QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross

Advanced backcross QTL analysis was used to identify quantitative trait loci (QTL) for agronomic performance in a population of BC₂F_3:5 introgression lines created from the cross of a Colombian large red-seeded commercial cultivar, ICA Cerinza, and a wild common bean accession, G24404. A total of 157 lines were evaluated for phenological traits, plant architecture, seed weight, yield and yield components in replicated trials in three environments in Colombia and genotyped with microsatellite, SCAR, and phaseolin markers that were used to create a genetic map that covered all 11 linkage groups of the common bean genome with markers spaced at an average distance of every 10.4 cM. Segregation distortion was most significant in regions orthologous for a seed coat color locus (R-C) on linkage group b08 and two domestication syndrome genes, one on linkage group b01 at the determinacy (fin) locus and the other on linkage group b02 at the seed-shattering (st) locus. Composite interval mapping analysis identified a total of 41 significant QTL for the eight traits measured of which five for seed weight, two for days to flowering, and one for yield were consistent across two or more environments. QTL were located on every linkage group with b06 showing the greatest number of independent loci. A total of 13 QTL for plant height, yield and yield components along with a single QTL for seed size showed positive alleles from the wild parent while the remaining QTL showed positive alleles from the cultivated parent. Some QTL co-localized with regions that had previously been described to be important for these traits. Compensation was observed between greater pod and seed production and smaller seed size and may have resulted from QTL for these traits being linked or pleiotropic. Although wild beans have been used before to transfer biotic stress resistance traits, this study is the first to attempt to simultaneously obtain a higher yield potential from wild beans and to analyze this trait with single-copy markers. The wild accession was notable for being from a unique center of diversity and for contributing positive alleles for yield and other traits to the introgression lines showing the potential that advanced backcrossing has in common bean improvement.     

Bacteriophages immunomodulate the response of monocytes

Bacteriophages are present in fluids from cirrhosis patients. However, their effect on the immune response is unknown. In this work, we explore the role of phages in the phenotype, function, and cytokine production of monocytes. We stimulated healthy monocytes with five different butanol-purified phage suspensions infective for Gram-negative and Gram-positive bacteria. We studied the expression of the monocyte markers involved in lipopolysaccharide recognition (LPS; CD14), antigen presentation (HLA-DR) and co-stimulation (CD86), and the concentration of induced cytokines (TNF-α, IFN-α, and IL-10) by phages. To confirm the direct role of phages without the interference of contaminating soluble LPS in phage suspensions, polymyxin B was added to the cell cultures. Phagocytosis experiments were assessed by flow cytometry using labeled phage suspensions. We observed that butanol-purified phages reduced the surface levels of CD14 and CD86 in monocytes and increased the secreted levels of TNF-α and IL-10 compared with the control sample containing only butanol buffer. All phage suspensions showed downregulation of HLA-DR expression but only Staphylococcus aureus phage contaminated with Escherichia coli reached statistical significance. The addition of polymyxin B did not restore the monocytic response induced by phages, suggesting that the effect was not caused by the presence of LPS. Monocytes were able to phagocyte phages in a dose- and time-dependent manner. To conclude, the phagocytosis of butanol-purified phages altered the phenotype and cytokine production of monocytes suggesting they become tolerogenic.     

Translational selection on codon usage in the genus Aspergillus

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression.     

Elevated CO<Subscript>2</Subscript> reduces stomatal and metabolic limitations on photosynthesis caused by salinity in <Emphasis Type="Italic">Hordeum vulgare</Emphasis>

The future environment may be altered by high concentrations of salt in the soil and elevated [CO₂] in the atmosphere. These have opposite effects on photosynthesis. Generally, salt stress inhibits photosynthesis by stomatal and non-stomatal mechanisms; in contrast, elevated [CO₂] stimulates photosynthesis by increasing CO₂ availability in the Rubisco carboxylating site and by reducing photorespiration. However, few studies have focused on the interactive effects of these factors on photosynthesis. To elucidate this knowledge gap, we grew the barley plant, Hordeum vulgare (cv. Iranis), with and without salt stress at either ambient or elevated atmospheric [CO₂] (350 or 700 μmol mol⁻¹ CO₂, respectively). We measured growth, several photosynthetic and fluorescence parameters, and carbohydrate content. Under saline conditions, the photosynthetic rate decreased, mostly because of stomatal limitations. Increasing salinity progressively increased metabolic (photochemical and biochemical) limitation; this included an increase in non-photochemical quenching and a reduction in the PSII quantum yield. When salinity was combined with elevated CO₂, the rate of CO₂ diffusion to the carboxylating site increased, despite lower stomatal and internal conductance. The greater CO₂ availability increased the electron sink capacity, which alleviated the salt-induced metabolic limitations on the photosynthetic rate. Consequently, elevated CO₂ partially mitigated the saline effects on photosynthesis by maintaining favorable biochemistry and photochemistry in barley leaves.     

Shiga toxin-producing Escherichia coli O104:H4: a new challenge for microbiology

In 2011, Germany experienced the largest outbreak with a Shiga toxin-producing Escherichia coli (STEC) strain ever recorded. A series of environmental and trace-back and trace-forward investigations linked sprout consumption with the disease, but fecal-oral transmission was also documented. The genome sequences of the pathogen revealed a clonal outbreak with enteroaggregative E. coli (EAEC). Some EAEC virulence factors are carried on the virulence plasmid pAA. From an unknown source, the epidemic strains acquired a lambdoid prophage carrying the gene for the Shiga toxin. The resulting strains therefore possess two different mobile elements, a phage and a plasmid, contributing essential virulence genes. Shiga toxin is released by decaying bacteria in the gut, migrates through the intestinal barrier, and is transported via the blood to target organs, like the kidney. In a mouse model, probiotic bifidobacteria interfered with transport of the toxin through the gut mucosa. Researchers explored bacteriophages, bacteriocins, and low-molecular-weight inhibitors against STEC. Randomized controlled clinical trials of enterohemorrhagic E. coli (EHEC)-associated hemolytic uremic syndrome (HUS) patients found none of the interventions superior to supportive therapy alone. Antibodies against one subtype of Shiga toxin protected pigs against fatal neurological infection, while treatment with a toxin receptor decoy showed no effect in a clinical trial. Likewise, a monoclonal antibody directed against a complement protein led to mixed results. Plasma exchange and IgG immunoadsoprtion ameliorated the condition in small uncontrolled trials. The epidemic O104:H4 strains were resistant to all penicillins and cephalosporins but susceptible to carbapenems, which were recommended for treatment.     

Differentiating ischemic from hemorrhagic stroke using plasma biomarkers: the S100B/RAGE pathway

Although neuroimaging is useful in differentiating ischemic (IS) from hemorrhagic (ICH) stroke in the Emergency Department, a wide-available rapid biochemical test would add advantages in the pre-hospital triage and management of stroke patients. Our aim was to examine the predictive value of a panel of blood-borne biomarkers to differentiate IS from ICH. Admission blood samples obtained within 24h from stroke symptoms onset were tested by ELISA for CRP, D-dimer, sRAGE, MMP9, S100B, BNP, NT-3, caspase-3, chimerin-II, secretagogin, cerebellin and NPY. The complete protocol was achieved in 915 patients (776 IS, 139 ICH). Among blood samples obtained <6 h from symptoms onset (n=337), S100B levels were increased in ICH (107.58 vs 58.70 pg/mL; p<0.001) whereas sRAGE levels were decreased (0.77 vs 1.02 ng/mL; p=0.009) as compared to IS. In this subset of patients S100B (OR 3.97 95% CI 1.82-8.68; p=0.001) and sRAGE (OR 0.22 95% CI 0.10-0.52; p<0.001) were independently associated with ICH. A regression tree was created by CART method showing good classification ability (AUC=0.762). Similar results were found for samples obtained within 3 h. In conclusion, a combination of biomarkers including those of the S100B/RAGE pathway seems promising to achieve a rapid biochemical diagnosis of IS versus ICH in the first hours from symptoms onset. This article is part of a Special Issue entitled: Translational Proteomics.     

Breast feeding, parity and breast cancer subtypes in a Spanish cohort

Background

Differences in the incidence and outcome of breast cancer among Hispanic women compared with white women are well documented and are likely explained by ethnic differences in genetic composition, lifestyle, or environmental exposures.

Methodolgy/Principal Findings

A population-based study was conducted in Galicia, Spain. A total of 510 women diagnosed with operable invasive breast cancer between 1997 and 2010 participated in the study. Data on demographics, breast cancer risk factors, and clinico-pathological characteristics were collected. The different breast cancer tumor subtypes were compared on their clinico-pathological characteristics and risk factor profiles, particularly reproductive variables and breastfeeding. Among the 501 breast cancer patients (with known ER and PR receptors), 85% were ER+/PR+ and 15% were ER-&PR-. Among the 405 breast cancer with known ER, PR and HER2 status, 71% were ER+/PR+/HER2- (luminal A), 14% were ER+/PR+/HER2+ (luminal B), 10% were ER−/PR−/HER2- (triple negative breast cancer, TNBC), and 5% were ER−/PR−/HER2+ (non-luminal). A lifetime breastfeeding period equal to or longer than 7 months was less frequent in case patients with TNBC (OR = 0.25, 95% CI = 0.08–0.68) compared to luminal A breast cancers. Both a low (2 or fewer pregnancies) and a high (3–4 pregnancies) number of pregnancies combined with a long breastfeeding period were associated with reduced odds of TNBC compared with luminal A breast cancer, although the association seemed to be slightly more pronounced among women with a low number of pregnancies (OR = 0.09, 95% CI = 0.005–0.54).

Conclusions/Significance

In case-case analyses with the luminal A cases as the reference group, we observed a lower proportion of TNBC among women who breastfed 7 or more months. The combination of longer breastfeeding duration and lower parity seemed to further reduce the odds of having a TNBC compared to a luminal A breast cancer.     

Reproductive traits of the small Patagonian octopus Octopus tehuelchus

This study evaluated the reproductive features of Octopus tehuelchus in three coastal environments of San Matías Gulf (Patagonia). Monthly samples of O. tehuelchus were used to estimate size at maturity, compare seasonal changes in oocyte size frequency distributions between sites as well as oocyte number and size between female maturity stage and sites. Females in Islote Lobos had a smaller size at maturity than females in San Antonio Bay and El Fuerte, probably as a consequence of a generally smaller body size. Males in San Antonio Bay were smaller at maturity than females. O. tehuelchus is a simultaneous terminal spawner. Fecundity (expressed as number of vitellogenic oocytes in ovary) was lower in Islote Lobos, and an increase in oocyte number in relation to female total weight was found. Females in San Antonio Bay had the largest oocytes, which may indicate higher energy reserves for the embryo and therefore higher juvenile survival. There was a close relationship between reproduction, growth and condition, represented as size at maturity, number and size of vitellogenic oocytes and period of maturity and spawning. Given the local variation in some reproductive features of O. tehuelchus, studies should focus on the environmental factors, which bring about this variation, and on how it affects the dynamics of local populations.