Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA‐dominated/TATA‐box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA‐like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA‐box promoters are more dynamic because TATA‐binding protein recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA‐box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.     

A new method for surface staining large slices of fixed brain using a copper phthalocyanine dye

Here we describe a method for gross staining of gray matter in slices of formaldehyde-fixed human brain. After protection of white matter with 4% phenol at 60°C for 5 min followed by a cold water wash, the gray matter was stained for 10-15 min at 20-25°C with 1% aqueous copper(II) phthalocyanine tetrasulfonic acid tetrasodium salt (CPTS). The staining resisted all attempts to be washed from the gray matter. Stained slices can be stored indefinitely in slightly acidified water, or plastinated as permanent dry specimens.     

Spontaneous coronary artery dissection: long stenting in a patient with polycythemia vera

Spontaneous coronary artery dissection is a rare cause of myocardial ischemia or sudden cardiac death. We describe a patient with polycythemia vera and a chronic spontaneous coronary artery dissection who was treated with successful angioplasty and long stenting.     

Thwarting of behaviour in different contexts and the gakel-call in the laying hen

Earlier studies have shown that thwarting of feeding behaviour in the laying hen is expressed through a specific vocalisation, the gakel-call. The first aim of this study was to investigate whether the effect of deprivation per se on the occurrence of gakel-calls can be distinguished from the effect of the additional frustration. Frustration is defined as the state of an animal that results from nonreward in the expectancy of reward. The second aim was to investigate whether the occurrence of gakel-calls is restricted to a food context or whether it can be regarded as an expression of frustration in general. For this purpose, 20 hens were deprived of food, water and dustbath. After deprivation at a fixed time, a cue was given and the hens were rewarded with access to food, water or dust during a 15-min session on 4 consecutive days. On the fifth day, they were thwarted in the associated behaviours by blocking the access to these commodities, after the hens had been presented the signal that previously preceded the reward. We then recorded behaviours that might reflect the state of frustration in three 15-min periods. The period "Pre-Frustration" started 15 min before "Frustration". This, in turn, was followed by the period "Post-frustration" in which the hens were rewarded again. Nesting behaviour was thwarted by blocking the access to the nest (Frustration) after a hen had reached the last stage of its prelaying behaviour.In the food, water and dustbath context, deprivation elicited gakel-calls. The additional frustration resulted in a higher number of gakel-calls in all contexts except the food context. However, together with the findings of previous experiments, the results of this study suggest that frustration, in general, is expressed through the gakel-call. Frustration in the nest context elicited more gakel-calls than the other contexts. This latter finding is discussed in the light of the occurrence of the gakel-call under natural circumstances.     

A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis

Background

Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analysed.

Results

Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE, the expression of NANOG, SOX2 and POU5F1 was increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was down-regulated.

Conclusion

The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent, epiblast-like state. The inability to culture ICM cells as stem cells in the presence of an inhibitor of MAPK activity together with the reported data indicates that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1448-x) contains supplementary material, which is available to authorized users.     

Aggregation patterns of helminth populations in the introduced fish, Liza haematocheilus (Teleostei: Mugilidae): disentangling host–parasite relationships

A number of hypotheses exist to explain aggregated distributions, but they have seldom been used to investigate differences in parasite spatial distribution between native and introduced hosts. We applied two aggregation models, the negative binomial distribution and Taylor’s power law, to study the aggregation patterns of helminth populations from Liza haematocheilus across its native (Sea of Japan) and introduced (Sea of Azov) distribution ranges. In accordance with the enemy release hypothesis, we predicted that parasite populations in the introduced host range would be less aggregated than in the native host area, because aggregation is tightly constrained by abundance. Contrary to our expectation, aggregation of parasite populations was higher in the introduced host range. However, the analyses suggested that the effect of host introduction on parasite aggregation depends on whether parasite species, or higher level taxonomic groups, were acquired in or carried into the new area. The revealed similarity in the aggregation parameters of co-introduced monogeneans can be attributed to the repeatability and identity of the host–parasite systems. In contrast, the degree of aggregation differed markedly between regions for higher level taxa, which are represented by the native parasites in the Sea of Japan versus the acquired species in the Sea of Azov. We propose that the host species plays a crucial role in regulating infra-population sizes of acquired parasites due to the high rate of host-induced mortality. A large part of the introduced host population may remain uninfected due to their resistance to native naïve parasites. The core concept of our study is that the comparative analysis of aggregation patterns of parasites in communities and populations, and macroecological relationships, can provide a useful tool to reveal cryptic relationships in host–parasite systems of invasive hosts and their parasites.     

Biometric variability of Hadwenius tursionis (Marchi, 1873) (Digenea,Campulidae) from the intestine of the bottlenose dolphin Tursiops truncatus (Montagu, 1821)

The species discrimination in the family Campulidae is largely based on morphometric characters (absolute measurements and ratios). To assess the variability of this characters we have studied the campulid species Hadwenius tursionis from four Mediterranean bottlenose dolphins Tursiops truncatus from the Western Mediterranean. In H. tursionis most absolute measurements differed significantly across the infrapopulations, showing high coefficients of variation. Only egg dimensions appeared to be fairly conservative. Body ratios were less variable than absolute measurements, but growth patterns did vary significantly between the infrapopulations studied. None of the ratios previously used in relation to other species of the family Campulidae indicated either isometric or allometric growth in this case. Only the ratios concerning the size of the gonads and the shape of the gonads and suckers showed isometry. It is concluded that absolute measurements and ratios should be used with caution in relation to the separation of species of the family Campulidae unless their intrinsic variability can be established beforehand.     

Native and invasive hosts play different roles in host–parasite networks

Parasites are often key players in biological invasions since they can mediate the impact of host invasions or can themselves become invasive species. However, the nature and extent of parasite-mediated invasions are often difficult to delineate. Here, we used individual-based, weighted bipartite networks to study the roles (degrees of interactions of individuals in a modular network according to their within- and among-module connections) played by native and invasive host individuals to their parasite communities. We studied two phylogenetically and ecologically close fish species, Mugil cephalus s.l. and Planiliza haematocheilus (Teleostei: Mugilidae). Planiliza haematocheilus is native to the Sea of Japan and invasive in the Sea of Azov whereas, M. cephalus s.l. is native to both seas. Based on the common evolutionary history that drives native host–parasite networks, we hypothesised that 1) native networks have higher modularity than invaded ones; and 2) invasive hosts in the invaded area play a peripheral role to structure parasite communities. We analysed the whole parasite community and subsets based on transmission strategy and host specificity of the parasite species to establish whether modularity and host roles are related to these features in the native and invaded areas. All networks were found to be modular. However, modularity tended to be higher in networks of the native area rather than those of the invaded area. Host individuals of both fish species played similar roles in the native area, whereas invasive hosts played a peripheral role in the networks of the invaded area. We propose that long-term monitoring of the roles of invasive hosts in parasite communities can be a useful proxy for estimating the maturity of the establishment of the invasive hosts in an ecosystem.     

IAA, ABA, polyamines and free amino acids associated with zygotic embryo development of Ocotea catharinensis

The aim of this work was to study morphological and biochemical aspects during zygotic embryogenesis in O. catharinensis, by measuring changes in the endogenous concentrations of proteins, amino acids, polyamines (PAs), indole-3-acetic acid (IAA) and abscisic acid (ABA). Buffer-soluble and insoluble protein contents were determined by spectrometry, and amino acids, PAs, IAA and ABA concentrations were determined by high performance liquid chromatography. Total amino acid accumulation, predominantly asparagine, occurred when the embryo showed completely developed cotyledons, with posterior reduction in the mature embryo. This decrease in total amino acid concentration in the mature embryo may result from their use in storage␣as well as for LEA protein synthesis. Free putrescine (Put) concentration decreased, while free spermine (Spm) increased during embryo development. This suggest a role for Put in the initial phases of embryogenesis when high rates of cell division occur, while elevated concentration of Spm are essential from the middle to the end of embryo development, when growth is mainly due to cell elongation. An IAA peak in zygotic embryos occurred during initial development, suggesting a link between growth and cellular division as well as with the establishment of bilateral symmetry. ABA concentration declined during initial stages of development then increased at the mature embryo stage, suggesting a possible relationship with dormancy and recalcitrance characteristics. Our results show that changes in the phytohormones (IAA, ABA and PAs) concentrations in combination with amino acids are likely important factors determining the developmental stages of O.␣catharinensis zygotic embryos.