Amino acid sequence versus morphological data and the interordinal relationships of mammals

To a large extent, the mutual affinities of the mammalian orders continue to puzzle systematists, even though comparative anatomy and amino acid sequencing offer a massive data base from which these relationships could potentially be adduced. In the present paper the consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular- sequence data. Consistency indices were calculated for previously published alpha crystallin A chain and myoglobin amino acid-sequence cladograms and for four original amino acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta hemoglobin); these were found to be comparable to the consistency indices of morphologically based cladograms. Qualitative comparisons between the morphologically based and molecularly based trees were also made; only moderate congruence between the two was observed. Moreover, there was a general lack of congruence between the cladograms specified by each of the four proteins. Amino acid-sequence and morphological data agreed on the placement of edentates as an early eutherian offshoot and on the grouping of hyracoids, proboscideans, and sirenians. Otherwise there was only limited congruence: morphology strongly supported the grouping of lagomorphs and rodents and the alliance of pholidotes and edentates, but sequence analyses did not. The placement of tubulidentates differed widely among proteins. Morphology indicated the close association of sirenians with proboscideans; proteins suggested a pairing of sirenians with hyracoids. Sequence data did not identify many (morphologically well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT TRUNCATED AT 250 WORDS)      

The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

Background  

The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues.     

Does Trapping Influence Decision-Making under Ambiguity in White-Lipped Peccary (Tayassu pecari)?

The white-lipped peccary (Tayassu pecari) is an endangered species whose bold anti-predator behaviour in comparison to related species may increase its vulnerability to hunting and predation. We used a judgement bias test to investigate whether captive peccaries that had recently experienced a trapping event made more ‘pessimistic’ decisions under ambiguity. If so, this would indicate (i) that the procedure may induce a negative affective state and hence have welfare implications, and (ii) that the species is able to adopt a cautious response style despite its bold phenotype. Eight individuals were trained to ‘go’ to a baited food bowl when a positive auditory cue (whistle; CS+) was given and to ‘no-go’ when a negative cue (horn A; CS-) was sounded to avoid a loud sound and empty food bowl. An ‘ambiguous’ auditory cue (bell; CSA) was presented to probe decision-making under ambiguity. Individuals were subjected to three tests in the order: T1 (control-no trap), T2 (24h after-trap procedure), and T3 (control-no trap). In each test, each animal was exposed to 10 judgement bias trials of each of the three cue types: CS+,CS-,CS_A. We recorded whether animals reached the food bowl within 60s (‘go’ response) and their response speed (m/s). The animals varied in their responses to the CS_A cue depending on test type. In all tests, animals made more ‘go’ responses to CS+ than CS_A. During control tests (T1 and T3), the peccaries showed higher proportions of ‘go’ responses to CS_A than to CS-. In T2, however, the animals showed similar proportions of ‘go’ responses to CS_A and CS-, treating the ambiguous cue similarly to the negative cue. There were differences in their response speed according to cue type: peccaries were faster to respond to CS+ than to CS- and CS_A. Trapping thus appeared to cause a ‘pessimistic’ judgement bias in peccaries, which may reflect a negative affective state with implications for the welfare and management of captive individuals, and also function to increase caution and survival chances following such an event in the wild environment.     

Stabilization of bacteriophage Mu repressor-operator complexes by the Escherichia coli integration host factor protein

All of the previously described effects of integration host factor (IHF) on bacteriophage Mu development have supported the view that IHF favours transposition-replication over the alternative state of lysogenic phage growth. In this report we show that, consistent with a model in which Mu repressor binding to its operators requires a particular topology of the operator DNA, IHF stimulates repressor binding to the O1 and O2 operators and enhances Mu repression. IHF would thus be one of the keys, besides supercoiling and the H-NS protein, that lock the operator region into the appropriate topological conformation for high-affinity binding not only of the phage transposase but also of the phage repressor.     

MAPK Signaling Pathway Regulates p27 Phosphorylation at Threonin 187 as Part of the Mechanism Triggered by Early-Weaning to Induce Cell Proliferation in Rat Gastric Mucosa

During rat postnatal development, gastric cell proliferation and differentiation depend on many elements, which include dietary pattern, hormones, growth factors and their signaling pathways. Among them, EGFR activity is increased through MAPK and Src cascades in response to early weaning that represents the abrupt transition from milk to solid food. We herein investigated the direct involvement of ERK pathway in the control of cell cycle progression during early weaning, and studied the specific role of p27. At 15 days, Wistar rats were separated from dams, fed with powdered chow and daily injected with PD98059 (MEK inhibitor, 300 µg/kg) or 0.5% DMSO (control). By using HE staining and immunohistochemistry for PCNA, we respectively detected mitotic (MI) and proliferative (PI) indices in 18-day-old pups, and observed that both were reduced by PD98059. As cell cycle-related proteins (cyclin E, CDK2, cyclin D1, CDK4, p21 and p27) are involved in proliferative regulation, we compared samples obtained at 17 days in the morning (17 d) and evening (17.5 d). We found that they were not altered after ERK inhibition, but cyclin D1, p21 and p27 levels changed throughout the day in the control group. As p27 activity depends on its integrity, we studied p27 phosphorylation (threonin 187), and observed that ERK inhibition reduced this process. We suggest that MAPK pathway interferes in the regulation of p27 function in the gastric mucosa during early weaning, possibly by controlling its degradation, and altogether this mechanism might contribute to the increase of epithelial proliferation at this condition.     

Physiological tonicity improves human chondrogenic marker expression through nuclear factor of activated T-cells 5 <Emphasis Type="Italic">in vitro</Emphasis>

Introduction  

Chondrocytes experience a hypertonic environment compared with plasma (280 mOsm) due to the high fixed negative charge density of cartilage. Standard isolation of chondrocytes removes their hypertonic matrix, exposing them to nonphysiological conditions. During in vitro expansion, chondrocytes quickly lose their specialized phenotype, making them inappropriate for cell-based regenerative strategies. We aimed to elucidate the effects of tonicity during isolation and in vitro expansion on chondrocyte phenotype.     

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.     

Growth and ion uptake in <Emphasis Type="Italic">Annona muricata</Emphasis> and <Emphasis Type="Italic">A. squamosa</Emphasis> subjected to salt stress

The effects of treatment with NaCl (3, 100 and 300 mM) for 1, 2, 3 and 7 d on plant growth and ion accumulation were analyzed in 2-week and 8-week-old Annona muricata and A. squamosa plants. Fresh mass and root growth inhibition were directly related to the increase in salinity, particularly for A. squamosa. Two-weeks old seedlings were sensitive to 100 and 300 mM NaCl particularly after 7 d, whereas 8-week-old plants were shown to be more resistant to NaCl even at 300 mM NaCl. Na⁺ and Cl^– mostly accumulated in young leaves. Our results suggest that A. squamosa is more sensitive than A. muricata to salt stress and that older seedlings of both species are more tolerant than younger seedlings.