Common misconceptions in molecular ecology: echoes of the modern synthesis

The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.     

Apoptosis may contribute to false-positive results in the in vitro micronucleus test performed in extreme osmolality, ionic strength and pH conditions

Conditions in which clastogens produce positive responses have been increasingly challenged, and several situations have been described in which clastogenic responses would be considered not to be relevant. For example, extreme culture conditions lead to high variations of pH, osmolality or ionic strength. Apoptosis is induced in extreme culture conditions and contributes to false-positive results in the in vitro micronucleus test performed with CTLL-2 cells. These cells can enter apoptosis when exposed to apoptosis stimuli or after IL-2 deprivation, whereas the CTLL-2 Bcl2 cell line is protected from apoptosis due to the over-expression of the apoptosis inhibitor Bcl2 in bcl2-transfected CTLL-2 cells. The two cell lines were treated in extreme culture conditions of either pH or osmolality or were submitted to high ionic strength. The apoptosis level was measured in parallel with the in vitro micronucleus test using the annexin V-FITC method. Data obtained in the two cell lines suggested that apoptosis caused by extreme culture condition induces the formation of micronucleated cells, which leads to false-positive results in the in vitro micronucleus test.     

Demography in stochastic environments. I. Exact distributions of age structure

The steady state distribution of age structure is studied for populations with two age classes and stochastic vital rates. For a serially uncorrelated dichotomic vital rate the distribution of age structure is found analytically to be a singular steplike function; outside a specific region of vital rate values the singular function crosses a threshold to a smooth function. For a vital rate following a correlated two state Markov process the joint distributions of age structure and environment are found analytically to be singular steplike functions; again a threshold marks a transition to a smooth function. For fecundities which are serially uncorrelated but continuously distributed the age structure distribution is obtained as a smooth analytic function for all parameter values. These explicit results have applications to studies of age structure and average growth rate.     

大湄公河次区域薇甘菊的防控技术

薇甘菊是大湄公河次区域的重要恶性入侵杂草,其种群跨境入侵扩张备受区域各国政府的高度重视和社会广泛关注。2011年以来在我国相关农业科研机构、团队和专家的科技支撑下,中国云南与周边五国科研机构成立“大湄公河次区域植物保护工作组”。本文简要介绍工作组围绕该入侵杂草在生态异质性条件下种群扩展与灾变过程的预警监测、阻截防控带建设、替代控制与选择性除草剂协同应用取得的阶段性成效,为积极主动融入国家“一带一路”倡议的实施,服务于中国云南的经济国境线、绿色国境线和生态国境线发挥建设性作用。     

Statistical considerations for in vitro research: II — Data to presentation

Summary The paper is the second of two papers about statistical considerations that researchers should make while doing in vitro plant biology research. The first paper focused on aspects from developing a plan to do research through the collection of data. This paper continues with information about editing data, handling outliers, analyzing quantitative and qualitative data, comparing treatment means, preparing graphs and tables, and presenting results.     

Reproducibility of a new signal processing technique to assess joint sway during standing

Postural control strategies can be investigated by kinematic analysis of joint movements. However, current research is focussing mainly on the analysis of centre of pressure excursion and lacks consensus on how to assess joint movement during postural control tasks. This study introduces a new signal processing technique to comprehensively quantify joint sway during standing and evaluates its reproducibility. Fifteen patients with non-specific low back pain and ten asymptomatic participants performed three repetitions of a 60-second standing task on foam surface. This procedure was repeated on a second day. Lumbar spine movement was recorded using an inertial measurement system. The signal was temporally divided into six sections. Two outcome variables (mean absolute sway and sways per second) were calculated for each section. The reproducibility of single and averaged measurements was quantified with linear mixed-effects models and the generalizability theory. A single measurement of ten seconds duration revealed reliability coefficients of .75 for mean absolute sway and .76 for sways per second. Averaging a measurement of 40 seconds duration on two different days revealed reliability coefficients higher than .90 for both outcome variables. The outcome variables’ reliability compares favourably to previously published results using different signal processing techniques or centre of pressure excursion. The introduced signal processing technique with two outcome variables to quantify joint sway during standing proved to be a highly reliable method. Since different populations, tasks or measurement tools could influence reproducibility, further investigation in other settings is still necessary. Nevertheless, the presented method has been shown to be highly promising.     

Cardiac resynchronisation therapy: results from daily practice in Rijnstate Hospital, Arnhem

BackgroundCardiac resynchronisation therapy (CRT) is an effective treatment to improve the clinical outcome of selected patients with heart failure. Clinical trials have studied clinical outcome and reported clinical improvements, but clinical consequences and results in daily practice are less well known. We evaluated clinical outcome in all patients with CRT implantation in our centre. MethodsData of 119 consecutive patients who met the criteria for CRT implantation in Rijnstate Hospital, Arnhem in the period 28 November 2000 until 1 January 2006 were collected. We analysed implantation procedure, hospitalisation for heart failure or other causes, mortality and device-related events. ResultsIn total 119 patients (83 men, 36 women; mean age 69 years) were eligible for CRT. Before implantation they had received optimal pharmacological therapy. Implantation was successful in 97% of patients. Procedural-related complications were seen in eight patients. During follow-up, 22 patients (18.5%: 14 men, 8 women) died. Causes of death were heart failure (11 patients), sudden cardiac death (4 patients) and noncardiac death (7 patients). Hospitalisation occurred 81 times, of which 77 for cardiac reasons. In follow-up the estimated five-year cumulative survival was 70%. ConclusionThis retrospective study from a single centre showed a high procedural success rate, low prevalence of complications and low mortality in comparison to other studies. Despite better functional capacity, the hospitalisation rate due to heart failure was high. (Neth Heart J 2009;17:6-8.)     

U7 snRNAs： A Computational Survey

U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for func- tional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both se- quence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short se- quence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.     

尿激酶原的性质、结构、功能及其药代动力学和临床应用效果

溶栓疗法不仅已被常规地用于急性心肌梗死的治疗,而且也已用于其它血栓病的治疗中,如急性缺血性脑血栓、肺栓塞、急性周围动脉血栓等。尿激酶原是双链尿激酶的单链前体,它主要激活纤维蛋白表面的纤溶蛋白原,所以具有选择性溶栓作用。临床结果表明它是一种安全有效的溶栓药物,与t-PA、链激酶或尿激酶伍用均有协同作用。本文综述它了的特性、结构与功能,以及它的药代动力学和临床的治疗效果。