two of the most critical questions in spatial pattern analysis: what is the appropriate scale to conduct the analysis, and what is the nature of the spatial structure? I review the techniques to evaluate categorical maps and spatial point data, and make observations about the interpretation of spatial pattern indices and the appropriate application of the techniques. Pattern analysis techniques are most useful when applied and interpreted in the context of the organism(s) and ecological processes of interest, and at appropriate scales, although some may be useful as coarse-filter indicators of ecosystem function. I suggest several important needs for future research, including continued investigation of scaling issues, development of indices that measure specific components of spatial pattern, and efforts to make point-data analysis more compatible with ecological theory.     

Conducting an Acute Intense Interval Exercise Session During the Ramadan Fasting Month: What Is the Optimal Time of the Day?

This study examines the effects of Ramadan fasting on performance during an intense exercise session performed at three different times of the day, i.e., 08:00, 18:00, and 21:00?h. The purpose was to determine the optimal time of the day to perform an acute high-intensity interval exercise during the Ramadan fasting month. After familiarization, nine trained athletes performed six 30-s Wingate anaerobic test (WAnT) cycle bouts followed by a time-to-exhaustion (T_exh) cycle on six separate randomized and counterbalanced occasions. The three time-of-day nonfasting (control, CON) exercise sessions were performed before the Ramadan month, and the three corresponding time-of-day Ramadan fasting (RAM) exercise sessions were performed during the Ramadan month. Note that the 21:00?h session during Ramadan month was conducted in the nonfasted state after the breaking of the day's fast. Total work (TW) completed during the six WAnT bouts was significantly lower during RAM compared to CON for the 08:00 and 18:00?h (p?<?.017; effect size [d]?=?.55 [small] and .39 [small], respectively) sessions, but not for the 21:00?h (p?=?.03, d?=?.18 [trivial]) session. The T_exh cycle duration was significantly shorter during RAM than CON in the 18:00 (p < .017, d?=?.93 [moderate]) session, but not in the 08:00 (p?=?.03, d?=?.57 [small]) and 21:00?h (p?=?.96, d?=?.02 [trivial]) sessions. In conclusion, Ramadan fasting had a small to moderate, negative impact on quality of performance during an acute high-intensity exercise session, particularly during the period of the daytime fast. The optimal time to conduct an acute high-intensity exercise session during the Ramadan fasting month is in the evening, after the breaking of the day's fast. (Author correspondence: abdul_rashid_aziz@ssc.gov.sg)     

Causation and the Origin of Life. Metabolism or Replication First?

The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.     

Drosophila Immunity: Is Antigen Processing the First Step?

A new genetic study has shown that the phagocytic ability of Drosophila blood cells, the hemocytes, may be important for the further induction of an antibacterial response in other tissues.     

Molecular Probes: What Is the Range of Their Interaction with the Environment?

We performed pressure-tuning hole-burning experiments on a modified cytochrome c protein in a glycerol/buffer glass. The shift and the broadening of the holes were investigated for various frequencies within the inhomogeneous band. On the basis of a simple model, we were able to estimate the interaction range between chromophore and protein. It is ~4.5 Å. The parameters that enter the model are the compressibility, the static mean-square displacement, the inhomogeneous width, and the average spectral shift per pressure. From this result and from our experiments on pressure-induced denaturing, we conclude that water molecules have to be brought very close to the chromophore during the denaturation process.     

What Is the Signal for the Posttranslational Arginylation of Proteins?

The N-terminal, posttranslational arginylation of proteins is ubiquitous in eukaryotic cells. Previous experiments, using purified components of the reaction incubated in the presence of exogenous substrates, have shown that only those proteins containing acidic residues at their N-terminals are arginylation substrates. However, data from experiments that used crude extracts of brain and nerve as the source of the arginylating molecules, suggest that the in vivo targets for arginylation are more complex than those demonstrated using purified components. One of the proposed functions for arginylation is as a signal for protein degradation and proteins that have undergone oxidative damage have been shown to be rapidly degraded. In the present experiments we have tested the hypothesis that the presence of an oxidatively damaged residue in a protein is a signal for its arginylation. These experiments have been performed by adding synthetic oxidized peptides to crude extracts of rat brain, incubating them with [³H]Arg and ATP and assaying for arginylated peptides using RP-HPLC. Results showed that while the oxidized A-chain of insulin was arginylated in this system, confirming previous experiments, other peptides containing oxidized residues were not. When a peptide containing Glu in the N-terminus was incubated under the same conditions it too was not a substrate for arginylation. These findings show that neither the presence of an N-terminal acidic residue nor an oxidized residue alone are sufficient to signal arginylation. Thus, another feature of the oxidized A-chain of insulin is required for arginylation. That feature remains to be identified.     

Microemboli-monitoring during the acute phase of ischemic stroke: Is it worth the time?

Background  

The prevalence of microembolic signals (MES) during the acute phase of ischemic stroke and its influence on outcome is not well studied. The aim of our study was to determine the prevalence of MES, the different factors that are associated with the presence of MES and the association between MES and outcomes in stroke patients investigated within 6 hours after the onset of ischemic stroke.     

What Are the Roles and Responsibilities of the Media in Disseminating Health Information?

BACKGROUND TO THE DEBATE: In December 2004 three news stories in the popular press suggested that the side effects of single-dose nevirapine, which has been proven to prevent mother-to-child transmission of HIV, had been covered up. Many HIV experts believed that the stories were unwarranted and that they would undermine use of the drug, leading to a rise in neonatal HIV infection. The controversy surrounding these stories prompted the PLoS Medicine editors to ask health journalists, and others with an interest in media reporting of health, to share their views on the roles and responsibilities of the media in disseminating health information.     

The Natural Progression of Gambiense Sleeping Sickness: What Is the Evidence?

Gambiense human African trypanosomiasis (HAT, sleeping sickness) is widely assumed to be 100% pathogenic and fatal. However, reports to the contrary exist, and human trypano-tolerance has been postulated. Furthermore, there is uncertainty about the actual duration of both stage 1 and stage 2 infection, particularly with respect to how long a patient remains infectious. Understanding such basic parameters of HAT infection is essential for optimising control strategies based on case detection. We considered the potential existence and relevance of human trypano-tolerance, and explored the duration of infectiousness, through a review of published evidence on the natural progression of gambiense HAT in the absence of treatment, and biological considerations. Published reports indicate that most gambiense HAT cases are fatal if untreated. Self-resolving and asymptomatic chronic infections probably constitute a minority if they do indeed exist. Chronic carriage, however, deserves further study, as it could seed renewed epidemics after control programmes cease.