Mathematical Modeling of Photo- and Thermomorphogenesis in Plants

Increased day lengths and warm conditions inversely affect plant growth by directly modulating nuclear phyB, ELF3, and COP1 levels. Quantitative measures of the hypocotyl length have been key to gaining a deeper understanding of this complex regulatory network, while similar quantitative data are the foundation for many studies in plant biology. Here, we explore the application of mathematical modeling, specifically ordinary differential equations (ODEs), to understand plant responses to these environmental cues. We provide a comprehensive guide to constructing, simulating, and fitting these models to data, using the law of mass action to study the evolution of molecular species. The fundamental principles of these models are introduced, highlighting their utility in deciphering complex plant physiological interactions and testing hypotheses. This brief introduction will not allow experimentalists without a mathematical background to run their own simulations overnight, but it will help them grasp modeling principles and communicate with more theory-inclined colleagues.

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity

Antibiotic-resistant Enterobacterales that produce oxacillinase (OXA)-48-like Class D β-lactamases are often linked to increased clinical mortality. Though the catalytic mechanism of OXA-48 is known, the molecular origin of its biphasic kinetics has been elusive. We here identify selective chloride binding rather than decarbamylation of the carbamylated lysine as the source of biphasic kinetics, utilizing isothermal titration calorimetry (ITC) to monitor the complete reaction course with the OXA-48 variant having a chemically stable N-acetyl lysine. Further structural investigation enables us to capture an unprecedented inactive acyl intermediate wedged in place by a halide ion paired with a conserved active site arginine. Supported by mutagenesis and mathematical simulation, we identify chloride as a "Janus effector" that operates by allosteric activation of the burst phase and by inhibition of the steady state in kinetic assays of β-lactams. We show that chloride-induced biphasic kinetics directly affects antibiotic efficacy and facilitates the differentiation of clinical isolates encoding Class D from Class A and B carbapenemases. As chloride is present in laboratory and clinical procedures, our discovery greatly expands the roles of chloride in modulating enzyme catalysis and highlights its potential impact on the pharmacokinetics and efficacy of antibiotics during in vivo treatment.

Demographic, clinical and microbiological characteristics of the first 30 human monkeypox confirmed cases attended in a tertiary hospital in Madrid (Spain), during the May-June 2022 international outbreak

The present outbreak of Human Monkeypox (HMPX) that has begun in May 2022 and has spread across all continents in less than two months has qualitative and quantitative characteristics that make it different from the pattern of human disease previously caused by this virus. It has spread with enormous ease, affects almost exclusively adults, behaves as a sexually transmitted disease and focuses on very specific groups and transmission conditions. The high incidence in the city of Madrid in males that have sex with males (MSM) has allowed us to observe and report the experience with the first 30 cases diagnosed in our institution. Patients presented with febrile symptoms, genital and paragenital skin lesions reminiscent of smallpox, but less extensive and severe. The disease may also cause proctitis, pharyngitis and perioral lesions. The PCR test for diagnostic confirmation has been shown to be very sensitive and effective, not only in skin lesions but also in blood and other fluids such as pharyngeal, rectal exudates and blood. A very high proportion of patients with HMPX also have other sexually transmitted diseases that must be actively detected in this context. The spontaneous evolution of our patients has been good and hospitalization has been practically unnecessary. Transmission to non-sexual cohabitants and health personnel has been nonexistent and the lesions have disappeared in less than 30 days without leaving sequelae and no need for specific antiviral treatment.

Monkeypox in humans: a new outbreak

Infection caused by Monkeypox Virus (MPVX) has small rodents as its natural reservoir and both monkeys and humans are occasional hosts. The causative agent is an Orthopoxvirus (MPVX) that was isolated in monkeys in 1958 and proved capable of passing to humans in 1970. It remained contained in Africa, causing isolated episodes of infection, until 2003 when an outbreak occurred in the United States following importation of animals from that continent. Since then, anecdotal cases have continued to be reported outside Africa, usually very clearly linked to travelers to those countries, but in May 2022, a broad outbreak of this disease has begun, now affecting several continents, with the emergence of human cases of MPVX (H-MPVX) infection mainly among Men that have Sex with Men (MSM). The disease has an incubation time ranging from 5 to 15 days and is characterized by the presence of pustules, fever, malaise and headache. The presence of significant regional lymphadenopathy is a differential feature with episodes of classical smallpox. Proctitis and pharyngitis, with minimal skin lesions, may be another form of presentation. Diagnosis can be confirmed by PCR testing of lesions or by demonstration of MPVX in other body fluids or tissues, although in the appropriate epidemiologic setting the clinical picture is highly suggestive of the disease. Effective drug treatment has been developed as part of programs to protect against potential bioterrorist agents and smallpox vaccinees are known to have high protection against monkeypox. New vaccines are available, but neither the drugs nor the vaccines are yet freely available on the market. The prognosis of the disease appears, at least in adults in developed countries, to be good, with very low mortality figures and much less aggressive behavior than that described in classical smallpox. Isolation measures, essential for the control of the outbreak, have been published by the health authorities.

COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation

As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.

High incidence of COVID-19 at nursing homes in Madrid, Spain, despite preventive measures

OBJECTIVE

To assess the impact of COVID-19 at nine nursing homes in Madrid, Spain, during the first wave of COVID-19 infection and lockdown period when preventive measures were taken to avoid transmission among residents.

METHODS

Nine hundred forty-two residents and 846 staff members from nine nursing homes participated in the study (April 18 to June 20, 2020). All participants were tested for SARS-CoV-2 in the nasopharynx by PCR and for IgG antibodies detection. Microbiological status at sampling was defined as active infection (positive PCR ± presence of antibodies), past infection (negative PCR + presence of antibodies), or naïve participants (negative PCR + absence of antibodies).

RESULTS

Laboratory results helped classify the residents as having active infection (n=224; 23.8%), past infection (n=462; 49.1%), or being naïve (n=256; 27.1%); staff members were actively infected (n=127; 15.1%), had had a past infection (n=290; 34.2%), or were naïve (n=429; 50.7%). Overall, the percentage of participants with COVID-19 was significantly higher in residents than in staff members (72.8% vs 49.2%; P=0.001). The clinical situation of residents vs staff at sampling was as follows: acute manifestations compatible with COVID-19 (7.3% vs 3.9%; P<0.01) and no manifestations of infection (92.7% vs 96.0%; P<0.01). A large proportion of both asymptomatic and symptomatic residents (69.4% vs 86.6%; P=0.015) had positive PCR results (mostly alongside positive IgG determinations).

CONCLUSIONS

COVID-19 affects 75% of the residents in nursing homes in Madrid. The high impact in these settings, despite the strict restrictions adopted during the lockdown, demonstrates the ability of SARS-CoV-2 to cause outbreaks.

Seeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata

Antibiotic resistance represents a growing medical concern where raw, clinical datasets are under-exploited as a means to track the scale of the problem. We therefore sought patterns of antibiotic resistance in the Antimicrobial Testing Leadership and Surveillance (ATLAS) database. ATLAS holds 6.5M minimal inhibitory concentrations (MICs) for 3,919 pathogen-antibiotic pairs isolated from 633k patients in 70 countries between 2004 and 2017. We show most pairs form coherent, although not stationary, timeseries whose frequencies of resistance are higher than other databases, although we identified no systematic bias towards including more resistant strains in ATLAS. We sought data anomalies whereby MICs could shift for methodological and not clinical or microbiological reasons and found artefacts in over 100 pathogen-antibiotic pairs. Using an information-optimal clustering methodology to classify pathogens into low and high antibiotic susceptibilities, we used ATLAS to predict changes in resistance. Dynamics of the latter exhibit complex patterns with MIC increases, and some decreases, whereby subpopulations' MICs can diverge. We also identify pathogens at risk of developing clinical resistance in the near future.

Effect of continuous positive airway pressure in very elderly with moderate-to-severe obstructive sleep apnea pooled results from two multicenter randomized controlled trials

STUDY OBJECTIVE

There is very limited information about the effect of continuous positive airway pressure (CPAP) in the very elderly. Here we aimed to analysed the effect of CPAP on a clinical cohort of patients with obstructive sleep apnea (OSA) ≥80 years old.

METHODS

Post-hoc pooled analysis of two open-label, multicenter clinical trials aimed to determine the effect of CPAP in a consecutive clinical cohort of elderly (≥70 years old) with moderate-to-severe OSA (apnea-hipopnea index ≥15 events/hour) randomized to receive CPAP or no CPAP for three months. Those consecutive patients ≥80 years old were included in the study. The primary endpoint was the change in Epworth Sleepiness scale (ESS). Secondary outcomes included sleep-related symptoms, quality of life, neurocognitive and mood status as well as office blood pressure measurements.

RESULTS

From the initial 369 randomized individuals with ≥70 years, 97 (26.3%) with ≥80 years old were included (47 in the CPAP group and 50 in the no-CPAP group). The mean (SD) age was 81.5 (2.4) years. Average use of CPAP was 4.3 (2.6) hours/night (53% with good adherence) Patients in the CPAP group significantly improved snoring and witnessed apneas as well as AHI (from 41.9 to 4.9 events/hour). However no clinical improvements were seen in ESS (-1.2 points, 95%CI, 0.2 to -2.6), any domain of QSQ, any neurocognitive test, OSA-related symptoms, depression/anxiety or blood pressure levels.

CONCLUSIONS

The present study does not support the use of CPAP in very elderly patients with moderate-to-severe OSA.

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.

The Antibiotic Dosage of Fastest Resistance Evolution: gene amplifications underpinning the inverted-U

To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an “inverted-U” pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.

SARS-CoV-2 screening of asymptomatic women admitted for delivery must be performed with a combination of microbiological techniques: an observational study

OBJECTIVE

The aim of this study is to assess the value of systematic screening in asymptomatic women admitted for spontaneous delivery with a combination of reverse transcription polymerase chain reaction (RT-PCR) and cycle threshold (Ct) and serum antibodies.

METHODS

Since May 6 all women admitted for spontaneous delivery underwent RT-PCR in nasopharyngeal swabs and specific antibodies IgG of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in serum that were performed as part of routine clinical care in our institution. Ct of the PCR was recorded. We analyzed the first 100 women consecutively admitted for spontaneous delivery at our institution.

RESULTS

Nine women were positive for SARS-CoV-2 in nasopharyngeal samples (9%) and 13 (13%) presented positive specific antibodies of the coronavirus. Overall, SARS-CoV-2 prior exposure was 15%. The Ct determination (RT-PCR test) of our 9 positive patients ranged from 36 to 41 cycles with a median of 40. Vaginal delivery occurred in 94% of the cases and only 6% underwent a cesarean section, always for obstetric reasons. No fetal transmission was observed and maternal and neonatal prognosis was excellent.

CONCLUSIONS

During epidemic episodes in asymptomatic women in labor, universal testing with RT-PCR (considering Ct determination), and the detection of antibodies, permits a better interpretation of the results and avoid unnecessary isolation procedures.

The first 100 cases of COVID-19 in a Hospital in Madrid with a 2-month follow-up

Background

There are few descriptions of the clinical presentation and evolution of consecutive SARS-CoV-2 infections with a long-enough follow up.

Methods

Description of the first consecutive 100 patients with microbiologically-proven COVID-19 in a large hospital in Madrid, Spain including a minimum of two-month follow up.

Results

The median age of the patients (52% males) was 61.5 years (IQR=39.5-82.0) and the median BMI was 28.8 kg/m² (IQR=24.7-33.7). Overall 72% of the patients had one or more co-morbid conditions with a median age-adjusted Charlson index of 2 (IQR=0-5.7). Five patients (5%) were immunosup-pressed. The most common symptoms at the time of diagnosis were fever (80.0%), cough (53.0%) and dyspnea (23.0%). The median O₂ saturation at the time of first examination was 94% (IQR=90-97). Chest X-ray on admission was compatible with pneumonia in 63% of the cases (bilateral in 42% and unilateral in 21%). Overall, 30% were managed at home and 70% were admitted to the hospital. Thirteen patients were admitted to the ICU with a median of 11 days of stay in the Unit (IQR=6.0-28.0). CALL score of our population ranged from 4 to 13. Overall, 60.0% of patients received antibiotic treatment and 66.0%, empirical antiviral treatment, mainly with lopina-vir/ritonavir (65%) or hydroxychloroquine (42%). Mortality, with a minimum of 60 days of follow up, was 23%. The median age of the deceased patients was 85 years (IQR=79-93).

Conclusions

We found a high mortality in the first 100 patients diagnosed with COVID-19 at our institution, associated with advanced age and the presence of serious underlying diseases.

Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map

The evolution of gene regulatory networks (GRNs) is of great relevance for both evolutionary and synthetic biology. Understanding the relationship between GRN structure and its function can allow us to understand the selective pressures that have shaped a given circuit. This is especially relevant when considering spatio-temporal expression patterns, where GRN models have been shown to be extremely robust and evolvable. However, previous models that studied GRN evolution did not include the evolution of protein and genetic elements that underlie GRN architecture. Here we use toyLIFE, a multilevel genotype-phenotype map, to show that not all GRNs are equally likely in genotype space and that evolution is biased to find the most common GRNs. toyLIFE rules create Boolean GRNs that, embedded in a one-dimensional tissue, develop a variety of spatio-temporal gene expression patterns. Populations of toyLIFE organisms choose the most common GRN out of a set of equally fit alternatives and, most importantly, fail to find a target pattern when it is very rare in genotype space. Indeed, we show that the probability of finding the fittest phenotype increases dramatically with its abundance in genotype space. This phenotypic bias represents a mechanism that can prevent the fixation in the population of the fittest phenotype, one that is inherent to the structure of genotype space and the genotype-phenotype map.

Data on samara morphology and wind dispersal in the invasive tree Ailanthus altissima

The data presented in this paper is supporting the research article “Estimating wind dispersal potential in Ailanthus altissima: The need to consider the three-dimensional structure of samaras” [1]. We analyzed the estimation of samara's wind dispersal potential through a group of morphological variables that succeed in describing the three-dimensional nature of samaras. We present here a dataset containing 8 morphological variables of 200 samaras belonging to 5 different individuals of the invasive tree Ailanthus altissima (Mill.) Swingle. Additionally, we present the average descent velocity of each of the samaras, which was recorded by releasing 5 times each samara under controlled and reproducible conditions. The data set is structured in a single spreadsheet where we also included the samara and the individual identity code of the tree.

The role of CPAP treatment in elderly patients with moderate obstructive sleep apnoea: a multicentre randomised controlled trial

The efficacy of continuous positive airway pressure (CPAP) treatment in elderly patients with nonsevere obstructive sleep apnoea (OSA) is controversial. The objective of this study was to assess the effect of CPAP treatment in elderly patients with moderate OSA in terms of clinical, quality-of-life and neurocognitive measures.This was an open-label, randomised, multicentre clinical trial in 145 elderly patients (≥70 years old) with confirmed moderate OSA (apnoea-hypopnoea index 15-29.9 events·h^-1) randomised to receive CPAP (n=73) or no CPAP (n=72) for 3 months. The primary end-point was the Epworth Sleepiness Scale (ESS) score, and the secondary end-points included quality of life (Quebec Sleep Questionnaire (QSQ) domain scores), sleep-related symptoms, presence of anxiety/depression, office-based blood pressure measurements and some neurocognitive tests. The analysis was performed according to the intention-to-treat principle.Mean±sd age was 74.9±4.6 years. The CPAP group achieved a greater improvement in the ESS score (adjusted difference of 2.6 (95% CI 3.6-1.6) points; effect size 1) in some sleep-related symptoms and in some dimensions of the QSQ questionnaire (nocturnal symptoms: -0.7 (95% CI -0.3--1.0) points; p<0.0001 and emotions: -0.4 (95% CI -0.1--0.7) points; p=0.023). However, CPAP did not demonstrate any effect on either neurocognitive tests (including anxiety and depression) or blood pressure levels. There was a positive correlation between the effect of CPAP and the improvement in ESS scores and quality of life domains.CPAP treatment resulted in a significant improvement in diurnal hypersomnia and some sleep-related symptoms and quality of life domains in elderly patients with moderate OSA.

Adding levels of complexity enhances robustness and evolvability in a multilevel genotype-phenotype map

Robustness and evolvability are the main properties that account for the stability and accessibility of phenotypes. They have been studied in a number of computational genotype-phenotype maps. In this paper, we study a metabolic genotype-phenotype map defined in toyLIFE, a multilevel computational model that represents a simplified cellular biology. toyLIFE includes several levels of phenotypic expression, from proteins to regulatory networks to metabolism. Our results show that toyLIFE shares many similarities with other seemingly unrelated computational genotype-phenotype maps. Thus, toyLIFE shows a high degeneracy in the mapping from genotypes to phenotypes, as well as a highly skewed distribution of phenotypic abundances. The neutral networks associated with abundant phenotypes are highly navigable, and common phenotypes are close to each other in genotype space. All of these properties are remarkable, as toyLIFE is built on a version of the HP protein-folding model that is neither robust nor evolvable: phenotypes cannot be mutually accessed through point mutations. In addition, both robustness and evolvability increase with the number of genes in a genotype. Therefore, our results suggest that adding levels of complexity to the mapping of genotypes to phenotypes and increasing genome size enhances both these properties.

Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo

Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.

Validation of clinical control in COPD as a new tool for optimizing treatment

Background

It has recently been proposed that the concept of clinical control in COPD may be useful for deciding treatment in COPD, but the original control criteria (OCC) were considered too restrictive.

Objective

Define and subsequently validate "modified" control criteria (MCC) of COPD.

Method

Prospective observational study in COPD patients with a 1-year follow-up. Control was defined as the presence of low clinical impact and clinical stability. To evaluate clinical impact, the following clinical parameters were assessed: the degree of dyspnea, use of rescue medication, physical activity, and sputum color. Stability was assessed by clinical changes and exacerbations in the last 3 months. The COPD assessment test score and their changes were also evaluated as alternative control criteria. To define the MCC, adjustment for disease severity using BODEx index (MCC-B) or FEV₁ (MCC-F) was evaluated, and the best cutoff point was established. Time to first combined event (emergency visit, hospitalization, or death) was analyzed to evaluate the predictive capacity of risk of the OCC, MCC-B, and MCC-F.

Results

We included 265 patients, 224 (83.9%) men, with a mean age (±SD) of 68±9 years and FEV₁ of 58%±17%. The proportion of controlled patients was higher using clinical MCC-B or MCC-F (61.5% and 59.6%) than OCC (27.5%). Similar percentages were found using COPD assessment test scores. The time to the first combined event was significantly greater in controlled patients using MCC criteria (P<0.001, all cases). The predictive capacity of risk was similar in MCC-B (c-statistic [C]=0.639) and MCC-F (C=0.637) and higher than OCC (C=0.589).

Conclusions

The new MCC identified a higher number of controlled COPD patients. These patients have a better quality of life and lower risk of poor outcomes. The concept of control and the new MCC could be a useful tool to optimize therapy.

On the networked architecture of genotype spaces and its critical effects on molecular evolution

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at the macroevolutionary, ecological and molecular level. Actually, when the complex architecture of genotype spaces is taken into account, the evolutionary dynamics of molecular populations becomes intrinsically non-uniform, sharing deep qualitative and quantitative similarities with slowly driven physical systems: nonlinear responses analogous to critical transitions, sudden state changes or hysteresis, among others. Furthermore, the phenotypic plasticity inherent to genotypes transforms classical fitness landscapes into multiscapes where adaptation in response to an environmental change may be very fast. The quantitative nature of adaptive molecular processes is deeply dependent on a network-of-networks multilayered structure of the map from genotype to function that we begin to unveil.

Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation

Background

Wright’s metaphor of the fitness landscape has shaped and conditioned our view of the adaptation of populations for almost a century. Since its inception, and including criticism raised by Wright himself, the concept has been surrounded by controversy. Among others, the debate stems from the intrinsic difficulty to capture important features of the space of genotypes, such as its high dimensionality or the existence of abundant ridges, in a visually appealing two-dimensional picture. Two additional currently widespread observations come to further constrain the applicability of the original metaphor: the very skewed distribution of phenotype sizes (which may actively prevent, due to entropic effects, the achievement of fitness maxima), and functional promiscuity (i.e. the existence of secondary functions which entail partial adaptation to environments never encountered before by the population).

Results

Here we revise some of the shortcomings of the fitness landscape metaphor and propose a new “scape” formed by interconnected layers, each layer containing the phenotypes viable in a given environment. Different phenotypes within a layer are accessible through mutations with selective value, while neutral mutations cause displacements of populations within a phenotype. A different environment is represented as a separated layer, where phenotypes may have new fitness values, other phenotypes may be viable, and the same genotype may yield a different phenotype, representing genotypic promiscuity. This scenario explicitly includes the many-to-many structure of the genotype-to-phenotype map. A number of empirical observations regarding the adaptation of populations in the light of adaptive multiscapes are reviewed.

Conclusions

Several shortcomings of Wright’s visualization of fitness landscapes can be overcome through adaptive multiscapes. Relevant aspects of population adaptation, such as neutral drift, functional promiscuity or environment-dependent fitness, as well as entropic trapping and the concomitant impossibility to reach fitness peaks are visualized at once. Adaptive multiscapes should aid in the qualitative understanding of the multiple pathways involved in evolutionary dynamics.

Reviewers

This article was reviewed by Eugene Koonin and Ricard Solé.

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.

Dinámicas de transferencia tecnológica en una universidad pública regional. El caso de la Universidad del Bío-Bío

Durante las últimas décadas, Chile ha experimentado un significativo crecimiento, resultando ello en un mayor bienestar socio-económico para su población. Sin embargo, su éxito se ve ensombrecido por diversos factores, principalmente su elevada desigualdad de ingresos, su excesiva centralización institucional y su baja capacidad de innovación. En este respecto, la transferencia tecnológica ha seguido una tendencia similar: el país no ha alcanzado, a pesar de su nueva riqueza, estándares internacionales, postergando de esta forma su entrada a la economía del conocimiento. El presente artículo tiene como objetivo analizar y explorar las dinámicas de transferencia tecnológica en una universidad pública y regional en Chile: la Universidad del Bío-Bío (UBB). La metodología utilizada considera herramientas cuantitativas y cualitativas, aplicando primero un modelo logit, para luego desarrollar, tres estudios de casos sobre proyectos de Investigación y Desarrollo (I+D) en UBB. El modelo a testear define como variable dependiente la ocurrencia de transferencia tecnológica e incluye cuatro variables independientes: i) Financiamiento Público en I+D; ii) Capacidad de Investigación; iii) Estructuras de Soporte de la Universidad; y iv) Redes. Los resultados muestran que la transferencia tecnológica en UBB depende de la Capacidad de Investigación de la Universidad – particularmente del número de patentes solicitadas por  el investigador principal y el desempeño, por parte del investigador principal, como director de un Centro o Laboratorio de I+D– , además de Redes, en relación al capital social del equipo del proyecto.

Obstructive sleep apnoea in the elderly: role of continuous positive airway pressure treatment

Almost all the information about the effect of continuous positive airway pressure (CPAP) in patients with obstructive sleep apnoea (OSA) comes from clinical trials involving only middle-aged patients. The objective of this study was to assess the effect of CPAP treatment in elderly patients with severe OSA on clinical, quality-of-life and neurocognitive spheres. We performed an open-label, randomised, multicentre clinical trial in a consecutive clinical cohort of 224 elderly (≥70 years old) patients with confirmed severe OSA (apnoea-hypopnea index ≥30) randomised to receive CPAP (n=115) or no CPAP (n=109) for 3 months. A sleep study was performed by either full polysomnography or respiratory polygraphy. CPAP titration was performed by an autoCPAP device. The primary endpoint was quality of life (Quebec Sleep Questionnaire) and secondary endpoints included sleep-related symptoms, presence of anxiety/depression, office-based blood pressure and some neurocognitive tests. The mean±sd age was 75.5±3.9 years. The CPAP group achieved a greater improvement in all quality-of-life domains (p<0.001; effect size: 0.41-0.98), sleep-related symptoms (p<0.001; effect size 0.31-0.91) as well as anxiety (p=0.016; effect size 0.51) and depression (p<0.001; effect size: 0.28) indexes and some neurocognitive tests (digit symbol test (p=0.047; effect size: 0.20) and Trail Making Test A (p=0.029; effect size: 0.44)) in an intention-to-treat analysis. In conclusion, CPAP treatment resulted in an improvement in quality of life, sleep-related symptoms, anxiety and depression indexes and some neurocognitive aspects in elderly people with severe OSA.

An algorithm to diagnose influenza infection: evaluating the clinical importance and impact on hospital costs of screening with rapid antigen detection tests

Rapid antigen detection tests (RADTs) are immunoassays that produce results in 15 min or less, have low sensitivity (50 %), but high specificity (95 %). We studied the clinical impact and laboratory savings of a diagnostic algorithm for influenza infection using RADTs as a first-step technique during the influenza season. From January 15th to March 31st 2014, we performed a diagnostic algorithm for influenza infection consisting of an RADT for all respiratory samples received in the laboratory. We studied all the patients with positive results for influenza infection, dividing them into two groups: Group A with a negative RADT but positive reference tests [reverse transcription polymerase chain reaction (RT-PCR) and/or culture] and Group B with an initial positive RADT. During the study period, we had a total of 1,156 patients with suspicion of influenza infection. Of them, 217 (19 %) had a positive result for influenza: 132 (11 %) had an initial negative RADT (Group A) and 85 (7 %) had a positive RADT (Group B). When comparing patients in Group A and Group B, we found significant differences, as follows: prescribed oseltamivir (67 % vs. 82 %; p = 0.02), initiation of oseltamivir before 24 h (89 % vs. 97 %; p = 0.03), antibiotics prescribed (89 % vs. 67 %; p = <0.01), intensive care unit (ICU) admissions after diagnosis (23 % vs. 14 %; p = 0.05), and need for supplementary oxygen (61 % vs. 47 %; p = 0.01). An influenza algorithm including RADTs as the first step improves the time of administration of proper antiviral therapy, reduces the use of antibiotics and ICU admissions, and decreases hospital costs.

Balearic insular isolation and large continental spread framed the phylogeography of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae)

Recent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero-Provençal belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub-structured into two geographically separated subgroups (SE + E Iberia and NE Iberia + SW France). Genetic diversity and spatial structure analyses suggested a mid-Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle-Late Pleistocene marine regressions, whereas the more recent single back-colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long-distance dispersal mediated by migratory marine birds or sea currents.

Association of torque teno virus (TTV) and torque teno mini virus (TTMV) with liver disease among patients coinfected with human immunodeficiency virus and hepatitis C virus

Torque teno virus (TTV) and torque teno mini virus (TTMV) have been potentially related to liver diseases. The aim of the study was to quantify TTV and TTMV in human immunodeficiency virus (HIV)/hepatitis C virus (HCV)-coinfected patients to study the relationship between the TTV and TTMV viral loads and the severity of liver disease. We carried out a cross-sectional study in 245 patients coinfected with HIV and HCV (HIV/HCV-group), 114 patients monoinfected with HIV (HIV-group), and 100 healthy blood donors (Control-group). Plasma samples were tested for TTV and TTMV by quantitative real-time polymerase chain reaction (PCR). The prevalences of TTV and TTMV infections in the HIV/HCV-group and the HIV-group were significantly higher than the Control-group (p < 0.05). Furthermore, TTV and TTMV coinfections were found in 92.2 % (226/245) in the HIV/HCV-group, 84.2 % (96/114) in the HIV-group, and 63 % (63/100 %) in the Control-group (p ≤ 0.05). HIV/HCV-coinfected patients with HIV viral load ≥50 copies/mL and patients with severe activity grade had the highest viral loads of TTV and TTMV (p ≤ 0.05). HIV/HCV-coinfected patients with high TTV load (>2.78 log copies/μL) had increased odds of having advanced fibrosis or severe necroinflammatory activity grade in the liver biopsy. Moreover, HIV/HCV-coinfected patients with high TTMV load (>1.88 log copies/μL) had decreased odds of having no/minimal fibrosis and no/mild activity grade, and increased odds of having a high fibrosis progression rate. In conclusion, TTV and TTMV might play a role in the development of liver disease in immunodeficiency patients, such as the patients coinfected with HIV and HCV.

Internal consistency and validity of the Spanish version of the quality of life questionnaire specific for obstructive sleep apnea: sleep apnea quality of life index

INTRODUCTION

The objective of the present study was to validate the Spanish version of the SAQLI, which is a health-related quality of life (HRQL) questionnaire specific for sleep apnea-hypopnea syndrome (SAHS), and to assess its sensitivity to change.

MATERIAL AND METHODS

A multicenter study performed in a group of patients with SAHS (apnea-hypopnea index [AHI] ≥5) who had been referred to the centers' Sleep Units. All patients completed the following questionnaires: SF-36, FOSQ, SAQLI and Epworth scale. The psychometric properties (internal consistency, construct validity, concurrent validity, predictive value, repeatability and responsiveness to change) of the SAQLI were assessed (four domains: daily function, social interactions, emotional function and symptoms; an optional fifth domain is treatment-related symptoms).

RESULTS

One hundred sixty-two patients were included for study (mean age: 58±12; Epworth: 10±4; BMI: 33±5.9kg m(-2); AHI: 37±15hour(-1)). The factorial analysis showed a construct of four factors with similar distribution to the original questionnaire domains. Internal consistency (Cronbach's alpha between 0.78 and 0.82 for the different domains), concurrent validity for SF-36, Epworth scale and FOSQ, and test-retest reliability were appropriate. The predictive validity of the questionnaire showed no significant correlations with the severity of SAHS. SAQLI showed good sensitivity to change in all the domains of the questionnaire (p<0,01).

CONCLUSIONS

The Spanish version of the SAQLI is a valid HRQL measurement with appropriate psychometric properties for use in patients with SAHS and it is sensitive to change.

The undiagnosed cases of Clostridium difficile infection in a whole nation: where is the problem?

Underdiagnosis of Clostridium difficile infection (CDI) because of lack of clinical suspicion or the use of non-sensitive diagnostic techniques is a known problem whose real magnitude has not yet been quantified. In order to estimate the extent of this underdiagnosis, we performed C. difficile cultures on all unformed stool specimens sent-irrespective of the type of request-to a series of laboratories in Spain on a single day. The specimens were cultured, and isolates were characterized at a central reference laboratory. A total of 807 specimens from 730 patients aged ≥ 2 years were selected from 118 laboratories covering 75.4% of the Spanish population. The estimated rate of hospital-acquired CDI was 2.4 episodes per 1000 admissions or 3.8 episodes per 10,000 patient-days. Only half of the episodes occurred in patients hospitalized for >2 days. Two of every three episodes went undiagnosed or were misdiagnosed, owing to non-sensitive diagnostic tests (19.0%) or lack of clinical suspicion and request (47.6%; mostly young people or non-hospitalized patients). The main ribotypes were 014/020 (20.5%), 001 (18.2%), and 126/078 (18.2%). No ribotype 027 strains were detected. Strains were fully susceptible to metronidazole and vancomycin. CDI was underdiagnosed in diarrhoeic stools in a high proportion of episodes, owing to the use of non-sensitive techniques or lack of clinical suspicion, particularly in people aged <65 years or patients with community-acquired diarrhoea. C. difficile toxins should be routinely sought in unformed stools of any origin sent for microbiological diagnosis. The ribotype 027 clone has not yet disseminated in Spain.

The undiagnosed cases of Clostridium difficile infection in a whole nation: where is the problem?

Underdiagnosis of Clostridium difficile infection (CDI) because of lack of clinical suspicion or the use of non-sensitive diagnostic techniques is a known problem whose real magnitude has not yet been quantified. In order to estimate the extent of this underdiagnosis, we performed C. difficile cultures on all unformed stool specimens sent-irrespective of the type of request-to a series of laboratories in Spain on a single day. The specimens were cultured, and isolates were characterized at a central reference laboratory. A total of 807 specimens from 730 patients aged ≥ 2 years were selected from 118 laboratories covering 75.4% of the Spanish population. The estimated rate of hospital-acquired CDI was 2.4 episodes per 1000 admissions or 3.8 episodes per 10,000 patient-days. Only half of the episodes occurred in patients hospitalized for >2 days. Two of every three episodes went undiagnosed or were misdiagnosed, owing to non-sensitive diagnostic tests (19.0%) or lack of clinical suspicion and request (47.6%; mostly young people or non-hospitalized patients). The main ribotypes were 014/020 (20.5%), 001 (18.2%), and 126/078 (18.2%). No ribotype 027 strains were detected. Strains were fully susceptible to metronidazole and vancomycin. CDI was underdiagnosed in diarrhoeic stools in a high proportion of episodes, owing to the use of non-sensitive techniques or lack of clinical suspicion, particularly in people aged <65 years or patients with community-acquired diarrhoea. C. difficile toxins should be routinely sought in unformed stools of any origin sent for microbiological diagnosis. The ribotype 027 clone has not yet disseminated in Spain.

[Double lumen tube insertion in awake patients through the AirTraq laryngoscope in 2 cases of expected difficult airway]

The likelihood of difficult airway in thoracic surgery increases in the presence of associated cancer of the pharynx or larynx. The difficulty is greater when a double lumen tube must be inserted in these conditions, and various newly developed optical devices offer solutions for managing such cases. We report on 2 patients with expected difficult airway who were scheduled for lung resection. In both cases, intubation was accomplished through the AirTraq laryngoscope while the patient remained awake. Awake patient tolerance is facilitated by this laryngoscope, because the tube can be inserted without changing the position of the tongue or placing pressure on the vallecula.

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.

Prolonged viral shedding in pandemic influenza A(H1N1): clinical significance and viral load analysis in hospitalized patients

The clinical significance of prolonged viral shedding (PVS) and viral load (VL) dynamics has not been sufficiently assessed in hospitalized patients with pandemic 2009 influenza A(H1N1). We performed a prospective study of adults with confirmed influenza A(H1N1) virus infection admitted to our hospital from 20 September 2009 to 31 December 2009. Consecutive nasopharyngeal swabs were collected every 2 days during the first week after diagnosis, and then every week or until viral detection was negative. Relative VL was measured on the basis of haemagglutinin and RNaseP gene analysis. PVS was defined as positive detection of influenza A(H1N1) virus by real-time RT-PCR at day 7 after diagnosis. We studied 64 patients: 16 (25%) presented PVS. The factors associated with PVS were admission to the intensive-care unit (69% vs. 33%, p 0.02), purulent expectoration (75% vs. 44%, p 0.04), higher dosage of oseltamivir (62.5% vs. 27%, p 0.016), corticosteroid treatment (50% vs. 21%, p 0.05), mechanical ventilation (MV) (50% vs. 12.5%, p 0.004), and longer stay (34 vs. 7 median days, p 0.003). Multivariate analysis revealed the factors independently associated with PVS to be immunosuppression (OR 5.15; 95% CI 1.2-22.2; p 0.03) and the need for MV (OR 11.7; 95% CI 2.5-54.4; p 0.002). VL at diagnosis correlated negatively with age and septic shock. VL dynamics of patients with acute respiratory distress syndrome and/or mortality were very different from those of other patients. PVS was detected in 25% of hospitalized patients with pandemic 2009 influenza A(H1N1) and was strongly associated with immunosuppression and the need for MV. Diagnostic VL and viral clearance varied with the clinical course.

Prolonged viral shedding in pandemic influenza A(H1N1): clinical significance and viral load analysis in hospitalized patients

The clinical significance of prolonged viral shedding (PVS) and viral load (VL) dynamics has not been sufficiently assessed in hospitalized patients with pandemic 2009 influenza A(H1N1). We performed a prospective study of adults with confirmed influenza A(H1N1) virus infection admitted to our hospital from 20 September 2009 to 31 December 2009. Consecutive nasopharyngeal swabs were collected every 2 days during the first week after diagnosis, and then every week or until viral detection was negative. Relative VL was measured on the basis of haemagglutinin and RNaseP gene analysis. PVS was defined as positive detection of influenza A(H1N1) virus by real-time RT-PCR at day 7 after diagnosis. We studied 64 patients: 16 (25%) presented PVS. The factors associated with PVS were admission to the intensive-care unit (69% vs. 33%, p 0.02), purulent expectoration (75% vs. 44%, p 0.04), higher dosage of oseltamivir (62.5% vs. 27%, p 0.016), corticosteroid treatment (50% vs. 21%, p 0.05), mechanical ventilation (MV) (50% vs. 12.5%, p 0.004), and longer stay (34 vs. 7 median days, p 0.003). Multivariate analysis revealed the factors independently associated with PVS to be immunosuppression (OR 5.15; 95% CI 1.2-22.2; p 0.03) and the need for MV (OR 11.7; 95% CI 2.5-54.4; p 0.002). VL at diagnosis correlated negatively with age and septic shock. VL dynamics of patients with acute respiratory distress syndrome and/or mortality were very different from those of other patients. PVS was detected in 25% of hospitalized patients with pandemic 2009 influenza A(H1N1) and was strongly associated with immunosuppression and the need for MV. Diagnostic VL and viral clearance varied with the clinical course.

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae)

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.

Decline in the workload associated with the serodiagnosis of syphilis in a general hospital: 1994-2004

Syphilis re-emergence is a cause of concern. Our objective was to quantify the laboratory workload, incident cases and patient follow-up that syphilis has generated for 11 years in a large teaching hospital. An ecologic study including all samples submitted for syphilis serodiagnosis at our hospital from January 1994 to December 2004 was undertaken. Our laboratory processed 58,832 samples for syphilis serodiagnosis. From 1994 to 2004, the number of samples submitted for syphilis testing dropped by 11% (95% confidence interval [CI] 10-12, p<0.001). Syphilis was diagnosed in 443 patients. The incidences were 11, 3 and 8 per 100,000 inhabitants/year in 1994, 2000 and 2004, respectively. Only 42% (185) of patients had repeat tests and in 79% (146) of cases, the 1-year follow-up data were missing. The median follow-up was 9 months (interquartile range [IQR] 3-26). We detected a reduction in the effort to detect syphilis, despite an increase in its incidence and the low cost of syphilis screening. Efforts should be intensified to improve physician compliance with syphilis screening and follow-up guidelines.

Identification of liver fibrosis in HIV/HCV-coinfected patients using a simple predictive model based on routine laboratory data

We constructed noninvasive models to predict significant fibrosis (F > or = 2) and advanced fibrosis (F > or = 3) among human immunodeficiency virus (HIV)/hepatitis C virus (HCV)-coinfected patients, naïve for anti-HCV treatment. A total of 296 patients with liver biopsy were randomly assigned to an estimation group (EG = 226; 70%) and a validation group (VG = 70; 30%). We developed the Hospital Gregorio Marañón (HGM)-1 index, based on platelet count, aspartate aminotransferase (AST) and glucose, to predict F > or = 2 and the HGM-2 index, based on platelet count, international normalized ratio, alkaline phosphatase and AST to predict F > or = 3. The area under the receiver operating characteristic curves (AUROCs) of the HGM-1 index for the EG and the VG were 0.807 and 0.712 respectively. The AUROCs of the HGM-2 index for the EG and the VG were 0.844 and 0.815 respectively. With the HGM-1 index applied to the VG, using best cutoff scores, the negative predictive value (NPV) to exclude F > or = 2 was 54.5% and the positive predictive value (PPV) to confirm F > or = 2 was 93.3%. With the HGM-2 index applied to the VG, using best cutoff scores, the NPV to exclude F > or = 3 was 92.3, and the PPV to confirm F > or = 3 was 64.3%. Thus, HGM-2 accurately predicted F > or = 3 among HIV/HCV-coinfected patients. HGM-1 was less accurate at predicting F > or = 2.

On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management

Borderea chouardii is a relictual and dioecious, strictly sexually reproducing, long-living geophyte of the Dioscoreaceae family. Previous biological and demographic studies have indicated the existence of a uniformly distributed panmictic population of this taxon at the southernmost Spanish pre-Pyrenean mountain ranges where it occurs in rather inaccessible crevices of a single limestone cliff. However, individuals of B. chouardii are spatially subdivided into two subpopulations located, respectively, on the upper and lower parts of the cliff, and vertically separated 150 m. Because of its extreme rarity, B. chouardii was the first Iberian taxon to have a specific conservation plan and has been included in several red lists under the category of critically endangered (CR). However, no previous attempts have been conducted to analyse the fine scale evolutionary mechanisms involved in its present microspatial distribution. Genetic diversity and population structure have been investigated through the analysis of neutral hypervariable markers such as simple sequence repeats (SSRs) and randomly amplified polymorphic DNAs (RAPDs) to unravel the impact of life history traits in the differentiation of the two subpopulations. Both types of molecular markers were unequivocal in distinguishing two genetically distinct groups of individuals corresponding to their spatial separation. However, SSRs detected a higher level of subpopulation differentiation (F(ST) = 0.35, R(ST) = 0.32) than RAPDs (F(ST) = 0.21). SSR data indicated significant deviation from random dispersal of genes and genotypes between the two groups, suggesting that mating occurs mainly among individuals within subpopulations, thus, favouring the divergence between the two groups. This microevolutionary differentiation scenario might have been caused by a coupled effect of past genetic drift and reproductive isolation, as a result of strong glacial age bottlenecks and inefficient dispersal system of pollen and seeds, respectively. The identification of such genetic structure in this narrow endemic prompts a modification of the management strategies of its single extant population.

Characterization of seven (CTT)(n) microsatellite loci in the Pyrenean endemic Borderea pyrenaica (Dioscoreaceae): remarks on ploidy level and hybrid origin assessed through allozymes and microsatellite analyses

We present the identification and characterization of microsatellite loci in the Pyrenean endemic Borderea pyrenaica Miégeville (Dioscoreaceae). Seven microsatellite loci were isolated from a (CTT)(n)-enriched partial genomic library. Electropherograms patterns suggest that B. pyrenaica is a tetraploid species, as is its congener B. chouardii. One microsatellite locus was monomorphic, whereas the remaining ones presented from 2 to 10 alleles when analyzed in a sample of 60 individuals. Microsatellites have revealed higher levels of genetic variability than those in previous studies based on allozymes. Levels of genetic diversity are discussed in terms of tetrasomic (autotetraploidy) or duplicated disomic (allotetraploidy) modes of allele segregation. According to the first hypothesis, mean levels of genetic variability (H(min)-H(max)) range between 0.36 and 0.41, whereas, according to the second hypothesis, the 7 primer pairs amplified 11 chromosomal loci, and mean levels of observed and expected heterozygosities were 0.217 and 0.229, respectively, and did not differ significantly from HW expectations. These results suggest a hybrid allopolyploid origin for the Borderea taxa.

"Second-look" cytotoxicity: an evaluation of culture plus cytotoxin assay of Clostridium difficile isolates in the laboratory diagnosis of CDAD

Clostridium difficile is one of the most frequent causes of hospital-acquired diarrhoea. Our objective was to prove that some stool samples with a direct negative cytotoxicity assay may indeed harbour toxigenic C. difficile and that this can be demonstrated by performing a "second-look" cytotoxicity assay using the isolated C. difficile strains. Over an eight-year period (1992-1999), the 8241 stool samples submitted for direct cell culture from patients with suspected C. difficile-associated diarrhoea (CDAD) were simultaneously plated on cycloserine cefoxitin fructose agar. C. difficile strains isolated from samples with a negative direct cell culture assay were re-tested for toxin production "second-look" cell culture assay). Using both methods 6423 samples (78%) were negative. Of the remaining 1818 samples, 127 (7%) yielded C. difficile isolates which were confirmed as non-producers of toxin by both methods, 1437 (85%) were positive in direct cell culture assay, and 254 were positive only after the "second-look" cell culture assay. Thus, our approach allowed us to detect an extra 15% of toxin-producing strains that could have gone undetected otherwise.The combination of direct-cell culture assay, culture for toxigenic C. difficile and "second-look" cell culture assay enhances the potential for diagnosis of CDAD and enables us to be more efficient with our patient care resources.