Insights into the historical construction of species-rich Mesoamerican seasonally dry tropical forests: the diversification of Bursera (Burseraceae, Sapindales)

? Mesoamerican arid biomes epitomize neotropical rich and complex biodiversity. To document some of the macroevolutionary processes underlying the vast species richness of Mesoamerican seasonally dry tropical forests (SDTFs), and to evaluate specific predictions about the age, geographical structure and niche conservatism of SDTF-centered woody plant lineages, the diversification of Bursera is reconstructed. ? Using a nearly complete Bursera species-level phylogeny from nuclear and plastid genomic markers, we estimate divergence times, test for phylogenetic and temporal diversification heterogeneity, test for geographical structure, and reconstruct habitat shifts. ? Bursera became differentiated in the earliest Eocene, but diversified during independent early Miocene consecutive radiations that took place in SDTFs. The late Miocene average age of Bursera species, the presence of phylogenetic geographical structure, and its strong conservatism to SDTFs conform to expectations derived from South American SDTF-centered lineages. ? The diversification of Bursera suggests that Mesoamerican SDTF richness derives from high speciation from the Miocene onwards uncoupled from habitat shifts, during a period of enhanced aridity resulting mainly from global cooling and regional rain shadows.     

Blood rheology of Weddell seals and bowhead whales

Red blood cell (RBC) aggregation and blood viscosity are important determinants of in vivo blood flow dynamics and, in marine mammals, these parameters may impact diving physiology by altering blood oxygen delivery during the diving response. Weddell seals are superb divers and exhibit age-related patterns in blood oxygen chemistry and diving ability. By contrast, bowhead whales are not long duration divers, and little is known of their blood properties relative to diving. The present study was designed to compare rheological characteristics of blood from Weddell seal pups, Weddell seal adults, and from adult bowhead whales: blood viscosity and RBC aggregation in plasma and in polymer solutions (i.e., RBC "aggregability") were measured. Salient findings included: (1) significant 4- to 8-fold greater aggregation in blood from adult seals compared with pups and human subjects; (2) 2-to 8-fold greater aggregation in bowhead whale blood compared with human blood; (3) compared to human red cells, enhanced RBC aggregability of RBC from adult seals and whales as determined by their greater aggregation in polymer solutions; (4) increasing RBC aggregation and aggregability of seal pup blood over a seven day period following birth; (5) significantly greater blood viscosity for adult seals compared with pups at both native and standardized hematocrits. These results indicate that, for both species, hemorheological parameters differ markedly from those of humans, and suggest progressive changes with seal age; the physiological implications of these differences have yet to be fully defined.     

Multiphasic Approach To Study the Bacterial Ecology of Fermented Sausages Inoculated with a Commercial Starter Culture

In this paper, the ability of a commercial starter culture to perform a sausage fermentation is evaluated. Molecular analysis revealed the presence of several strains of the same species contained in the starter culture with different behavior during the fermentation, and the contribution of Lactobacillus curvatus, which was only marginally isolated during the transformation.     

The activation of liver X receptors inhibits toll‐like receptor‐9‐induced foam cell formation

Toll‐like receptors (TLRs) are related to foam cell formation (FCF), key event in the establishment/progression of atherosclerosis. The activation of TLR2 and TLR4 can increase FCF. The aim of this study was to evaluate the role of TLR9 in FCF. Murine macrophages were treated with CpG‐ODN, TLR9 agonist, and oxidized particles of LDL (Paz‐PC) and FCF was analyzed by means of Oil Red O staining. The administration of CpG‐ODN plus Paz‐PC onto macrophages increased the amount of lipid droplets, correlated to increased levels of tumor necrosis factor (TNF)‐α, IFNβ, and IP‐10. The underlying mechanism by which TLR9 ligation influenced Paz‐PC in the FCF was NF‐κB‐ and IRF7‐dependent, as observed by higher levels of phosphorylated IκBα, increased nuclear translocation of the p65 subunit, lower levels of the total IKKα protein and higher release of interferon‐dependent cytokines, such as IP‐10. Liver X receptors (LXRs) regulate lipid cellular transport and negatively modulate TLR‐dependent signaling pathways. Indeed, the addition of GW3965, synthetic LXRs agonist, significantly reduced FCF after CpG‐ODN plus Paz‐PC stimulation. In this condition, we observed decreased levels of the nuclear translocation of the p65 subunit, related to the higher presence of LXRα into the nucleus. TNF‐α, IP‐10, and IFNβ levels were reduced by the administration of GW3965 following CpG‐ODN and Paz‐PC treatment. In conclusion, the activation of TLR9 facilitates the formation of foam cells in an NF‐κB‐ and IRF7‐dependent manner, countered by the activation of LXRs. This study further support LXRs as potential anti‐atherosclerotic target. J. Cell. Physiol. 223: 158–167, 2010. © 2009 Wiley‐Liss, Inc.     

Study of the ecology of fresh sausages and characterization of populations of lactic acid bacteria by molecular methods

In this study, a polyphasic approach was used to study the ecology of fresh sausages and to characterize populations of lactic acid bacteria (LAB). The microbial profile of fresh sausages was monitored from the production day to the 10th day of storage at 4 degrees C. Samples were collected on days 0, 3, 6, and 10, and culture-dependent and -independent methods of detection and identification were applied. Traditional plating and isolation of LAB strains, which were subsequently identified by molecular methods, and the application of PCR-denaturing gradient gel electrophoresis (DGGE) to DNA and RNA extracted directly from the fresh sausage samples allowed the study in detail of the changes in the bacterial and yeast populations during storage. Brochothrix thermosphacta and Lactobacillus sakei were the main populations present. In particular, B. thermosphacta was present throughout the process, as determined by both DNA and RNA analysis. Other bacterial species, mainly Staphylococcus xylosus, Leuconostoc mesenteroides, and L. curvatus, were detected by DGGE. Moreover, an uncultured bacterium and an uncultured Staphylococcus sp. were present, too. LAB strains isolated at day 0 were identified as Lactococcus lactis subsp. lactis, L. casei, and Enterococcus casseliflavus, and on day 3 a strain of Leuconostoc mesenteroides was identified. The remaining strains isolated belonged to L. sakei. Concerning the yeast ecology, only Debaryomyces hansenii was established in the fresh sausages. Capronia mansonii was initially present, but it was not detected after the first 3 days. At last, L. sakei isolates were characterized by randomly amplified polymorphic DNA PCR and repetitive DNA element PCR. The results obtained underlined how different populations took over at different steps of the process. This is believed to be the result of the selection of the particular population, possibly due to the low storage temperature employed.     

MADS-box gene expression in lateral primordia,meristems and differentiated tissues of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> roots

Although MADS-box genes involved in flower and fruit development have been well characterized, the function of MADS-box genes expressed in vegetative structures has yet to be explored. At least seven members of this family are grouped in clades of genes that are preferentially expressed in roots of Arabidopsis thaliana (L.) Heynh.. We report here the cloning of the AGL21 MADS-box gene, which belongs to the ANR1 clade, and the mRNA in situ expression patterns of this and two other root MADS-box genes. AGL17 appears to be a lateral root cap marker in the root tip, and towards the elongation zone this gene is expressed in the epidermal cells. AGL21 is highly expressed in lateral root primordia and it has a punctate expression pattern in the primary root meristem. AGL12 also has a punctate expression pattern in the primary root meristem. AGL12 and AGL21 are also expressed in the central cylinder of differentiated roots and both are expressed in developing embryos. This study, combined with previous phylogenetic analyses, indicates that these MADS-box genes may play distinct regulatory roles during root development.     

Positively charged surfaces increase the flexibility of DNA

Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how ions change the flexibility of DNA in solution, but when considering macromolecules such as chromatin in which the DNA contacts the nucleosome core each turn of the double helix, it may be more appropriate to assess the flexibility of DNA on charged surfaces. Mica coated with positively charged molecules is a convenient substrate upon which the flexibility of DNA may be directly measured with a scanning force microscope. In the experiments described below, the flexibility of DNA increased as much as fivefold depending on the concentration and type of polyamine used to coat mica. Using theory that relates charge neutralization to flexibility, we predict that phosphate repulsions were attenuated by approximately 50% in the most flexible DNA observed. This simple method is an important tool for investigating the physiochemical causes and molecular biological effects of DNA flexibility, which affects DNA biochemistry ranging from chromatin stability to viral encapsulation.     

Electrophysiological Responses of Nucleus Tractus Solitarius Neurons to CCK and Gastric Distension in Newborn Lambs

The effect of cervical vagus nerve stimulation, gastric distension and CCK-8S administration was studied on the activity of 120 neurons located in the nucleus tractus solitarius (NTS) of anesthetized newborn lambs. One hundred cells responded to the three different inputs.The distribution of the cells in the NTS was from 3 mm rostral to 3 mm caudal to the obex, the major responsive cells being located at the level of the obex. Neurons were either excited or inhibited by gastric distension and CCK-8S, and the responses to these two stimuli were always in the same direction. A small number of cells responded to gastric distension and CCK-8S but not to vagus nerve stimulation.Injection of the CCK-A receptor antagonist 2-NAP abolished both the responses to CCK-8S and to gastric distension. The results are consistent with the idea that CCK-8S acts directly on vagal mechanoreceptive endings in the gastric corpus close to duodenum.These results from lambs may reflect the pathway by which gastric distension and peripheral CCK-8S modulate NTS cells activity during colostrum ingestion, which could in turn activate structures related to learning and memory processes involved in the development of mother preference.     

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina''s MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.