Short-snouted toothless ichthyosaur from China suggests Late Triassic diversification of suction feeding ichthyosaurs

Background

Ichthyosaurs were an important group of Mesozoic marine reptiles and existed from the Early Triassic to the early Late Cretaceous. Despite a great diversity in body shapes and feeding adaptations, all share greatly enlarged eyes, an elongated rostrum with numerous conical teeth, and a streamlined body.

Methodology/Principal Findings

Based on new material from China and the restudy of Shastasaurus pacificus, we here reinterpret the classical large-bodied Late Triassic ichthyosaur genus Shastasaurus to differ greatly from the standard ichthyosaurian body plan, indicating much greater morphological diversity and range of feeding adaptations in ichthyosaurs than previously recognized. Phylogenetic analysis indicates a monophyletic clade consisting of the giant Shonisaurus sikanniensis, Guanlingsaurus liangae, and Shastasaurus pacificus to which the genus name Shastasaurus is applied. Shastasaurus liangae comb. nov. is from the Late Triassic (Carnian) Xiaowa Formation of Guizhou Province, southwestern China. The species combines a diminutive head with an entirely toothless and greatly reduced snout. The species also has by far the highest vertebral count among ichthyosaurs (86 presacral vertebrae and >110 caudal vertebrae), a count that is also very high for tetrapods in general. A reduced toothless snout and a diminutive head is also apparently present in the giant S. sikanniensis and presumably in S. pacificus.

Conclusions/Significance

In analogy to many modern odontocetes, Shastasaurus is interpreted as a specialized suction feeder on unshelled cephalopods and fish, suggesting a unique but widespread Late Triassic diversification of toothless, suction-feeding ichthyosaurs. Suction feeding has not been hypothesized for any of the other diverse marine reptiles of the Mesozoic before, but in Shastasaurus may be linked to the Late Triassic minimum in atmospheric oxygen.     

First diagnostic marine reptile remains from the aalenian (middle jurassic): a new ichthyosaur from southwestern Germany

Background

The Middle Jurassic was a critical time in the evolutionary history of ichthyosaurs. During this time interval, the diverse, well-studied faunas of the Lower Jurassic were entirely replaced by ophthalmosaurids, a new group that arose sometime prior to the Aalenian-Bajocian boundary and by the latest middle Jurassic comprised the only surviving group of ichthyosaurs. Thus, the Middle Jurassic Aalenian-Bathonian interval (176–165 million years ago) comprises the time frame during which ophthalmosaurids not only originated but also achieved taxonomic dominance. However, diagnostic ichthyosaur remains have been described previously from only a single locality from this interval, from the Bajocian of Argentina.

Methodology/Principal Findings

In this paper, we describe a new species of ichthyosaur based on a partial articulated specimen from the Middle Jurassic of southwestern Germany. This specimen was recovered from the Opalinuston Formation (early Aalenian) and is referable to Stenopterygius aaleniensis sp. nov. reflecting features of the skull and forefin. The genus Stenopterygius is diverse and abundant in the Lower Jurassic of Europe, but its presence has not previously been confirmed in younger (Middle Jurassic) rocks from the northern hemisphere.

Conclusions/Significance

This specimen represents the only diagnostic ichthyosaur remains reported from the Aalenian. It bears numerous similarities in size and in morphology to the Lower Jurassic species of the genus Stenopterygius and provides additional evidence that the major ecological changes hypothesized to have occurred at the end of the Toarcian took place sometime after this point and most likely did not occur suddenly. There is currently no evidence for the presence of ophthalmosaurids in the northern hemisphere during the Aalenian-Bathonian interval.     

A New Look at Ichthyosaur Long Bone Microanatomy and Histology: Implications for Their Adaptation to an Aquatic Life

Background

Ichthyosaurs are Mesozoic reptiles considered as active swimmers highly adapted to a fully open-marine life. They display a wide range of morphologies illustrating diverse ecological grades. Data concerning their bone microanatomical and histological features are rather limited and suggest that ichthyosaurs display a spongious, “osteoporotic-like” bone inner structure, like extant cetaceans. However, some taxa exhibit peculiar features, suggesting that the analysis of the microanatomical and histological characteristics of various ichthyosaur long bones should match the anatomical diversity and provide information about their diverse locomotor abilities and physiology.

Methodology/Principal Findings

The material analyzed for this study essentially consists of mid-diaphyseal transverse sections from stylopod bones of various ichthyosaurs and of a few microtomographic (both conventional and synchrotron) data. The present contribution discusses the histological and microanatomical variation observed within ichthyosaurs and the peculiarities of some taxa (Mixosaurus, Pessopteryx). Four microanatomical types are described. If Mixosaurus sections differ from those of the other taxa analyzed, the other microanatomical types, characterized by the relative proportion of compact and loose spongiosa of periosteal and endochondral origin respectively, seem to rather especially illustrate variation along the diaphysis in taxa with similar microanatomical features. Our analysis also reveals that primary bone in all the ichthyosaur taxa sampled (to the possible exception of Mixosaurus) is spongy in origin, that cyclical growth is a common pattern among ichthyosaurs, and confirms the previous assumptions of high growth rates in ichthyosaurs.

Conclusions/Significance

The occurrence of two types of remodelling patterns along the diaphysis, characterized by bone mass decrease and increase respectively is described for the first time. It raises questions about the definition of the osseous microanatomical specializations bone mass increase and osteoporosis, notably based on the processes involved, and reveals the difficulty in determining the true occurrence of these osseous specializations in ichthyosaurs.     

A basal thunnosaurian from Iraq reveals disparate phylogenetic origins for Cretaceous ichthyosaurs

Cretaceous ichthyosaurs have typically been considered a small, homogeneous assemblage sharing a common Late Jurassic ancestor. Their low diversity and disparity have been interpreted as indicative of a decline leading to their Cenomanian extinction. We describe the first post-Triassic ichthyosaur from the Middle East, Malawania anachronus gen. et sp. nov. from the Early Cretaceous of Iraq, and re-evaluate the evolutionary history of parvipelvian ichthyosaurs via phylogenetic and cladogenesis rate analyses. Malawania represents a basal grade in thunnosaurian evolution that arose during a major Late Triassic radiation event and was previously thought to have gone extinct during the Early Jurassic. Its pectoral morphology appears surprisingly archaic, retaining a forefin architecture similar to that of its Early Jurassic relatives. After the initial latest Triassic radiation of early thunnosaurians, two subsequent large radiations produced lineages with Cretaceous representatives, but the radiation events themselves are pre-Cretaceous. Cretaceous ichthyosaurs therefore include distantly related lineages, with contrasting evolutionary histories, and appear more diverse and disparate than previously supposed.     

Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers

Background

Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact on conservation and genetic improvement as well as on breeding. Using 84 polymorphic SSRs, we genotyped 213 M. rubra individuals (99 male individuals, 113 female varieties and 1 monoecious) and compared the difference in genetic diversity between the female and the male populations.

Results

Neighbour-joining cluster analysis separated M. rubra from three related species, and the male from female populations within M. rubra. By structure analysis, 178 M. rubra accessions were assigned to two subpopulations: Male dominated (98) and Female dominated (80). The well-known cultivars ‘Biqi’ and ‘Dongkui’, and the landraces ‘Fenhong’ are derived from three different gene pools. Female population had a slightly higher values of genetic diversity parameters (such as number of alleles and heterozygosity) than the male population, but not significantly different. The SSR loci ZJU062 and ZJU130 showed an empirical Fst value of 0.455 and 0.333, respectively, which are significantly above the 95 % confidence level, indicating that they are outlier loci related to sex separation.

Conclusion

The male and female populations of Chinese bayberry have similar genetic diversity in terms of average number of alleles and level of heterozygosity, but were clearly separated by genetic structure analysis due to two markers associated with sex type, ZJU062 and ZJU130. Zhejiang Province China could be the centre of diversity of M. rubra in China, with wide genetic diversity coverage; and the two representative cultivars ‘Biqi’ and ‘Dongkui’, and one landrace ‘Fenhong’ in three female subpopulations. This research provides genetic information on male and female Chinese bayberry and will act as a reference for breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1602-5) contains supplementary material, which is available to authorized users.     

A Giant Chelonioid Turtle from the Late Cretaceous of Morocco with a Suction Feeding Apparatus Unique among Tetrapods

Background

Secondary adaptation to aquatic life occurred independently in several amniote lineages, including reptiles during the Mesozoic and mammals during the Cenozoic. These evolutionary shifts to aquatic environments imply major morphological modifications, especially of the feeding apparatus. Mesozoic (250–65 Myr) marine reptiles, such as ichthyosaurs, plesiosaurs, mosasaurid squamates, crocodiles, and turtles, exhibit a wide range of adaptations to aquatic feeding and a broad overlap of their tooth morphospaces with those of Cenozoic marine mammals. However, despite these multiple feeding behavior convergences, suction feeding, though being a common feeding strategy in aquatic vertebrates and in marine mammals in particular, has been extremely rarely reported for Mesozoic marine reptiles.

Principal Findings

A relative of fossil protostegid and dermochelyoid sea turtles, Ocepechelon bouyai gen. et sp. nov. is a new giant chelonioid from the Late Maastrichtian (67 Myr) of Morocco exhibiting remarkable adaptations to marine life (among others, very dorsally and posteriorly located nostrils). The 70-cm-long skull of Ocepechelon not only makes it one of the largest marine turtles ever described, but also deviates significantly from typical turtle cranial morphology. It shares unique convergences with both syngnathid fishes (unique long tubular bony snout ending in a rounded and anteriorly directed mouth) and beaked whales (large size and elongated edentulous jaws). This striking anatomy suggests extreme adaptation for suction feeding unmatched among known turtles.

Conclusion/Significance

The feeding apparatus of Ocepechelon, a bony pipette-like snout, is unique among tetrapods. This new taxon exemplifies the successful systematic and ecological diversification of chelonioid turtles during the Late Cretaceous. This new evidence for a unique trophic specialization in turtles, along with the abundant marine vertebrate faunas associated to Ocepechelon in the Late Maastrichtian phosphatic beds of Morocco, further supports the hypothesis that marine life was, at least locally, very diversified just prior to the Cretaceous/Palaeogene (K/Pg) biotic crisis.     

Neurocognition,Insight and Medication Nonadherence in Schizophrenia: A Structural Equation Modeling Approach

Objective

The aim of this study was to examine the complex relationships among neurocognition, insight and nonadherence in patients with schizophrenia.

Methods

Design: Cross-sectional study. Inclusion criteria: Diagnosis of schizophrenia according to the DSM-IV-TR criteria. Data collection: Neurocognition was assessed using a global approach that addressed memory, attention, and executive functions; insight was analyzed using the multidimensional ‘Scale to assess Unawareness of Mental Disorder;’ and nonadherence was measured using the multidimensional ‘Medication Adherence Rating Scale.’ Analysis: Structural equation modeling (SEM) was applied to examine the non-straightforward relationships among the following latent variables: neurocognition, ‘awareness of positive symptoms’ and ‘negative symptoms’, ‘awareness of mental disorder’ and nonadherence.

Results

One hundred and sixty-nine patients were enrolled. The final testing model showed good fit, with normed χ² = 1.67, RMSEA = 0.063, CFI = 0.94, and SRMR = 0.092. The SEM revealed significant associations between (1) neurocognition and ‘awareness of symptoms,’ (2) ‘awareness of symptoms’ and ‘awareness of mental disorder’ and (3) ‘awareness of mental disorder’ and nonadherence, mainly in the ‘attitude toward taking medication’ dimension. In contrast, there were no significant links between neurocognition and nonadherence, neurocognition and ‘awareness of mental disorder,’ and ‘awareness of symptoms’ and nonadherence.

Conclusions

Our findings support the hypothesis that neurocognition influences ‘awareness of symptoms,’ which must be integrated into a higher level of insight (i.e., the ‘awareness of mental disorder’) to have an impact on nonadherence. These findings have important implications for the development of effective strategies to enhance medication adherence.     

Re-Visiting Trichuris trichiura Intensity Thresholds Based on Anemia during Pregnancy

Background

The intensity categories, or thresholds, currently used for Trichuris trichiura (ie. epg intensities of 1–999 (light); 1,000–9,999 epg (moderate), and ≥10,000 epg (heavy)) were developed in the 1980s, when there were little epidemiological data available on dose-response relationships. This study was undertaken to determine a threshold for T. trichiura-associated anemia in pregnant women and to describe the implications of this threshold in terms of the need for primary prevention and chemotherapeutic interventions.

Methodology/Principal Findings

In Iquitos, Peru, 935 pregnant women were tested for T. trichiura infection in their second trimester of pregnancy; were given daily iron supplements throughout their pregnancy; and had their blood hemoglobin levels measured in their third trimester of pregnancy. Women in the highest two T. trichiura intensity quintiles (601–1632 epg and ≥1633 epg) had significantly lower mean hemoglobin concentrations than the lowest quintile (0–24 epg). They also had a statistically significantly higher risk of anemia, with adjusted odds ratios of 1.67 (95% CI: 1.02, 2.62) and 1.73 (95% CI: 1.09, 2.74), respectively.

Conclusions/Significance

This analysis provides support for categorizing a T. trichiura infection ≥1,000 epg as ‘moderate’, as currently defined by the World Health Organization. Because this ‘moderate’ level of T. trichiura infection was found to be a significant risk factor for anemia in pregnant women, the intensity of Trichuris infection deemed to cause or aggravate anemia should no longer be restricted to the ‘heavy’ intensity category. It should now include both ‘heavy’ and ‘moderate’ intensities of Trichuris infection. Evidence-based deworming strategies targeting pregnant women or populations where anemia is of concern should be updated accordingly.     

Impact on Clinical and Cost Outcomes of a Centralized Approach to Acute Stroke Care in London: A Comparative Effectiveness Before and After Model

Background

In July 2010 a new multiple hub-and-spoke model for acute stroke care was implemented across the whole of London, UK, with continuous specialist care during the first 72 hours provided at 8 hyper-acute stroke units (HASUs) compared to the previous model of 30 local hospitals receiving acute stroke patients. We investigated differences in clinical outcomes and costs between the new and old models.

Methods

We compared outcomes and costs ‘before’ (July 2007–July 2008) vs. ‘after’ (July 2010–June 2011) the introduction of the new model, adjusted for patient characteristics and national time trends in mortality and length of stay. We constructed 90-day and 10-year decision analytic models using data from population based stroke registers, audits and published sources. Mortality and length of stay were modelled using survival analysis.

Findings

In a pooled sample of 307 patients ‘before’ and 3156 patients ‘after’, survival improved in the ‘after’ period (age adjusted hazard ratio 0.54; 95% CI 0.41–0.72). The predicted survival rates at 90 days in the deterministic model adjusted for national trends were 87.2% ‘before’ % (95% CI 86.7%–87.7%) and 88.7% ‘after’ (95% CI 88.6%–88.8%); a relative reduction in deaths of 12% (95% CI 8%–16%). Based on a cohort of 6,438 stroke patients, the model produces a total cost saving of £5.2 million per year at 90 days (95% CI £4.9-£5.5 million; £811 per patient).

Conclusion

A centralized model for acute stroke care across an entire metropolitan city appears to have reduced mortality for a reduced cost per patient, predominately as a result of reduced hospital length of stay.     

Association between Obesity and Cardiometabolic Health Risk in Asian-Canadian Sub-Groups

Objectives

To quantify and compare the association between the World Health Organizations’ Asian-specific trigger points for public health action [‘increased risk’: body mass index (BMI) ≥23 kg/m², and; ‘high risk’: BMI ≥27.5 kg/m²] with self-reported cardiovascular-related conditions in Asian-Canadian sub-groups.

Methods

Six cycles of the Canadian Community Health Survey (2001–2009) were pooled to examine BMI and health in Asian sub-groups (South Asians, Chinese, Filipino, Southeast Asians, Arabs, West Asians, Japanese and Korean; N = 18 794 participants, ages 18–64 y). Multivariable logistic regression, adjusting for demographic, lifestyle characteristics and acculturation measures, was used to estimate the odds of cardiovascular-related health (high blood pressure, heart disease, diabetes, ‘at least one cardiometabolic condition’) outcomes across all eight Asian sub-groups.

Results

Compared to South Asians (OR = 1.00), Filipinos had higher odds of having ‘at least one cardiometabolic condition’ (OR = 1.29, 95% CI: 1.04–1.62), whereas Chinese (0.63, 0.474–0.9) and Arab-Canadians had lower odds (0.38, 0.28–0.51). In ethnic-specific analyses (with ‘acceptable’ risk weight as the referent), ‘increased’ and ‘high’ risk weight categories were the most highly associated with ‘at least one cardiometabolic condition’ in Chinese (‘increased’: 3.6, 2.34–5.63; ‘high’: 8.9, 3.6–22.01). Compared to normal weight South Asians, being in the ‘high’ risk weight category in all but the Southeast Asian, Arab, and Japanese ethnic groups was associated with approximately 3-times the likelihood of having ‘at least one cardiometabolic condition’.

Conclusion

Differences in the association between obesity and cardiometabolic health risks were seen among Asian sub-groups in Canada. The use of WHO’s lowered Asian-specific BMI cut-offs identified obesity-related risks in South Asian, Filipino and Chinese sub-groups that would have been masked by traditional BMI categories. These findings have implications for public health messaging, especially for ethnic groups at higher odds of obesity-related health risks.     

The Effectiveness of the Cardiovascular Disease Prevention Programme ‘KardioPro’ Initiated by a German Sickness Fund: A Time-to-Event Analysis of Routine Data

Background

Cardiovascular disease is the leading cause of morbidity and mortality in the developed world. To reduce this burden of disease, a German sickness fund (‘Siemens-Betriebskrankenkasse’, SBK) initiated the prevention programme ‘KardioPro’ including primary (risk factor reduction) and secondary (screening) prevention and guideline-based treatment. The aim of this study was to assess the effectiveness of ‘KardioPro’ as it is implemented in the real world.

Methods

The study is based on sickness fund routine data. The control group was selected from non-participants via propensity score matching. Study analysis was based on time-to-event analysis via Cox proportional hazards regression with the endpoint ‘all-cause mortality, acute myocardial infarction (MI) and ischemic stroke (1)’, ‘all-cause mortality (2)’ and ‘non-fatal acute MI and ischemic stroke (3)’.

Results

A total of 26,202 insurants were included, 13,101 participants and 13,101 control subjects. ‘KardioPro’ enrolment was associated with risk reductions of 23.5% (95% confidence interval (CI) 13.0–32.7%) (1), 41.7% (95% CI 30.2–51.2%) (2) and 3.5% (hazard ratio 0.965, 95% CI 0.811–1.148) (3). This corresponds to an absolute risk reduction of 0.29% (1), 0.31% (2) and 0.03% (3) per year.

Conclusion

The prevention programme initiated by a German statutory sickness fund appears to be effective with regard to all-cause mortality. The non-significant reduction in non-fatal events might result from a shift from fatal to non-fatal events.     

A Meta-Analysis of the Effects of the 5-Hydroxytryptamine Transporter Gene-Linked Promoter Region Polymorphism on Susceptibility to Lifelong Premature Ejaculation

Objective

Premature ejaculation (PE) has been reported as the most common male sexual dysfunction with global prevalence rates estimated at approximately 30%. The neurobiogenesis of ejaculation is very complex and involves the serotoninergic (5-hydroxytryptamine, 5-HT) system. Recently, genetic polymorphisms located on SLC6A4 gene codifying for 5-HT transporter (5-HTT), the major regulator of serotonic neurotransmission, have been linked with the pathogenesis and risk of PE. Apparently studies of this type of polymorphism in PE have show conflicting results.

Methods

A meta-analysis was performed that are available in relation with 5-HTT gene-linked promoter region (5-HTTLPR) polymorphism and the risk of lifelong PE (LPE) in men to clarify this relationship. We searched Pubmed and Embase (last search updated on Aug 2012) using ‘premature ejaculation’, ‘polymorphism or variant’, ‘genotype’, ‘ejaculatory function’, and ‘rapid ejaculation’ as keywords and reference lists of studies corresponded to the inclusion criteria for meta-analysis. These studies involved the total number of 481 LPE men and 466 health control men subjects. Odds ratio (OR) and 95% confidence intervals (CIs) were used to evaluate this relationship.

Results

In the overall analysis, significant associations between LPE risk and 5-HTTLPR polymorphism were found (L-allele vs. S-allele OR = 0.86, 95% CI = 0.79–0.95, P = 0.002; LL vs. SS: OR = 0.80, 95% CI = 0.68–0.95, P = 0.009; LS vs. SS: OR = 0.85, 95% CI = 0.76–0.97, P = 0.012 and LL+LS vs. SS: OR = 0.88, 95% CI = 0.81–0.95, P = 0.002). Moreover, in subgroup analysis based on ethnicity, similar significant associations were detected. The Egger’s test did not reveal presence of a publication bias.

Conclusions

Our investigations demonstrate that 5-HTTLPR (L>S) polymorphism might protect men against LPE risk. Further studies based on larger sample size and gene-environment interactions should be conducted the role of 5-HTTLPR polymorphism and LPE risk.     

Fasting for 24 Hours Heightens Reward from Food and Food-Related Cues

Introduction

We examined the impact of a 24 hour complete fast (vs. fed state) on two measures of food reward: 1) ‘wanting’, as measured by response to food images and by the relative-reinforcing value of food (RRV), and 2) ‘liking’, as measured by response to food images and the hedonic evaluation of foods consumed.

Methods

Utilizing a randomized crossover design, 15 subjects (9 male; 6 female) aged 28.6±4.5 yrs with body mass index 25.3±1.4 kg/m² were randomized and counterbalanced to normal feeding (FED) and 24-hour fast (FASTED) conditions. Trait characteristics were measured with the Three Factor Eating Questionnaire. Two computer tasks measured food reward: 1) RRV progressive ratio task, 2) explicit ‘liking’ and ‘wanting’ (Leeds Food Preference Questionnaire, LFPQ). Also measured were ad libitum energy intake (EI; buffet) and food ‘liking’ (visual analogue scale) of personalized stimuli.

Results

There were no significant anthropometric changes between conditions. Appetite scores, hedonic ratings of ‘liking’, and ad libitum EI all significantly increased under the FASTED condition (p<0.05). Under the FASTED condition there were significant increases in the RRV of snack foods; similarly, explicit ‘wanting’ and ‘liking’ significantly increased for all food categories. ‘Liking’ of sweet foods remained high across-meals under FASTED, but savory foods decreased in hedonic saliency.

Conclusion

Relative to a fed state, we observed an increase in hedonic ratings of food, the rewarding value of food, and food intake after a 24 hr fast. Alliesthesia to food and food cues is suggested by heightened hedonic ratings under the FASTED condition relative to FED.     

Towards an ontogenetic understanding of inflorescence diversity

Backgrounds and Aims

Conceptual and terminological conflicts in inflorescence morphology indicate a lack of understanding of the phenotypic diversity of inflorescences. In this study, an ontogeny-based inflorescence concept is presented considering different meristem types and developmental pathways. By going back to the ontogenetic origin, diversity is reduced to a limited number of types and terms.

Methods

Species from 105 genera in 52 angiosperm families are investigated to identify their specific reproductive meristems and developmental pathways. Based on these studies, long-term experience with inflorescences and literature research, a conceptual framework for the understanding of inflorescences is presented.

Key Results

Ontogeny reveals that reproductive systems traditionally called inflorescences fall into three groups, i.e. ‘flowering shoot systems’ (FSS), ‘inflorescences’ sensu stricto and ‘floral units’ (FUs). Our concept is, first, based on the identification of reproductive meristem position and developmental potential. The FSS, defined as a seasonal growth unit, is used as a reference framework. As the FSS is a leafy shoot system bearing reproductive units, foliage and flowering sequence play an important role. Second, the identification of two different flower-producing meristems is essential. While ‘inflorescence meristems’ (IMs) share acropetal primordia production with vegetative meristems, ‘floral unit meristems’ (FUMs) resemble flower meristems in being indeterminate. IMs produce the basic inflorescence types, i.e. compound and simple racemes, panicles and botryoids. FUMs give rise to dense, often flower-like units (e.g. heads). They occur solitarily at the FSS or occupy flower positions in inflorescences, rendering the latter thyrses in the case of cymose branching.

Conclusions

The ontogenetic concept differs from all existing inflorescence concepts in being based on meristems and developmental processes. It includes clear terms and allows homology statements. Transitional forms are an explicit part of the concept, illustrating the ontogenetic potential for character transformation in evolution.     

galign: A Tool for Rapid Genome Polymorphism Discovery

Background

Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale. However, the development of customized software to analyze data produced by these methods has lagged behind.

Methods/Principal Findings

Here I describe a tool, ‘galign’, designed to identify polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome. The ‘galign’ alignment tool does not use Smith-Waterman matrices for sequence comparisons. Instead, a simple algorithm comparing parsed sequence reads to parsed reference genome sequences is used. ‘galign’ output is geared towards immediate user application, displaying polymorphism locations, nucleotide changes, and relevant predicted amino-acid changes for ease of information processing. To do so, ‘galign’ requires several accessory files easily derived from an annotated reference genome. Direct sequencing as well as in silico studies demonstrate that ‘galign’ provides lesion predictions comparable in accuracy to available prediction programs, accompanied by greater processing speed and more user-friendly output. We demonstrate the use of ‘galign’ to identify mutations leading to phenotypic consequences in C. elegans.

Conclusion/Significance

Our studies suggest that ‘galign’ is a useful tool for polymorphism discovery, and is of immediate utility for sequence mining in C. elegans.     

A canopy architectural model to study the competitive ability of chickpea with sowthistle

Background and Aims

Improving the competitive ability of crops is a sustainable method of weed management. This paper shows how a virtual plant model of competition between chickpea (Cicer arietinum) and sowthistle (Sonchus oleraceus) can be used as a framework for discovering and/or developing more competitive chickpea cultivars.

Methods

The virtual plant models were developed using the L-systems formalism, parameterized according to measurements taken on plants at intervals during their development. A quasi-Monte Carlo light-environment model was used to model the effect of chickpea canopy on the development of sowthistle. The chickpea–light environment–sowthistle model (CLES model) captured the hypothesis that the architecture of chickpea plants modifies the light environment inside the canopy and determines sowthistle growth and development pattern. The resulting CLES model was parameterized for different chickpea cultivars (viz. ‘Macarena’, ‘Bumper’, ‘Jimbour’ and ‘99071-1001’) to compare their competitive ability with sowthistle. To validate the CLES model, an experiment was conducted using the same four chickpea cultivars as different treatments with a sowthistle growing under their canopy.

Results and Conclusions

The growth of sowthistle, both in silico and in glasshouse experiments, was reduced most by ‘99071-1001’, a cultivar with a short phyllochron. The second rank of competitive ability belonged to ‘Macarena’ and ‘Bumper’, while ‘Jimbour’ was the least competitive cultivar. The architecture of virtual chickpea plants modified the light inside the canopy, which influenced the growth and development of the sowthistle plants in response to different cultivars. This is the first time that a virtual plant model of a crop–weed interaction has been developed. This virtual plant model can serve as a platform for a broad range of applications in the study of chickpea–weed interactions and their environment.Key words: Plant architecture, virtual plant modelling, L-systems formalism, crop/weed competition, integrated weed management, chickpea, Cicer arietinum, sowthistle, Sonchus oleraceus     

High Levels of Heterogeneity in the HIV Cascade of Care across Different Population Subgroups in British Columbia,Canada

Background

The HIV cascade of care (cascade) is a comprehensive tool which identifies attrition along the HIV care continuum. We executed analyses to explicate heterogeneity in the cascade across key strata, as well as identify predictors of attrition across stages of the cascade.

Methods

Using linked individual-level data for the population of HIV-positive individuals in BC, we considered the 2011 calendar year, including individuals diagnosed at least 6 months prior, and excluding individuals that died or were lost to follow-up before January 1^st, 2011. We defined five stages in the cascade framework: HIV ‘diagnosed’, ‘linked’ to care, ‘retained’ in care, ‘on HAART’ and virologically ‘suppressed’. We stratified the cascade by sex, age, risk category, and regional health authority. Finally, multiple logistic regression models were built to predict attrition across each stage of the cascade, adjusting for stratification variables.

Results

We identified 7621 HIV diagnosed individuals during the study period; 80% were male and 5% were <30, 17% 30–39, 37% 40–49 and 40% were ≥50 years. Of these, 32% were MSM, 28% IDU, 8% MSM/IDU, 12% heterosexual, and 20% other. Overall, 85% of individuals ‘on HAART’ were ‘suppressed’; however, this proportion ranged from 60%–93% in our various stratifications. Most individuals, in all subgroups, were lost between the stages: ‘linked’ to ‘retained’ and ‘on HAART’ to ‘suppressed’. Subgroups with the highest attrition between these stages included females and individuals <30 years (regardless of transmission risk group). IDUs experienced the greatest attrition of all subgroups. Logistic regression results found extensive statistically significant heterogeneity in attrition across the cascade between subgroups and regional health authorities.

Conclusions

We found that extensive heterogeneity in attrition existed across subgroups and regional health authorities along the HIV cascade of care in B.C., Canada. Our results provide critical information to optimize engagement in care and health service delivery.     

Individual Correlates of Podoconiosis in Areas of Varying Endemicity: A Case-Control Study

Background

Podoconiosis is a non-filarial form of elephantiasis resulting in lymphedema of the lower legs. Previous studies have suggested that podoconiosis arises from the interplay of individual and environmental factors. Here, our aim was to understand the individual-level correlates of podoconiosis by comparing 460 podoconiosis-affected individuals and 707 unaffected controls.

Methods/principal findings

This was a case-control study carried out in six kebeles (the lowest governmental administrative unit) in northern Ethiopia. Each kebele was classified into one of three endemicity levels: ‘low’ (prevalence <1%), ‘medium’ (1–5%) and ‘high’ (>5%). A total of 142 (30.7%) households had two or more cases of podoconiosis. Compared to controls, the majority of the cases, especially women, were less educated (OR = 1.7, 95% CI = 1.3 to 2.2), were unmarried (OR = 3.4, 95% CI = 2.6–4.6) and had lower income (t = −4.4, p<0.0001). On average, cases started wearing shoes ten years later than controls. Among cases, age of first wearing shoes was positively correlated with age of onset of podoconiosis (r = 0.6, t = 12.5, p<0.0001). Among all study participants average duration of shoe wearing was less than 30 years. Between both cases and controls, people in ‘high’ and ‘medium’ endemicity kebeles were less likely than people in ‘low’ endemicity areas to ‘ever’ have owned shoes (OR = 0.5, 95% CI = 0.4–0.7).

Conclusions

Late use of shoes, usually after the onset of podoconiosis, and inequalities in education, income and marriage were found among cases, particularly among females. There were clustering of cases within households, thus interventions against podoconiosis will benefit from household-targeted case tracing. Most importantly, we identified a secular increase in shoe-wearing over recent years, which may give opportunities to promote shoe-wearing without increasing stigma among those at high risk of podoconiosis.