Bean Genome Diversity Reveals the Genomic Consequences of Speciation, Adaptation, and Domestication

Here we review whether genomic islands of speciation are repeatedly more prone to harbor within-species differentiation due to genomic features, such as suppressed recombination, smaller effective population size, and increased drift, across repeated hierarchically nested levels of divergence. Our discussion focuses on two species of Phaseolus beans with strong genepool and population substructure and multiple independent domestications each. We overview regions of species-associated divergence, as well as divergence recovered in within-species between-genepool comparisons and in within-genepool wild-cultivated comparisons. We discuss whether regions with overall high relative differentiation coincide with sections of low SNP density and with between-species pericentric inversions, since these convergences would suggest that shared variants are being recurrently fixed at replicated comparisons, and in a similar manner across different hierarchically nested levels of divergence, likely as the result of genomic features that make certain regions more prone to accumulate islands of speciation as well as within-species divergence. We conclude that neighboring signatures of speciation, adaptation, and domestication in Phaseolus beans seem to be influenced by ubiquitous genomic constrains, which may continue shaping, fortuitously, genomic differentiation at various other scales of divergence. This pattern also suggests that genomic regions important for adaptation may frequently be sheltered from recombination

Diversidad de faseolinas en frijol común cultivado del caribe

Se evaluó el tipo de faseolina en 180 accesiones cultivadas de Phaseolus vulgaris del Caribe de la colección del Centro Internacional de Agricultura Tropical (CIAT). En fríjoles de Cuba (25 accesiones) predominó el tipo S (68%, semilla pequeña, roja o negra y hábito de crecimiento de tipos II y III), seguidos por fríjoles con faseolina T (20 %) y con un bajo porcentaje los tipos B, CH y Sd. En Haití (108 accesiones) las faseolinas más comunes fueron T (48.1%, semilla grande, rojo moteado y hábito arbustivo) y S (42.6%, semilla pequeña, negra), y unas pocas mostraron faseolinas B, Sb y Sd. En los fríjoles de Puerto Rico (21 accesiones) las faseolinas más comunes fueron T (57.14%, semilla grande, rojo moteada) y S (42.86%, semilla pequeña amarilla, negra o blanca). En los de República Dominicana (21 accesiones) abundó el tipo T (85.7%, semilla grande o mediana rojomoteada). En los fríjoles de Jamaica (5) predominaron las faseolinas T y B (40% de cada una). Los patrones de faseolina indicaron la prevalencia tanto de fríjoles Mesoamericanos como Andinos.In this study, 180 genotypes of cultivated Phaseolus vulgaris from the Caribbean were evaluated with the phaseolin marker. All the accessions belonged to the germplasm collection of the International Center for Tropical Agriculture (CIAT). Beans from Cuba were mostly S phaseolin (68.0 %) type, with small seed size, red and black seed color and type II or type III growth habit. These were followed by beans with T phaseolin (20.0 %) and finally by those with B, CH and Sd phaseolin. In Haiti, the most common phaseolin was T (48.1%), the majority of which were large seeded bush beans, mostly of the red mottled seed color class. Many of the remaining accessions were S phaseolin (42.6%) and had small black seed, although a few had B, Sb and Sd phaseolin (4.6, 2.8 and 1.9% of genotypes, respectively). In Puerto Rico, T phaseolin was in the majority with 57.1%, most of these with large red or red mottled seed. S phaseolin was represented by 42.9 % of landraces some of which had small yellow, black or white seed. In the Dominican Republic, the T phaseolin was very abundant (85.7%) the majority of which were medium to large seeded bush beans all of which were red mottled. A smaller proportion of Dominican landraces had S and B phaseolin (9.5% and 4.8% respectively). Finally, in Jamaica, T phaseolin was found for 40.0 % of the landraces, B phaseolin was equally common and 20% of the landraces had S phaseolin although this was based on a small sample of genotypes. The phaseolin patterns indicated the prevalence of both Andean and Mesoamerican beans in the Caribbean

Social Determinants of Health and Parenting Self-Efficacy Among Mothers of Preterm Infants

Objective: To explore the relationships between social and environmental factors and parenting self-efficacy (PSE) among mothers of preterm infants hospitalized in neonatal intensive care units (NICUs) using a social determinants of health (SDoH) framework. Method: We analyzed data from a prospective cohort study that included 187 mother-infant dyads admitted to four NICUs in the Mountain West region between June 2017 and December 2019. We used multivariable linear regression models to assess the independent associations between maternal and infant characteristics and PSE. Results: Our final multiple linear regression model predicting the efficacy score including maternal race/ethnicity, age, insurance, employment status before giving birth, gestational age, depression, and having other children was significant (F(12,160) = 3.17, p = .0004, adjusted R¬2 = .131). Significant predictors of PSE were race/ethnicity (β= 3.3, p = .022), having another child/children (β= 4.2, p = .005), and depression (β= -4.2, p = .004). Conclusions: Findings suggest that social workers and medical practitioners should consider SDoH, such as insurance type, household income, and employment, along with traditional clinical indicators when assessing families’ infant care needs. Social workers, medical practitioners, and researchers should be mindful of how implicit bias may influence the allocation of care and parental supports

Physical activity levels, ownership of goods promoting sedentary behaviour and risk of myocardial infarction: results of the INTERHEART study

Aims: To evaluate the association between occupational and leisure-time physical activity (PA), ownership of goods promoting sedentary behaviour, and the risk of myocardial infarction (MI) in different socio-economic populations of the world. Studies in developed countries have found low PA as a risk factor for cardiovascular disease, however, the protective effect of occupational PA is less certain. Moreover, ownership of goods promoting sedentary behaviour may be associated with an increased risk. Methods: In INTERHEART, a casecontrol study of 10 043 cases of first MI and 14 217 controls who did not report previous angina or physical disability completed a questionnaire on work and leisure-time PA. Results: Subjects whose occupation involved either light [multivariable-adjusted odds ratio (OR) 0.78, confidence interval (CI) 0.710.86] or moderate (OR 0.89, CI 0.800.99) PA were at a lower risk of MI, whereas those who did heavy physical labour were not (OR 1.02, CI 0.881.19), compared with sedentary subjects. Mild exercise (OR 0.87, CI 0.810.93) as well as moderate or strenuous exercise (OR 0.76, CI 0.690.82) was protective. The effect of PA was observed across countries with low, middle, and high income. Subjects who owned both a car and a television (TV) (multivariable-adjusted OR 1.27, CI 1.051.54) were at higher risk of MI compared with those who owned neither. Conclusion: Leisure-time PA and mild-to-moderate occupational PA, but not heavy physical labour, were associated with a reduced risk, while ownership of a car and TV was associated with an increased risk of MI across all economic regions

The role of diet and other environmental factors in the causation of gastric cancer in Iran—A population based study

Despite a declining trend in the incidence of gastric cancer (GC), it is still a major global public health concern of the 21st century. The rates of GC reported from Ardabil Province, Iran, are among the highest in the world. To investigate risk factors for GC in Ardabil, we undertook a population-based case-control study. The study aimed to recruit all Ardabil residents newly diagnosed with GC in the time period of 2004–2005, and 2 controls per case. Participants were interviewed using a structured questionnaire. Ten milliliters of blood was collected for blood grouping and investigating the presence of IgG antibodies against Helicobacter pylori. During the study period, 217 people with GC and 394 controls were recruited. In multivariate analysis, diet and Helicobacter pylori infection (OR 5 2.41; 95% CI: 1.35–4.32) were found to be the factors that were most strongly related to GC. High intake of Allium vegetables (OR 5 0.35) and fruit, especially citrus fruit (OR 5 0.31) and consumption of fresh fish (OR 5 0.37) were significantly protective. On the other hand, consumption of red meat (OR 5 3.40) and dairy products (OR 5 2.28) were positively associated with the risk of GC. People who had a preference for higher salt intake (OR 5 3.10) and drinking strong and hot tea (OR 5 2.64 and 2.85, respectively) were at higher risk. In conclusion, Helicobacter pylori infection as measured by serum IgG as well as the consumption of red meat and dairy products increases the risk of GC in Ardabil, while the intake of fresh fruit and fresh fish decrease the risk

An aortic aneurysm model for the evaluation of endovascular exclusion prostheses

Abstract Purpose: The purpose of this study was to develop an aortic aneurysm (AA) model with a predictable tendency for rupture for the evaluation of the efficacy of endovascular prostheses in preventing rupture and their long-term outcome after implantation. Methods: An infrarenal AA measuring two to three times the diameter of the proximal aorta was created in 18 dogs with a full-thickness patch of jejunum. Seven dogs were allowed to survive without aneurysm exclusion. In 11 dogs the aneurysm was immediately excluded with a stented 8 mm Dacron graft mounted in a 14F delivery system introduced through the femoral artery with aortographic guidance. The pressure differential between the aorta and the excluded aneurysm was measured, and angiography, necropsy, and histologic examination were performed at 3- and 6-month survival. Results: All animals survived aneurysm implantation. Without aneurysm exclusion, six dogs died of rupture within 1 to 6 days of surgery. In three dogs the exclusion failed because of graft-to-aorta size mismatch or misplacement demonstrated on angiography and by a low pressure differential between the aorta and the aneurysm (p < 0.023) in dogs with successfully excluded aneurysms (n = 6) compared with that in dogs without exclusion or with failed aneurysm exclusion (n = 7). Conclusion: This aneurysm model demonstrates that without effective aneurysm exclusion all animals die of rupture and that successfully placed endovascular prostheses can prevent AA rupture with long-term graft patency and stability. Endovascular aortic Dacron grafts in dogs undergo complete incorporation at 3 months from implantation. This aneurysm model is useful for the evaluation of endovascular devices designed for the treatment of AAs. (J VASC SURG 1995;22:306-15.

Mechanisms of TSC-mediated Control of Synapse Assembly and Axon Guidance

Tuberous sclerosis complex is a dominant genetic disorder produced by mutations in either of two tumor suppressor genes, TSC1 and TSC2; it is characterized by hamartomatous tumors, and is associated with severe neurological and behavioral disturbances. Mutations in TSC1 or TSC2 deregulate a conserved growth control pathway that includes Ras homolog enriched in brain (Rheb) and Target of Rapamycin (TOR). To understand the function of this pathway in neural development, we have examined the contributions of multiple components of this pathway in both neuromuscular junction assembly and photoreceptor axon guidance in Drosophila. Expression of Rheb in the motoneuron, but not the muscle of the larval neuromuscular junction produced synaptic overgrowth and enhanced synaptic function, while reductions in Rheb function compromised synapse development. Synapse growth produced by Rheb is insensitive to rapamycin, an inhibitor of Tor complex 1, and requires wishful thinking, a bone morphogenetic protein receptor critical for functional synapse expansion. In the visual system, loss of Tsc1 in the developing retina disrupted axon guidance independently of cellular growth. Inhibiting Tor complex 1 with rapamycin or eliminating the Tor complex 1 effector, S6 kinase (S6k), did not rescue axon guidance abnormalities of Tsc1 mosaics, while reductions in Tor function suppressed those phenotypes. These findings show that Tsc-mediated control of axon guidance and synapse assembly occurs via growth-independent signaling mechanisms, and suggest that Tor complex 2, a regulator of actin organization, is critical in these aspects of neuronal development

Italian guidelines for primary headaches: 2012 revised version

The first edition of the Italian diagnostic and therapeutic guidelines for primary headaches in adults was published in J Headache Pain 2(Suppl. 1):105–190 (2001). Ten years later, the guideline committee of the Italian Society for the Study of Headaches (SISC) decided it was time to update therapeutic guidelines. A literature search was carried out on Medline database, and all articles on primary headache treatments in English, German, French and Italian published from February 2001 to December 2011 were taken into account. Only randomized controlled trials (RCT) and meta-analyses were analysed for each drug. If RCT were lacking, open studies and case series were also examined. According to the previous edition, four levels of recommendation were defined on the basis of levels of evidence, scientific strength of evidence and clinical effectiveness. Recommendations for symptomatic and prophylactic treatment of migraine and cluster headache were therefore revised with respect to previous 2001 guidelines and a section was dedicated to non-pharmacological treatment. This article reports a summary of the revised version published in extenso in an Italian version

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Effects of fluoxetine on functional outcomes after acute stroke (FOCUS): a pragmatic, double-blind, randomised, controlled trial

Background Results of small trials indicate that fluoxetine might improve functional outcomes after stroke. The FOCUS trial aimed to provide a precise estimate of these effects. Methods FOCUS was a pragmatic, multicentre, parallel group, double-blind, randomised, placebo-controlled trial done at 103 hospitals in the UK. Patients were eligible if they were aged 18 years or older, had a clinical stroke diagnosis, were enrolled and randomly assigned between 2 days and 15 days after onset, and had focal neurological deficits. Patients were randomly allocated fluoxetine 20 mg or matching placebo orally once daily for 6 months via a web-based system by use of a minimisation algorithm. The primary outcome was functional status, measured with the modified Rankin Scale (mRS), at 6 months. Patients, carers, health-care staff, and the trial team were masked to treatment allocation. Functional status was assessed at 6 months and 12 months after randomisation. Patients were analysed according to their treatment allocation. This trial is registered with the ISRCTN registry, number ISRCTN83290762. Findings Between Sept 10, 2012, and March 31, 2017, 3127 patients were recruited. 1564 patients were allocated fluoxetine and 1563 allocated placebo. mRS data at 6 months were available for 1553 (99·3%) patients in each treatment group. The distribution across mRS categories at 6 months was similar in the fluoxetine and placebo groups (common odds ratio adjusted for minimisation variables 0·951 [95% CI 0·839–1·079]; p=0·439). Patients allocated fluoxetine were less likely than those allocated placebo to develop new depression by 6 months (210 [13·43%] patients vs 269 [17·21%]; difference 3·78% [95% CI 1·26–6·30]; p=0·0033), but they had more bone fractures (45 [2·88%] vs 23 [1·47%]; difference 1·41% [95% CI 0·38–2·43]; p=0·0070). There were no significant differences in any other event at 6 or 12 months. Interpretation Fluoxetine 20 mg given daily for 6 months after acute stroke does not seem to improve functional outcomes. Although the treatment reduced the occurrence of depression, it increased the frequency of bone fractures. These results do not support the routine use of fluoxetine either for the prevention of post-stroke depression or to promote recovery of function. Funding UK Stroke Association and NIHR Health Technology Assessment Programme