Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.     

Beech versus spruce deadwood as forest microhabitat: does it make any difference to bryophytes?

The presence data of 153 bryophyte species, recorded on beech (BDW) and spruce (SDW) deadwood in the managed forests within a montane watershed, were analysed by controlling for different plot size, substrate pH and elevation. Only three pleurocarpous species, which were probably remnant epiphytes from live wood, showed relative specificity for BDW, but none to SDW. The few species displaying preference for BDW or SDW were generally true epixylic, mosses and hepatics, respectively. The chances of occurrence of epiphytic (early successional) and epixylic (mid-late successional) taxa on either deadwood species increased and respectively, decreased with the substrate pH. There was no consistent relationship between bryophyte preference to BDW/SDW and elevation. Neither total nor threatened species richness was related to deadwood species identity. However, at 100 cm² resolution and within certain extension range, the cumulative number of bryophyte species was significantly higher on BDW than on SDW, despite no significant difference in species pool size. Threatened species richness increased monotonically towards lower elevations, suggesting that valley bottoms might act as refugia with high air humidity. The number of threatened species and in particular, the presence of Lophozia ascendens, were good predictors of total bryophyte richness regardless of deadwood species identity.     

What does it take to make a heart?

Ever increasing advances are being made in our quest to understand what it takes to direct pluripotent precursor cells to adopt a specific developmental fate. Eventually, the obvious goal is that targeted manipulation of these precursor cells will result in an efficient and reliable production of tissue‐specific cells, which can be safely employed for therapeutic purposes. We have gained an incredible insight as to which molecular pathways are involved in governing neural, skeletal and cardiac muscle fate decisions. However, we still face the challenge of how to direct, for example, a cardiac fate in stem cells in the amounts needed to be employed for regenerative means. Equally importantly, we need to resolve critical questions such as: can the in vitro generated cardiomyocytes actually functionally replace damaged heart tissue? Here I will provide an overview of the molecules and signalling pathways that have first been demonstrated in embryological studies to function in cardiogenesis, and summarize how this knowledge is being applied to differentiate mouse and human embryonic stem cells into cardiomyocytes.     

Frequency of bird hybrids: does detectability make all the difference?

The number of hybrids recorded in the field may be biased because these data may simply reflect the detectability of a hybrid pairing. A questionnaire was constructed for assessing the detectability of natural avian hybrids. Ratings from 17 independent experienced observers were subjected to factor analysis and all observers loaded onto the same single factor. The reliability was extremely high (Cronbachs alpha=0.96). Initially, I found a weak positive and significant correlation between the number of hybrids and their detectability index (r_s=0.268; P=0.015; n=81). However, the respective correlations within three orders and one family containing enough hybrids for analysis revealed non-significant results. Significant differences existed among orders with respect to both detectability and hybrid frequency. At the family level, differences existed in detectability, but not in the number of hybrids recorded. Furthermore, I found no publication bias. These results suggest a general influence of detectability and on higher taxonomic levels, and that either detectability or the number of hybrids vary between orders possibly due to phylogenetic effects. Data about hybrids should be used in a cautious manner in analyses across a wide range of species, but seem unbiased when restricted to analyses within orders and families. As a rule of thumb, distinctness of hybrids seems to be a function of the plumage difference between the hybridising species.Communicated by F. Bairlein     

The intracellular region of Notch ligands: does the tail make the difference?

   

The cytoplasmic tail of Notch ligands drives endocytosis, mediates association with proteins implicated in the organization of cell-cell junctions and, through regulated intra-membrane proteolysis, is released from the membrane as a signaling fragment. We survey these findings and discuss the role of Notch ligands intracellular region in bidirectional signaling and possibly in signal modulation in mammals.     

Cardiac operative risk evaluation: The EuroSCORE II,does it make a real difference?

Background

The EuroSCORE, worldwide used as a model for prediction of mortality after cardiac surgery, has recently been renewed. Since October 2011, the EuroSCORE II calculator is available at the EuroSCORE website and recommended for clinical use. The intention of this paper is to compare the use of the initial EuroSCORE and EuroSCORE II as a risk evaluation tool.

Methods

100 consecutive patients who underwent combined mitral valve and coronary bypass surgery (MVR + CABG) and 100 consecutive patients undergoing combined aortic valve surgery and coronary bypass surgery (AVR + CABG) at the Radboud University Nijmegen Medical Center before 10 October 2011 were included. For both groups the initial EuroSCORE and the EuroSCORE II model were used for risk calculation and based on the calculated risks, cumulative sum charts (CUSUM) were constructed to evaluate the impact on performance monitoring.

Results

For the MVR + CABG group the calculated risk using the initial logistic EuroSCORE was 9.95 ± 8.47 (1.51–45.37) versus 5.08 ± 4.03 (0.67–19.76) for the EuroSCORE II. For the AVR + CABG group 9.50 ± 8.6 (1.51–69.5) versus 4.77 ± 6.6 (0.96–64.24), respectively. For both groups the calculated risk by the EuroSCORE II was statistically lower compared with the initial EuroSCORE (p < 0.001). This lower expected risk has influence on performance monitoring, using risk-adjusted CUSUM analysis.

Conclusion

The EuroSCORE II, based on a recently updated database, reduces the overestimation of the calculated risk by the initial EuroSCORE. This difference is statistically significant and the EuroSCORE II may also reflect better current surgical performance.     

Quality of care in family practice: does residency training make a difference?

As the proportion of physicians who enter residency training in family practice steadily increases, so does the need to evaluate the impact of their training and postgraduate education on the quality of care in their practices. We audited the practices of 120 randomly selected family physicians in Ontario, who were separated into four groups: nonmembers of the College of Family Physicians of Canada (CFPC), members of the CFPC with no certification in family medicine, certificated members without residency training in family medicine and certificated members with residency training in family medicine. The practices were assessed according to predetermined criteria for charting, procedures in periodic health examination, quality of medical care and use of indicator drugs. Generally the scores were significantly higher for CFPC members with residency training in family medicine than for those in the other groups, nonmembers having the lowest scores. Patient questionnaires indicated no difference in satisfaction with specific aspects of care between the four groups. Self-selection into residency training and CFPC membership may account for some of the results; nevertheless, the findings support the contention that residency training in family medicine should be mandatory for family physicians.     

Single‐ or multistage regulation in complex life cycles: does it make a difference?

Data on the different stages of complex life cycles are often rather unbalanced, especially those concerning the effects of density. How does this affect our understanding of a species’ population dynamics? Two discrete three‐stage models with overlapping generations and delayed maturation are constructed to address this question. They assume that survival or emigration in any life stage and/or reproduction can be density dependent. A typical pond‐breeding amphibian species with a well‐studied larval stage serves as an example. Numerical results show that the population dynamics resulting from density dependence at a single (e.g. the larval) stage can be decisively and unpredictably modified by density dependence in additional stages. Superposition of density‐dependent processes could thus be one reason for the difficulties in identifying density dependence in the field. Moreover, in a simulated source‐refuge system with habitat‐specific density‐dependent dispersal of juveniles density dependence in multiple stages can stabilize or destabilize the dynamics and produce misleading age structures. From an applied perspective this model shows that excluding multistage regulation prematurely clearly affects our ability to predict consequences of human impacts.     

Pre-counseling education materials for BRCA testing: does tailoring make a difference?

Although tailored print materials (TPMs) have been assessed for a variety of behavioral targets, their effectiveness as decision aids for genetic testing had not been evaluated at the time this study began. We compared TPMs and non-tailored print material (NPMs) that included similar content about genetic testing for breast and ovarian cancer susceptibility. TPMs were prepared especially for an individual based on information from and about her. We mailed baseline surveys to 461 women referred by physicians or identified through a tumor registry. All had personal and family histories of breast and/or ovarian cancer and, on the basis of these histories, an estimated > or =10% probability of carrying a mutation in the breast/ovarian cancer genes BRCA1 or BRCA2. The 325 (70%) who responded were randomly assigned to receive TPM or NPM. Followup surveys, mailed 2 weeks following receipt of print materials, were returned by 262 women (81% of baseline responders). Participants were predominately white (94%) and well-educated (50% college graduates). The mean age was 49 years. At follow-up, TPM recipients exhibited significantly greater improvement in percent of correct responses for the 13-item true/false measure of knowledge (24% increase for TPM vs. 16% for NPM; p < 0.0001) and significantly less over-estimation of risk of being a mutation carrier (40% TPM group overestimated vs. 70% NPM; p < 0.0001). Anxiety did not differ significantly between groups. Reactions to materials differed on two items: "seemed to be prepared just for me" (76% TPM vs. 52% NPM; p < 0.001) and "told me what I wanted to know about BRCA1 and 2 testing" (98% TPM vs. 91% NPM; p < 0.05). TPMs showed an advantage in increasing knowledge and enhancing accuracy of perceived risk. Both are critical components of informed decision making.     

Gene therapy for HIV infection: what does it need to make it work?

The efficacy of antiviral drug therapy for HIV infection is limited by toxicity and viral resistance. Thus, alternative therapies need to be explored. Several gene therapeutic strategies for HIV infection have been developed, but in clinical testing therapeutically effective levels of the transgene product were not achieved. This review focuses on the determinants of therapeutic efficacy and discusses the potential and also the limits of current gene therapy approaches for HIV infection.     

HLA-DQ system and insulin-dependent diabetes mellitus in Japanese: does it contribute to the development of IDDM as it does in Caucasians?

Fifty-six unrelated Japanese patients with insulin-dependent diabetes mellitus (IDDM) were HLA-typed, and restriction fragment length polymorphism (RFLP) analysis was performed after enzyme digestion with Bam HI and Taq I by using both DR and DQ probes. As previously reported, increased frequencies of Bw54, Cw1, DR4, and DRw53, which are in strong linkage disequilibrium in the Japanese population and make the characteristic Japanese haplotype, were confirmed. DQw4, a new allele of the DQ system recognized by the monoclonal antibody HU-46 and in linkage disequilibrium with this haplotype, presented the highest IDDM association. The RFLP analysis also showed the strongest correlation to IDDM when the DQ probe was applied. These results indicate that HLA-DQ might play the most important role in the development of IDDM in Japanese as well as in Caucasians. The correlation of DQ amino acid sequences strongly associated with IDDM in Japanese are discussed in this study, and contrasting results were found when such sequences were compared with those of Caucasians.Abbreviations used in this paper IDDM insulin-dependent diabetes mellitus - RFLP restriction fragment length polymorphism - Asp aspartic acid - Asp-57 aspartic acid at the 57th residue of the DQ chain - non-Asp-57 nonaspartic acid at the 57th residue of the DQ chain - R.R. relative risk of Woolf and Haldane     

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more‐individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual‐based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more‐individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS‐curve has the potential to quantify the underlying factors influencing most aspects of diversity change.     

Invasive species as a new food source: does a nudibranch predator prefer eating an invasive bryozoan?

Membranipora membranacea is an invasive bryozoan that was first found in the Gulf of Maine in 1987 and within two years became the dominant organism living on kelps. Membranipora may have become dominant so quickly because it had little competition in a relatively unoccupied niche; however, lack of predation has also probably played a major role. Where Membranipora is native, there is usually a specialist nudibranch predator that keeps the population in check. For example, in European populations, the nudibranch Polycera quadrilineata prefers Membranipora while Onchidoris muricata is known to prefer another bryozoan, Electra pilosa. Electra, Membranipora, and Onchidoris are all now found in the Gulf of Maine while Polycera is not. We tested whether Onchidoris would (1) eat Membranipora at all, (2) eat Membranipora and Electra at different rates, and (3) show a preference for eating Membranipora or Electra when given a choice. We found that Onchidoris does eat Membranipora, and it generally eats Membranipora faster than Electra. However, when given a choice, Onchidoris prefers Electra. Onchidoris typically reproduces in the spring and grows over the fall and winter, but has recently been found reproducing in the winter in New Hampshire. Although it does not survive the winter as well as Electra, Membranipora is the dominant organism living on many macroalgae in the late summer and fall. Thus, the large Membranipora food source now available in the summer and fall may allow Onchidoris to reproduce earlier.     

Why do species abundance distributions of individuals and of biomass behave differently under sampling?

A surprising and important difference between species abundance distributions (SADs) of individuals and of biomass has been found in a wide variety of taxa. On sampling, individuals SADs are ‘veiled’, the left tail is missing, to an extent depending on the sampling intensity, while biomass SADs appear not to be veiled. The explanation offered here is that sampling is always of individuals, biomass is sampled only indirectly. Graphs of the community of birds in an English wood show how the explanation works. Biomass SADs are different from individuals SADs.     

How long does it take to equilibrate the unfolded state of a protein?

How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.     

Quality of life in adolescents born small for gestational age: does growth hormone make a difference?

BACKGROUND/AIMS: To evaluate quality of life (QoL) in adolescents born SGA without spontaneous catch-up growth, treated with and without long-term growth hormone (GH) therapy. Additionally, to assess whether GH treatment has a positive effect on QoL, besides improving adult height and height SDS during childhood. METHODS: Two groups of adolescents born SGA without spontaneous catch-up growth participated in the QoL evaluation; a GH-treated group (n = 44, mean GH duration: 8.8 (1.7) years) and an untreated group (n = 28), both mean age 15.8 (2.1) years. QoL was measured by self-reports of the TACQOL-S, a disorder-specific questionnaire, and the CHQ, a generic questionnaire. RESULTS: The GH group scored significantly better health status and health-related QoL on several scales of the TACQOL-S. On all TACQOL-S scales the GH group scored better QoL than the untreated group, with effect sizes of moderate to large, not all differences reaching statistical significance. The generic CHQ did not reveal significant differences in QoL between the GH group and the untreated group. CONCLUSIONS: Firstly, adolescents born SGA, with a GH-induced improved height, had in many aspects a better QoL than untreated adolescents born SGA, according to the disorder-specific questionnaire. Secondly, we advise to use, in addition to a generic questionnaire, a disorder-specific questionnaire for measuring QoL in children treated for short stature, as the generic CHQ did not reveal such differences.     

Surrogate species versus landscape metric: does presence of a raptor species explains diversity of multiple taxa more than patch area?

Prioritizing conservation areas is a central theme in conservation biology. The use of surrogate species and landscape metrics to identify areas with high conservation value is common. However, few studies have examined the relative efficacy of these two surrogates. In this study, we compared the efficacy of the presence/absence (PA) of a top predator (Eastern Marsh Harrier, Circus spilonotus) and wetland patch area on species richness, total abundance, and community composition of birds, plants, and small mammals, but species richness and community composition only for plants, in a fragmented wetland landscape. Although harrier PA was an effective indicator of the distribution of birds, it had no significant efficacy on the distributions of plants and small mammals. Patch area was more effective indicator of the distributions of plants and small mammals. These results suggest that surrogate species can be more effective indicators than landscape surrogates when there are ecological linkages between surrogate species and the focal taxa (e.g., similarity of habitat requirements between surrogate species and focal taxa or hetero-specific attraction). On the other hand, landscape surrogates would be useful when ecological knowledge about the relationships is limited.     

Calcitonin, an enigmatic hormone: does it have a function?

This editorial presents our view of the status of thyroidal calcitonin (TCT) in mammalian physiology. The discovery of calcitonin (CT) enabled the development of a valuable therapeutic agent but the early experiments most likely misled us with regard to its physiological significance. These early purported roles for TCT, first as an agent important in blood calcium regulation and later as an agent to prevent hypercalcemia, are no longer considered as physiological functions. While large supraphysiological doses of CT have an effect on the morphology and function of osteoclasts, it is unlikely that these effects of CT are important in the normal physiology of osteoclasts or bone remodeling. It is surprising that 38 years after the discovery of TCT there is no consensus as to its role in normal mammalian physiology. This editorial concerns three possibilities with respect to TCT: 1) the hormone is vestigial; 2) the hormone plays a role in water metabolism, ionic concentrations, and/or acid-base balance, actions that may not involve calcium metabolism at all; and 3) TCT acts to store phosphate postprandially on bone surfaces as a labile calcium-phosphate colloid, an action that may provide calcium needed for use in non-feeding periods or to reduce postprandial loss of phosphate when dietary phosphate is limited. Also discussed are recent publications indicating that CT synthesized in non-thyroidal tissues (NTCT) may have paracrine actions.