Curling during desiccation protects the foliose lichen Lobaria pulmonaria against photoinhibition

This study aims to assess the photoprotective potential of desiccation-induced curling in the light-susceptible old forest lichen Lobaria pulmonaria by using chlorophyll fluorescence imaging. Naturally curled thalli showed less photoinhibition-induced limitations in primary processes of photosynthesis than artificially flattened specimens during exposures to 450 μmol m⁻² s⁻¹ in the laboratory after both 12- (medium dose treatment) and 62-h duration (high dose treatment). Thallus areas shaded by curled lobes during light exposure showed unchanged values of measured chlorophyll fluorescence parameters (F _V/F _M, Φ_{PS II}), whereas non-shaded parts of curled thalli, as well as the mean for the entire flattened thalli, showed photoinhibitory limitation after light treatments. Furthermore, the chlorophyll fluorescence imaging showed that the typical small-scale reticulated ridges on the upper side of L. pulmonaria caused a spatial, small-scale reduction in damage due to minor shading. Severe dry-state photoinhibition readily occurred in flattened and light-treated L. pulmonaria, although the mechanisms for such damage in a desiccated and inactive stage are not well known. Natural curling is one strategy to reduce the chance for serious photoinhibition in desiccated L. pulmonaria thalli during high light exposures.     

A human cell surface receptor activated by free fatty acids and thiazolidinedione drugs

Fatty acids, which are essential nutritional components, are also involved in cardiovascular and metabolic diseases. Here we report a human cell surface receptor that we name free fatty acid receptor (FFAR), because it is specifically activated by medium to long-chain free fatty acids. The receptor belongs to the class of seven-transmembrane, G-protein coupled receptors (GPCRs) and also mediates responses to antidiabetic drugs of the thiazolidinedione type. It is expressed in skeletal muscle, heart, liver, and pancreatic beta-cells. Stimulation of FFAR increases the intracellular calcium concentration in cells expressing the receptor in a native (pancreatic beta-cell line) or in a recombinant form. In view of the nature of the activating substances, their physiological role in the body, and the tissue distribution of FFAR we suggest the term "nutrient sensing receptor" for receptors acting at the interface between dietary components and signalling molecules.     

Seasonal N uptake and N2fixation by common and adzuki bean at various spacings

The adzuki bean (Vigna angularis (Wild.) Ohwi and Ohashi) and common bean (Phaseolus vulgaris L.) have a high physiological demand for N. A 2-year field study was conducted to investigate the seasonal change of available soil N and symbiotic N₂ fixation usage. The beans were seeded at two densities, 22.2 plants m^–2 with a row spacing of 0.3 m and 11.1 plants m^–2 with a row spacing of 0.6 m. The amount of fixed N₂ in the shoot was calculated using the ¹⁵N natural abundance method. The common bean demonstrated low N₂ fixation and the ability to accumulate high levels of soil N. Soil nitrate under the common bean was continually absorbed. The adzuki bean, on the other hand, had a remarkable peak of N accumulation in the early reproductive stage. This was mainly due to N₂ fixation, though the soil nitrate level was high. Narrowing the plant row spacing increased the dry matter yield of both species, but the origin of the increased N differed between the species. For the first 77 DAP in 1999 (73 DAP in 2000) the N increase for both beans was due to both soil and atmospheric N₂. At harvest, though, the increase of N in common bean was mainly due to soil N, while that in adzuki bean was mainly due to atmospheric N₂. It can be concluded that the low symbiotic N₂ fixation ability of common bean was due to its high soil N uptake ability and constant N accumulation, which enabled an efficient soil N absorption. Adzuki bean absorbed N mainly for a short period and depended more on symbiotically fixed N₂ and, in contrast to common bean, left a high level of NO₃-N remaining in the soil after cropping.     

Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics

Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In this paper we propose for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an integer linear program (ILP). In addition we describe a branch-and-cut algorithm to effectively solve the ILP to optimality. We evaluate the performances of our approach in terms of running time and quality of the alignments using the BAliBase database of reference alignments. The results show that our implementation ranks amongst the best programs developed so far.     

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background

The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B.

Methodology/Principal Findings

As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212–216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers.

Conclusions/Significance

Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B'' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation.     

Long-term survival from adenocarcinoma of the esophagus after transthoracic and transhiatal esophagectomy

ABSTRACT: BACKGROUND: The effects of transthoracic or transhiatal esophagectomy on the long-term survival of patients who had adenocarcinoma of the esophagus were compared, as were factors applicable in preoperative stratification of patient treatment. METHODS: A cohort of 147 consecutive patients with adenocarcinoma of the esophagus was evaluated for esophagectomy between 1984 and 2000. The patients were followed prospectively and observed survival rates of patients with a transthoracic or transhiatal approach to esophagectomy were compared by standardized mortality ratio (SMR) and relative mortality ratio (RMR) using the expected survival of a matched Norwegian population. RESULTS: A R0 resection was performed by transthoracic (n = 33) or a transhiatal (n = 55) esophagectomy in 88 (60%) patients with a median age of 61 (range: 35-77) and 70 (42-88) years, respectively (P <0.001). Tumor stages and other possible risk factors were similar in the two groups. Transthoracic or transhiatal esophagectomy resulted in a median survival time of 20.5 (95% confidence interval (CI): 10.4-57.6) and 16.4 (10.6-28.7) months, respectively. The respective survival rates were 31.2% and 27.8% by 5 years, and 21.3% and 16.6% by 10 years with an overall RMR of 1.14 (P = 0.63). Median survival time in the absence or presence of lymph node metastases was 74.0 (95% CI: 17.5-166.4) and 10.7 (7.9- 14.9) months. The corresponding survival rates by 10 years with non-involved or involved nodes were 48.9% and 3.8% respectively (RMR 2.22, P = 0.007). Patients with a pT1-tumor were few and the survival rate was not very different from that of the general population (SMR = 1.7, 95% CI: 0.7-4.1). The median survival time of patients with a pT2-tumor was 30.4 (95% CI: 9.0-142) months and with a pT3-tumor 14 (9.2-16.4) months. The survival rates by 10 years among patients with a pT1 tumor were 57.0% (95% CI: 14.9-78.9), pT2 33.3% (11.8-52.2), and pT3 7.1% (1.9-15.5). The relative mortality for T3 stages compared to T1 stages was statistically significant (RMR = 3.22, P = 0.024). CONCLUSION: Transthoracic and transhiatal esophagectomy are both effective approaches for treatment of adenocarcinoma of the esophagus and survival of more than 10 years can be expected without adjuvant chemotherapy. However, increasing depth of tumor invasion and lymph node metastases reduce life expectancy.     

The Association of Alcohol and Alcohol Metabolizing Gene Variants with Diabetes and Coronary Heart Disease Risk Factors in a White Population

Background

Epidemiological studies have shown a J- or U-shaped relation between alcohol and type 2 diabetes and coronary heart disease (CHD). The underlying mechanisms are not clear. The aim was to examine the association between alcohol intake and diabetes and intermediate CHD risk factors in relation to selected ADH and ALDH gene variants.

Methodology/Principal Findings

Cross-sectional study including 6,405 Northern European men and women aged 30–60 years from the general population of Copenhagen, Denmark. Data were collected with self-administered questionnaires, a physical examination, a 2 hour oral glucose tolerance test, and various blood tests. J shaped associations were observed between alcohol and diabetes, metabolic syndrome (MS), systolic and diastolic blood pressure, triglyceride, total cholesterol, and total homocysteine. Positive associations were observed with insulin sensitivity and HDL cholesterol, and a negative association with insulin release. Only a few of the selected ADH and ALDH gene variants was observed to have an effect. The ADH1c (rs1693482) fast metabolizing CC genotype was associated with an increased risk of impaired glucose tolerance (IGT)/diabetes compared to the CT and TT genotypes. Significant interactions were observed between alcohol and ADH1b (rs1229984) with respect to LDL and between alcohol and ALDH2 (rs886205) with respect to IGT/diabetes.

Conclusions/Significance

The selected ADH and ALDH gene variants had only minor effects, and did not seem to markedly modify the health effects of alcohol drinking. The observed statistical significant associations would not be significant, if corrected for multiple testing.     

Removal of acidic residues of the prodomain of PCSK9 increases its activity towards the LDL receptor

Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the low density lipoprotein receptor (LDLR) at the cell surface and mediates intracellular degradation of the LDLR. The amino-terminus of mature PCSK9, residues 31–53 of the prodomain, has an inhibitory effect on this function of PCSK9, but the underlying mechanism is not fully understood. In this study, we have identified two highly conserved negatively charged segments (residues 32–40 and 48–50, respectively) within this part of the prodomain and performed deletions and substitutions to study their importance for degradation of the LDLRs.Deletion of the acidic residues of the longest negatively charged segment increased PCSK9’s ability to degrade the LDLR by 31%, whereas a modest 8% increase was observed when these residues were mutated to uncharged amino acids. Thus, both the length and the charge of this part of the prodomain were important for its inhibitory effect. Deletion of the residues of the shorter second negatively charged segment only increased PCSK9’s activity by 8%. Substitution of the amino acids of both charged segments to uncharged residues increased PCSK9’s activity by 36%. These findings indicate that the inhibitory effect of residues 31–53 of the prodomain is due to the negative charge of this segment. The underlying mechanism could involve the binding of this peptide segment to positively charged structures which are important for PCSK9’s activity. One possible candidate could be the histidine-rich C-terminal domain of PCSK9.