An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

Klebsiella pneumoniae is a Gram-negative bacterium of the family Enterobacteriaceae that possesses diverse metabolic capabilities: many strains are leading causes of hospital-acquired infections that are often refractory to multiple antibiotics, yet other strains are metabolically engineered and used for production of commercially valuable chemicals. To study its metabolism, we constructed a genome-scale metabolic model (iYL1228) for strain MGH 78578, experimentally determined its biomass composition, experimentally determined its ability to grow on a broad range of carbon, nitrogen, phosphorus and sulfur sources, and assessed the ability of the model to accurately simulate growth versus no growth on these substrates. The model contains 1,228 genes encoding 1,188 enzymes that catalyze 1,970 reactions and accurately simulates growth on 84% of the substrates tested. Furthermore, quantitative comparison of growth rates between the model and experimental data for nine of the substrates also showed good agreement. The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism.     

Rhizobia enhance acquisition of phosphorus from different sources by soybean plants

Aims

Some rhizobia can convert insoluble P into available forms for plant growth but the underlying mechanisms for this are not understood. In this study, the function of rhizobia in P acquisition from P sources for soybean was studied.

Methods

Four rhizobial strains were employed to evaluate their phosphate-solubilizing (PS) activity, their ability to mediate pH changes in growth medium for different P sources, and IAA production. A sand culture experiment using different P sources was carried out to characterize P acquisition changes of soybean plants with or without rhizobium inoculation. Rhizospheric acidification in soybean was further analyzed in hydroponics.

Results

Our results showed that all the tested rhizobial strains exhibited significant PS activity for different P sources in the order of Ca-P>Al-P>Phy-P??Fe-P as indicated by the halo/colony ratio technique and increased Pi percentage in the solid and liquid phases, respectively. Furthermore, all of the rhizobial strains could acidify the growth medium for all P sources except Phy-P, but only three of them produced IAA. Compared to non-nodulated plants, the nodulated plants had greater plant biomass and P content in sand culture for all the tested P sources, especially for Ca-P. Moreover, H⁺ and total acid exudation was more significantly enhanced in the nodulated plants in hydroponics.

Conclusions

Our results suggested that the PS ability of rhizobia is more related to acidification of the growth medium than IAA production. Rhizobium inoculation could enhance P acquisition in soybean, especially on soils where Ca-P is the primary P source, and the primary mechanism for rhizobial-mediated P solubilization appears to be via Pi remobilization of nodulated roots through rhizospheric acidification.     

Cloning, expression, and characterization of a new beta-agarase from Vibrio sp. strain CN41

A new agarase, AgaA(CN41), cloned from Vibrio sp. strain CN41, consists of 990 amino acids, with only 49% amino acid sequence identity with known β-agarases. AgaA(CN41) belongs to the GH50 (glycoside hydrolase 50) family but yields neoagarotetraose as the end product. AgaA(CN41) was expressed and characterized.     

<Emphasis Type="Italic">BRAF</Emphasis> V600E mutation and resistance to anti-EGFR monoclonal antibodies in patients with metastatic colorectal cancer: a meta-analysis

Epidemiologic studies have evaluated the association between BRAF mutations and resistance to the treatment of anti-EGFR monoclonal antibodies (MoAb) in patients with metastatic colorectal cancer (mCRC). However, the results are still inconclusive. To derive a more precise estimation of the relationship, we performed this meta-analysis. A total of 11 studies were included in the final meta-analysis. There were seven studies for unselected mCRC patients and four studies for patients with wild type KRAS mCRC. Among unselected mCRC patients, BRAF V600E mutation was detected in 48 of 546 primary tumors (8.8%). The objective response rate (ORR) of patients with mutant BRAF was 29.2% (14/48), whereas the ORR of patients with wild-type BRAF was 33.5% (158/472).The overall RR for ORR of mutant BRAF patients over wild-type BRAF patients was 0.86 (95% CI = 0.57–1.30; P = 0.48). For patients with KRAS wild-type mCRC, BRAF V600E mutation was detected in 40 of 376 primary tumors (10.6%). The ORR of patients with mutant BRAF was 0.0% (0/40), whereas the ORR of patients with wild-type BRAF was 36.3% (122/336). The pooled RR of mutant BRAF patients over wild-type BRAF patients was 0.14 (95% CI = 0.04–0.53; P = 0.004). In conclusion, this meta-analysis provides evidence that BRAF V600E mutation is associated with lack of response in wild-type KRAS mCRC treated with anti-EGFR MoAbs. BRAF mutation may be used as an additional biomarker for the selection of mCRC patients who might benefit from anti-EGFR MoAbs therapy.     

The presence of co-flowering species facilitates reproductive success of Pedicularis monbeigiana (Orobanchaceae) through variation in bumble-bee foraging behaviour

Background and Aims The presence of co-flowering species can alter pollinator foraging behaviour and, in turn, positively or negatively affect the reproductive success of the focal species. Such interactions were investigated between a focal species, Pedicularis monbeigiana, and a co-flowering species, Vicia dichroantha, which was mediated by behaviour alteration of the shared bumble-bee pollinator. Methods Floral display size and floral colour change of P. monbeigiana were compared between pure (P. monbeigiana only) and mixed (P. monbeigiana and V. dichroantha) plots in two populations. Pollinator visitation rates, interspecific floral switching and successive within-plant pollinator visits were recorded. In addition, supplemental pollination at plant level was performed, and the fruit set and seed set were analysed in pure and mixed plots with different densities of P. monbeigiana. Key Results Pollinator visitation rates were dramatically higher in mixed plots than in pure plots. The higher pollinator visitation rates were recorded in both low- and high-density plots. In particular, successive flower visits within an individual plant were significantly lower in mixed plots. Supplemental pollination significantly increased fruit set and seed set of individuals in pure plots, while it only marginally increased seed set per fruit of plants in mixed plots. Conclusions The presence of V. dichroantha can facilitate pollination and increase female reproductive success of P. monbeigiana via both quantity (mitigating pollinator limitation) and quality (reducing geitonogamy) effects. This study suggests that successive pollinator movements among flowers within a plant, as well as pollinator visitation rates and interspecific flower switching, may be important determinants of the direction and mechanisms of interaction between species.     

Protective effects of adenosine in rabbit sinoatrial node ischemia–reperfusion model in vivo: control of arrhythmia by hyperpolarization-activated cyclic nucleotide-gated (HCN)4 channels

Disturbance of cardiac rhythm is one of the consequences of myocardial ischemia/reperfusion injury. Many researchers have prompted considerable interests in developing therapeutic approaches for its control. In present study, we want to determine whether that adenosine pre- and postconditioning have protective effects on sinoatrial node ischemia/reperfusion injury on morphology, arrhythmia score, serological markers (CK-MB and cTnT), SOD activities, MDA levels and expression of HCN4 channels in SA node cells. According to the arrhythmia score recorded, whether adenosine used in terms of ischemia or reperfusion, the total number of arrhythmia was significantly reduced, as well as the number of its episodes was also markedly decreased. We have also shown a clear correlation between HCN4 channels expression and the dysfunction of SA node cells. HCN4 immunoreactivity decreased after adenosine pre- and postconditioning, but changes were significantly smaller in the cells of the SA node compared with cells of I/R group. The content of cTnT, CK-MB and MDA in adenosine pre- and postconditioning group reduced significantly; but the level of SOD increased significantly. Histological examination and electron microscopy observations found in adenosine pre- and postconditioning group sinoatrial node injury also mitigated. These findings suggested that adenosine pre- or postconditioning were to reduce the incidence of ischemia/reperfusion arrhythmias, reduce myocardial ischemia reperfusion injury. The mechanism was to stabilize the SA node cells membrane and one possible mechanism involves modulation of HCN4 channels in pacemaker cells of the sinoatrial node.     

Micropropagation of bromeliad <Emphasis Type="Italic">Aechmea fasciata</Emphasis> via floral organ segments and effects of acclimatization on plantlet growth

Although suckers and seedlings can be used for the propagation of bromeliads, the low number of propagules and cross-variation limit their uniformity and mass cultivation. In this study, high-efficiency shoot organogenesis and plant regeneration were achieved on callus derived from petal and ovary explants of Aechmea fasciata (Bromeliaceae). Calluses were induced on half-strength Murashige and Skoog inorganic salts (1/2MS) supplemented with 1.0–1.5 mg l⁻¹ 2,4-dichlorophenoxyacetic acid in combination with 1.0 or 0.5 mg l⁻¹ α-naphthaleneacetic acid (NAA), and shoots regenerated after transfer to 1/2MS basal medium containing the combination of 1.0 mg l⁻¹ NAA + 0.5 mg l⁻¹ 1-phenyl-3-(1,2,3-thiadiazol-5-yl) urea. Those plantlets grown under a middle light intensity (50 μmol m⁻² s⁻¹) showed a dramatic increase in survival percentage (up to 95%) and the maximum number of newly developing roots. The plantlets that were transplanted onto pots were successfully grown in the greenhouse.     

Structure,composition and mechanical properties of the silk fibres of the egg case of the Joro spider, <Emphasis Type="Italic">Nephila clavata</Emphasis> (Araneae,Nephilidae)

The silk egg case and orb web of spiders are elaborate structures that are assembled from a number of components. We analysed the structure, the amino acid and fibre compositions, and the tensile properties of the silk fibres of the egg case of Nephila clavata. SEM shows that the outer and inner covers of the egg case consist of thick, medium and thin silk fibres. The silk fibres of the outer cover of the egg case are probably produced by the major and minor ampullate glands. The silk fibres of the inner cover of the egg case from cylindrical glands appears to be distinct from the silk fibres of the major ampullate glands based on their micro-morphology, mole percent amino acid composition and types, and tensile behaviour and properties. Collectively, our investigations show that N. clavata uses silk fibres from relatively few glands in varying combinations to achieve different physical and chemical properties (e.g., color, diameter, morphology and amino acid composition) and functional and mechanical properties in the different layers of the egg case.