Lipoprotein lipase activity in neonatal-rat liver cell types.

The lipoprotein lipase activity in the liver of neonatal (1 day old) rats was about 3 times that in the liver of adult rats. Perfusion of the neonatal liver with collagenase decreased the tissue-associated activity by 77%. When neonatal-rat liver cells were dispersed, hepatocyte-enriched (fraction I) and haemopoietic-cell-enriched (fraction II) populations were obtained. The lipoprotein lipase activity in fraction I was 7 times that in fraction II. On the basis of those activities and the proportion of both cell types in either fraction, it was estimated that hepatocytes contained most, if not all, the lipoprotein lipase activity detected in collagenase-perfused neonatal-rat livers. From those calculations it was also concluded that haemopoietic cells did not contain lipoprotein lipase activity. When the hepatocyte-enriched cell population was incubated at 25 degrees C for up to 3 h, a slow but progressive release of enzyme activity to the incubation medium was found. However, the total activity (cells + medium) did not significantly change through the incubation period. Cycloheximide produced a time-dependent decrease in the cell-associated activity. Heparin increased the amount of lipoprotein lipase activity released to the medium. Because the cell-associated activity was unchanged, heparin also produced a time-dependent increase in the total activity. In those cells incubated with heparin, cycloheximide did not affect the initial release of lipoprotein lipase activity to the medium, but blocked further release. The cell-associated activity was also decreased by the presence of cycloheximide in those cells. It is concluded that neonatal-rat hepatocytes synthesize active lipoprotein lipase.     

Hepatic lipoate uptake

Uptake of [35S]lipoate was studied in perfused rat liver and in isolated rat hepatocytes. During single-pass perfusion of [35S]lipoate about 30% of the radioactivity is retained in the liver. A substantial amount of 5,5'-dithiobis(2-nitrobenzoic acid)-reactive material appears in the effluent perfusate, while hepatic efflux of GSH is unchanged. The hepatic uptake of lipoate, the release of thiols, and also the biliary excretion of 35S-labeled compounds are suppressed by octanoate. In isolated hepatocytes the uptake of lipoate follows saturation kinetics showing a Km value of 38 microM and a Vmax of 180 pmol/mg X 10 s. The uptake is temperature-dependent; from the Arrhenius plot an activation energy of 14.8 kcal/mol at 20 microM lipoate is calculated. At high concentrations of lipoate (above 75 microM) a nonsaturable uptake component becomes predominant. Lipoate uptake is selectively inhibited by medium-chain fatty acids. Only slight inhibition is seen in the presence of long-chain fatty acids, and there is no inhibition with acetate or lactate. Substantial inhibition is also observed with acetylsalicylic acid, but not with taurocholate, bromosulfophthalein or biotin. Lipoate uptake can be inhibited by high concentrations of phloretin (200 microM) and is rather insensitive to 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (200 microM). The results indicate that hepatic uptake of lipoate at physiological concentrations is largely carrier-mediated.     

A cross-scale framework to support a mechanistic understanding and modelling of marine climate-driven species redistribution,from individuals to communities

Climate-driven species redistribution is pervasive and accelerating, yet the complex mechanisms at play remain poorly understood. The implications of large-scale species redistribution for natural systems and human societies have resulted in a large number of studies exploring the effects on individual species and ecological communities worldwide. Whilst many studies have investigated discrete components of species redistribution, the integration required for a more complete mechanistic understanding is lacking. In this paper, we provide a framework for synthesising approaches to more robustly understand and predict marine species redistributions. We conceptualise the stages and processes involved in climate-driven species redistribution at increasing levels of biological organisation, and synthesize the laboratory, field and modelling approaches used to study redistribution related processes at individual, population and community levels. We then summarise links between scales of biological organisation and methodological approaches in a hierarchical framework that represents an integrated mechanistic assessment of climate-driven species redistributions. In a rapidly expanding field of research, this framework provides direction for: 1) guiding future research, 2) highlighting key knowledge gaps, 3) fostering data exchange and collaboration between disciplines and 4) improving shared capacity to predict and therefore, inform the proactive management of climate impacts on natural systems.     

In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae

Background

The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynamics. The principle of these new molecular tools is based on the comparison of melting profiles, after denaturation of a DNA double strand. Until now, the secondary structure of single-stranded nucleic acids has not been exploited to develop identification systems based on PCR. To test the potential of single-strand RNA denaturation as a new alternative to detect specific nucleic acid variations, sequences from viruses of the Totiviridae family were compared using a new in silico melting curve approach. This family comprises double-stranded RNA virus, with a genome constituted by two ORFs, ORF1 and ORF2, which encodes the capsid/RNA binding proteins and an RNA-dependent RNA polymerase (RdRp), respectively.

Results

A phylogenetic tree based on RdRp amino acid sequences was constructed, and eight monophyletic groups were defined. Alignments of RdRp RNA sequences from each group were screened to identify RNA regions with conserved secondary structure. One region in the second half of ORF2 was identified and individually modeled using the RNAfold tool. Afterwards, each DNA or RNA sequence was denatured in silico using the softwares MELTSIM and RNAheat that generate melting curves considering the denaturation of a double stranded DNA and single stranded RNA, respectively. The same groups identified in the RdRp phylogenetic tree were retrieved by a clustering analysis of the melting curves data obtained from RNAheat. Moreover, the same approach was used to successfully discriminate different variants of Trichomonas vaginalis virus, which was not possible by the visual comparison of the double stranded melting curves generated by MELTSIM.

Conclusion

In silico analysis indicate that ssRNA melting curves are more informative than dsDNA melting curves. Furthermore, conserved RNA structures may be determined from analysis of individuals that are phylogenetically related, and these regions may be used to support the reconstitution of their phylogenetic groups. These findings are a robust basis for the development of in vitro systems to ssRNA melting curves detection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-243) contains supplementary material, which is available to authorized users.     

Regulation of IFN response gene activity during infliximab treatment in rheumatoid arthritis is associated with clinical response to treatment

Introduction  

Cross-regulation between TNF and type I IFN has been postulated to play an important role in autoimmune diseases. Therefore, we determined the effect of TNF blockade in rheumatoid arthritis (RA) on the type I IFN response gene activity in relation to clinical response.     

Disease-modifying antirheumatic drugs are associated with a reduced risk for cardiovascular disease in patients with rheumatoid arthritis: a case control study

Rheumatoid arthritis (RA) is characterized by inflammation and an increased risk for cardiovascular disease (CVD). This study investigates possible associations between CVD and the use of conventional disease-modifying antirheumatic drugs (DMARDs) in RA. Using a case control design, 613 RA patients (5,649 patient-years) were studied, 72 with CVD and 541 without CVD. Data on RA, CVD and drug treatment were evaluated from time of RA diagnosis up to the first cardiovascular event or the end of the follow-up period. The dataset was categorized according to DMARD use: sulfasalazine (SSZ), hydroxychloroquine (HCQ) or methotrexate (MTX). Odds ratios (ORs) for CVD, corrected for age, gender, smoking and RA duration, were calculated per DMARD group. Patients who never used SSZ, HCQ or MTX were used as a reference group. MTX treatment was associated with a significant CVD risk reduction, with ORs (95% CI): 'MTX only', 0.16 (0.04 to 0.66); 'MTX and SSZ ever', 0.20 (0.08 to 0.51); and 'MTX, SSZ and HCQ ever', 0.20 (0.08 to 0.54). The risk reductions remained significant after additional correction for the presence of rheumatoid factor and erosions. After correction for hypertension, diabetes and hypercholesterolemia, 'MTX or SSZ ever' and 'MTX, SSZ and HCQ ever' showed significant CVD risk reduction. Rheumatoid factor positivity and erosions both increased CVD risk, with ORs of 2.04 (1.02 to 4.07) and 2.36 (0.92 to 6.08), respectively. MTX and, to a lesser extent, SSZ were associated with significantly lower CVD risk compared to RA patients who never used SSZ, HCQ or MTX. We hypothesize that DMARD use, in particular MTX use, results in powerful suppression of inflammation, thereby reducing the development of atherosclerosis and subsequently clinically overt CVD.     

Phylogeography of the Calonectris shearwaters using molecular and morphometric data

We investigated phylogenetic relationships and the biogeographic history of the Calonectris species complex, using both molecular and biometric data from one population of the Cape Verde shearwater Calonectris edwardsii (Cape Verde Islands), one from the streaked shearwater C. leucomelas (western Pacific Ocean) and 26 from Cory's shearwater populations distributed across the Atlantic (C. d. borealis) and the Mediterranean (C. d. diomedea). The streaked shearwater appeared as the most basal and distant clades, whereas the genetic divergences among the three main clades within the Palearctic were similar. Clock calibrations match the first speciation event within Calonectris to the Panama Isthmus formation, suggesting a vicariant scenario for the divergence of the Pacific and the Palearctic clades. The separation between the Atlantic and Mediterranean clades would have occurred in allopatry by range contraction followed by local adaptation during the major biogeographic events of the Pleistocene. The endemic form from Cape Verde probably evolved as a result of ecological divergence from the Mediterranean subspecies. Finally, one Mediterranean population (Almeria) was unexpectedly grouped into the Atlantic subspecies clade, both by genetic and by morphometric analyses, pointing out the Almeria-Oran oceanographic front (AOOF) as the actual divide between the two Cory's shearwater subspecies. Our results highlight the importance of oceanographic boundaries as potentially effective barriers shaping population and species phylogeographical structure in pelagic seabirds.     

Recovery of soil phosphorus on former bauxite mines through tropical forest restoration

Soil phosphorus (P) is a major driver of forest development and a critically limited nutrient in tropical soils, especially when topsoil is removed by mining. This nutrient can be present in soils in the form of different fractions, which have direct consequences for P availability to plants and, consequently, for restoration success. Therefore, understanding how the stocks of different soil P fractions change over the restoration process can be essential for guiding restoration interventions, monitoring, and adaptive management. Here, we investigated the recovery of soil P fractions by forest restoration interventions on bauxite mine sites in the Brazilian Atlantic Forest. We assessed the concentration of different fractions of soil organic and inorganic P at (1) a bauxite mine prepared for restoration; (2) two former bauxite mines undergoing forest restoration for 6 and 24 years; and (3) an old‐growth forest remnant. Overall, restored areas recovered levels of labile organic P (P_o‐NaHCO₃) at 5–40 cm and of moderately labile organic P (P_o‐NaOH) at different depths, exhibiting concentrations similar to those found in a conserved forest. The use of P‐rich fertilizers and forest topsoil may have greatly contributed to this outcome. Some other fractions, however, recovered only after 24 years of restoration. Other inorganic P fractions did not differ among mined, restored, and conserved sites: nonlabile P_i (residual P and P‐HCl), labile P_i (P_i‐NaHCO₃), and moderately labile P_i (P_i‐NaOH). Forest restoration was able to promote efficient recovery of important soil P fractions, highlighting the value of restoration efforts to mitigate soil degradation by mining.     

Loss of the K+ channel Kv2.1 greatly reduces outward dark current and causes ionic dysregulation and degeneration in rod photoreceptors

Vertebrate retinal photoreceptors signal light by suppressing a circulating “dark current” that maintains their relative depolarization in the dark. This dark current is composed of an inward current through CNG channels and NCKX transporters in the outer segment that is balanced by outward current exiting principally from the inner segment. It has been hypothesized that K_v2.1 channels carry a predominant fraction of the outward current in rods. We examined this hypothesis by comparing whole cell, suction electrode, and electroretinographic recordings from K_v2.1 knockout (K_v2.1^−/−) and wild-type (WT) mouse rods. Single cell recordings revealed flash responses with unusual kinetics, and reduced dark currents that were quantitatively consistent with the measured depolarization of the membrane resting potential in the dark. A two-compartment (outer and inner segment) physiological model based on known ionic mechanisms revealed that the abnormal K_v2.1^−/− rod photoresponses arise principally from the voltage dependencies of the known conductances and the NCKX exchanger, and a highly elevated fraction of inward current carried by Ca²⁺ through CNG channels due to the aberrant depolarization. K_v2.1^−/− rods had shorter outer segments than WT and dysmorphic mitochondria in their inner segments. Optical coherence tomography of knockout animals demonstrated a slow photoreceptor degeneration over a period of 6 mo. Overall, these findings reveal that K_v2.1 channels carry 70–80% of the non-NKX outward dark current of the mouse rod, and that the depolarization caused by the loss of K_v2.1 results in elevated Ca²⁺ influx through CNG channels and elevated free intracellular Ca²⁺, leading to progressive degeneration.