Attenuation of liver ischemia-reperfusion-induced atrial dysfunction by external pacing but not by isoproterenol

Remote ischemia-reperfusion detrimentally affects myocardial function by initially interfering with the rate of contraction. We investigated the usefulness of isoproterenol versus external electrical pacing in attenuating secondary functional damage of isolated Wistar rat atria. Atrial strips (n = 10/group) were bathed within oxygenated Krebs-Henseleit solution that exited from isolated livers that had been either perfused normally (controls) or underwent no flow (ischemia) for 2 h. In addition to one noninterventional ischemia-exposed strip group, a second group was externally paced at a fixed rate (55 pulses.min-1, 6 V) and a third "ischemia" group was treated with isoproterenol (0.1 mM), both interventions commencing upon the strips' exposure to the hepatic effluents. Control strips displayed unaltered contraction rate and systolic-generated tension during the 2-h exposure. Nontreated strips exposed to ischemic reperfusate experienced bradycardia compared with baseline values (7 +/- 2 vs. 50 +/- 12 beats.min-1, p < 0.05), followed <1-min later by a fall in the generated tension (11 +/- 4 vs. 20 +/- 6 mmHg, p < 0.05). The paced-ischemic strips displayed unaltered rate and force of contraction, whereas the addition of isoproterenol did not prevent deterioration in the rate and force of contraction (8 +/- 3 beats.min-1, 12 +/- 4 mmHg, respectively; p < 0.05 vs. baseline control ischemia-paced strips). Thus, external electrical pacing prevented liver ischemia-reperfusion-induced atrial strips' bradycardia and loss of contractility, while isoproterenol did not.     

Interactive effects of grazing and shrubs on the annual plant community in semi‐arid Mediterranean shrublands

Question: We studied the interactive effects of grazing and dwarf shrub cover on the structure of a highly diverse annual plant community. Location: Mediterranean, semi‐arid shrubland in the Northern Negev desert, Israel. Methods: Variation in the biomass and plant density of annual species in the shrub and open patches was monitored during four years, inside and outside exclosures protected from sheep grazing, in two contrasting topographic sites: north and south‐facing slopes that differed in their dominant dwarf shrubs species: Sarcopoterium spinosus and Corydothymus capitatus, respectively. Results: Above‐ground biomass, density and richness of annual species were lower under the canopy of both shrub species compared to the adjacent open patches in the absence of grazing. Grazing reduced the biomass of annuals in open patches of both topographic sites, but not in the shrub patches. On the north‐facing slope, grazing also reduced plant density and richness in the open patches, but increased plant density in the shrub patches. At the species level, various response patterns to the combined effects of grazing and patch type were exhibited by different annuals. Protection against the direct impacts of grazing by shrub cover as well as species‐specific interactions between shrubs and annuals were observed. A conceptual mechanistic model explaining these interactions is proposed. Conclusion: In semi‐arid Mediterranean shrublands grazing and dwarf shrub cover interact in shaping the structure of the annual plant community through (1) direct impacts of grazing restricted to the open patches, (2) species‐specific facilitation/ interference occurring in the shrub patches and (3) subsequent further processes occurring among the interconnected shrub and open patches mediated through variation in seed flows between patches.     

Lists2Networks: Integrated analysis of gene/protein lists

Background  

Systems biologists are faced with the difficultly of analyzing results from large-scale studies that profile the activity of many genes, RNAs and proteins, applied in different experiments, under different conditions, and reported in different publications. To address this challenge it is desirable to compare the results from different related studies such as mRNA expression microarrays, genome-wide ChIP-X, RNAi screens, proteomics and phosphoproteomics experiments in a coherent global framework. In addition, linking high-content multilayered experimental results with prior biological knowledge can be useful for identifying functional themes and form novel hypotheses.     

Crustacean Species Richness in Temporary Pools: Relationships with Habitat Traits

We examined species richness separately for cladocerans and ostracods in 52 temporary pools in a small geographical area, relating species richness with habitat traits using multiple regressions. Habitat traits considered included surface area, water depth, permanence and sediment depth. Permanence was an important predictor of species richness of both cladocerans and ostracods. Additionally, variation in ostracod species richness was significantly explained by water depth (negative relationship) and sediment depth (positive relationship). Surface area was not a statistically significant factor in any of our analyses. The importance of permanence supports the hypothesis that extinction due to pool drying is a major driving force behind the structuring of microcrustacean communities in temporary pools.     

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

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Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological systems. Consequently, a large number of computational methods for extracting dynamic information from such data have been developed. One example is RNA velocity analysis, in which spliced and unspliced RNA abundances are jointly modeled in order to infer a ‘direction of change’ and thereby a future state for each cell in the gene expression space. Naturally, the accuracy and interpretability of the inferred RNA velocities depend crucially on the correctness of the estimated abundances. Here, we systematically compare five widely used quantification tools, in total yielding thirteen different quantification approaches, in terms of their estimates of spliced and unspliced RNA abundances in five experimental droplet scRNA-seq data sets. We show that there are substantial differences between the quantifications obtained from different tools, and identify typical genes for which such discrepancies are observed. We further show that these abundance differences propagate to the downstream analysis, and can have a large effect on estimated velocities as well as the biological interpretation. Our results highlight that abundance quantification is a crucial aspect of the RNA velocity analysis workflow, and that both the definition of the genomic features of interest and the quantification algorithm itself require careful consideration.     

Resolution of parallel and antiparallel oligonucleotide triple helices formation and melting processes by multivariate curve resolution

A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are successfully estimated from Multivariate Curve Resolution analysis of UV absorbance spectra recorded along acid-base titrations and melting experiments of single stranded, hairpin and their mixtures. The dependence of formation constants upon pH was successfully estimated. The hairpin h26 (5'-GAAGGAGGAGA-TTTT-TCTCCTCCTTC-3'), and the single stranded oligonucleotides s11CT (5'-CTTCCTCCTCT-3'), s11AG (5'-AGAGGAGGAAG-3') and s11TG (5'-TGTGGTGGTTG-3') were synthesized and their protonation and conformational equilibria were studied in detail. The procedure was shown to be especially useful for the study of triplexes with a low hypochromism upon formation.     

Role of xanthine oxidase, lactoperoxidase, and NO in the innate immune system of mammary secretion during active involution in dairy cows: manipulation with casein hydrolyzates

The aims of this study were to test whether xanthine oxidase, lactoperoxidase, and NO are components of the innate immune system of mammary secretion during active involution in dairy cows, and whether the innate immune system is activated by casein hydrolysates. Our laboratory has shown recently that infusion of CNH into mammary glands induced involution and was associated with earlier increases in the concentrations of components of the innate immune system. Intact casein is inactive and served as control. Half of the glands of 8 Holstein cows scheduled for dry off (approximately 60 days before parturition) were injected for 3 days with a single dose of casein hydrolyzates and the contralateral glands with a single dose of intact casein with the same concentration. Involution elicited marked increases in xanthine oxidase and lactoperoxidase activities, and accumulation of urate and nitrate. NO and H(2)O(2) were constantly produced in the mammary gland secretion. Nitrite formed either by autooxidation of NO or by conversion of nitrate to nitrite by xanthine oxidase was converted into the powerful nitric dioxide radical by lactoperoxidase and H(2)O(2) that is derived from the metabolism of xanthine oxidase. Nitric dioxide is most likely responsible for the formation of nitrosothiols on thiol-bearing groups, which allows an extended NO presence in mammary secretion. Nitrite is effectively converted to nitrate, which accumulated in the range of approximately 25 microM -1 mM from the start of the experiment to the complete involution of glands. The mammary secretion in all glands was bactericidal and bacteriostatic during established involution, and this appeared sooner and more acutely in glands treated with casein hydrolyzates, within 8 to 24 h. It is concluded that xanthine oxidase, lactoperoxidase, and NO are components of the mammary innate immune system that form bactericidal and bacteriostatic activities in mammary secretions. The innate immune system play a major role in preventing intramammary infection during milk stasis and its activation may increase its effectiveness.     

Influence of pH, temperature and the cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5'-(C3TA2)4-3' sequence of the human telomere

The influence of pH, temperature and the cationic porphyrin TMPyP4 on the conformational equilibria of the cytosine-rich strand of the human telomeric sequence 5′-(C₃TA₂)₄-3′, as well as those of the sequence 5′-(C₃TT₂)₄-3′, was studied. The presence of adenine bases at the loops causes the formation of two different intramolecular i-motif structures with a pH-transition midpoint around 4.6, which stability is lower than the i-motif formed by the sequence 5′-(C₃TT₂)₄-3′. The stoichiometries of the complexes formed by these i-motif structures with TMPyP4 are also influenced by the presence of adenine at the loops.     

Bird and mammal species composition in distinct geographic regions and their relationships with environmental factors across multiple spatial scales

Global patters of species distributions and their underlying mechanisms are a major question in ecology, and the need for multi‐scale analyses has been recognized. Previous studies recognized climate, topography, habitat heterogeneity and disturbance as important variables affecting such patterns. Here we report on analyses of species composition – environment relationships among different taxonomic groups in two continents, and the components of such relationships, in the contiguous USA and Australia. We used partial Canonical Correspondence Analysis of occurrence records of mammals and breeding birds from the Global Biodiversity Information Facility, to quantify relationships between species composition and environmental variables in remote geographic regions at multiple spatial scales, with extents ranging from 10⁵ to 10⁷ km² and sampling grids from 10 to 10,000 km². We evaluated the concept that two elements contribute to the impact of environmental variables on composition: the strength of species' affinity to an environmental variable, and the amount of variance in the variable. To disentangle these two elements, we analyzed correlations between resulting trends and the amount of variance contained in different environmental variables to isolate the mechanisms behind the observed relationships. We found that climate and land use‐land cover are responsible for most explained variance in species composition, regardless of scale, taxonomic group and geographic region. However, the amount of variance in species composition attributed to land use / land cover (LULC) was closely related to the amount of intrinsic variability in LULC in the USA, but not in Australia, while the effect of climate on species composition was negatively correlated to the variability found in the climatic variables. The low variance in climate, compared to LULC, suggests that species in both taxonomic groups have strong affinity to climate, thus it has a strong effect on species distribution and community composition, while the opposite is true for LULC.