Two-state intermittency near a symmetric interaction of saddle-node and Hopf bifurcations: a case study from dynamo theory

We consider a model of a Hopf bifurcation interacting as a codimension 2 bifurcation with a saddle-node on a limit cycle, motivated by a low-order model for magnetic activity in a stellar dynamo. This model consists of coupled interactions between a saddle-node and two Hopf bifurcations, where the saddle-node bifurcation is assumed to have global reinjection of trajectories. The model can produce chaotic behaviour within each of a pair of invariant subspaces, and also it can show attractors that are stuck-on to both of the invariant subspaces. We investigate the detailed intermittent dynamics for such an attractor, investigating the effect of breaking the symmetry between the two Hopf bifurcations, and observing that it can appear via blowout bifurcations from the invariant subspaces. We give a simple Markov chain model for the two-state intermittent dynamics that reproduces the time spent close to the invariant subspaces and the switching between the different possible invariant subspaces; this clarifies the observation that the proportion of time spent near the different subspaces depends on the average residence time and also on the probabilities of switching between the possible subspaces

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes

Conserved elements within open reading frames of mammalian Hox genes

A recent study in BMC Evolutionary Biology shows that many of the open reading frames in mammalian Hox genes are more conserved than expected on the basis of their protein sequence. The presence of highly conserved DNA elements is thus not confined to the noncoding DNA in neighboring regions but clearly overlaps with coding sequences. These findings support an emerging view that gene regulatory and coding sequences are likely to be more intermingled than once believed

Essential and checkpoint functions of budding yeast ATM and ATR during meiotic prophase are facilitated by differential phosphorylation of a meiotic adaptor protein, Hop1

A hallmark of the conserved ATM/ATR signalling is its ability to mediate a wide range of functions utilizing only a limited number of adaptors and effector kinases. During meiosis, Tel1 and Mec1, the budding yeast ATM and ATR, respectively, rely on a meiotic adaptor protein Hop1, a 53BP1/Rad9 functional analog, and its associated kinase Mek1, a CHK2/Rad53-paralog, to mediate multiple functions: control of the formation and repair of programmed meiotic DNA double strand breaks, enforcement of inter-homolog bias, regulation of meiotic progression, and implementation of checkpoint responses. Here, we present evidence that the multi-functionality of the Tel1/Mec1-to-Hop1/Mek1 signalling depends on stepwise activation of Mek1 that is mediated by Tel1/Mec1 phosphorylation of two specific residues within Hop1: phosphorylation at the threonine 318 (T318) ensures the transient basal level Mek1 activation required for viable spore formation during unperturbed meiosis. Phosphorylation at the serine 298 (S298) promotes stable Hop1-Mek1 interaction on chromosomes following the initial phospho-T318 mediated Mek1 recruitment. In the absence of Dmc1, the phospho-S298 also promotes Mek1 hyper-activation necessary for implementing meiotic checkpoint arrest. Taking these observations together, we propose that the Hop1 phospho-T318 and phospho-S298 constitute key components of the Tel1/Mec1- based meiotic recombination surveillance (MRS) network and facilitate effective coupling of meiotic recombination and progression during both unperturbed and challenged meiosis

An interlaboratory study of TEX86 and BIT analysis of sediments, extracts and standard mixtures.

Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round-robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility ±3-4°C when translated to temperature) but a large spread in BIT measurements (reproducibility ±0.41 on a scale of 0-1). Here we report results of a second round-robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round-robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0°C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the "true" (i.e., molar-based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar-based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar-based, BIT values

Mine Injury Casualties Report from the Iraq-Kuwait DMZ

After the implementation of the UN Iraq-Kuwait Observation Mission (UNIKOM) at the end of the first Gulf War in 1990, a medical team was set up in 1991 to support the UN troops in their difficult tasks in the demilitarised zone (DMZ), a remote desert area between Kuwait and Iraq. The medical team was designed to take care of the medical treatment for the UNIKOM members and the nomadic people living in the DMZ as pointed out in UN Secretary-General reports S/2001/287 and S/2001/913 on the official UN website

Plasmodium falciparum metacaspase PfMCA-1 triggers a z-VAD-fmk inhibitable protease to promote cell death.

Activation of proteolytic cell death pathways may circumvent drug resistance in deadly protozoan parasites such as Plasmodium falciparum and Leishmania. To this end, it is important to define the cell death pathway(s) in parasites and thus characterize proteases such as metacaspases (MCA), which have been reported to induce cell death in plants and Leishmania parasites. We, therefore, investigated whether the cell death function of MCA is conserved in different protozoan parasite species such as Plasmodium falciparum and Leishmania major, focusing on the substrate specificity and functional role in cell survival as compared to Saccharomyces cerevisae. Our results show that, similarly to Leishmania, Plasmodium MCA exhibits a calcium-dependent, arginine-specific protease activity and its expression in yeast induced growth inhibition as well as an 82% increase in cell death under oxidative stress, a situation encountered by parasites during the host or when exposed to drugs such as artemisins. Furthermore, we show that MCA cell death pathways in both Plasmodium and Leishmania, involve a z-VAD-fmk inhibitable protease. Our data provide evidence that MCA from both Leishmania and Plasmodium falciparum is able to induce cell death in stress conditions, where it specifically activates a downstream enzyme as part of a cell death pathway. This enzymatic activity is also induced by the antimalarial drug chloroquine in erythrocytic stages of Plasmodium falciparum. Interestingly, we found that blocking parasite cell death influences their drug sensitivity, a result which could be used to create therapeutic strategies that by-pass drug resistance mechanisms by acting directly on the innate pathways of protozoan cell death

Sequential fusion of information from two portable spectrometers for improved prediction of moisture and soluble solids content in pear fruit

Near infrared (NIR) spectroscopy allows rapid estimation of quality traits in fresh fruit. Several portable spectrometers are available in the market as a low-cost solution to perform NIR spectroscopy. However, portable spectrometers, being lower in cost than a benchtop counterpart, do not cover the complete near infrared (NIR) spectral range. Often portable sensors either use silicon-based visible and NIR detector to cover 400–1000 nm, or InGaAs-based short wave infrared (SWIR) detector covering the 900–1700 nm. However, these two spectral regions carry complementary information, since the 400–1000 nm interval captures the color and 3rd overtones of most functional group vibrations, while the 1st and the 2nd overtones of the same transitions fall in the 1000–1700 nm range. To exploit such complementarity, sequential data fusion strategies were used to fuse the data from two portable spectrometers, i.e., Felix F750 (~400–1000 nm) and the DLP NIR Scan Nano (~900–1700 nm). In particular, two different sequential fusion approaches were used, namely sequential orthogonalized partial-least squares (SO-PLS) regression and sequential orthogonalized covariate selection (SO-CovSel). SO-PLS improved the prediction of moisture content (MC) and soluble solids content (SSC) in pear fruit, leading to an accuracy which was not obtainable with models built on any of the two spectral data set individually. Instead, SO-CovSel was used to select the key wavelengths from both the spectral ranges mostly correlated to quality parameters of pear fruit. Sequential fusion of the data from the two portable spectrometers led to an improved model prediction (higher R2 and lower RMSEP) of MC and SSC in pear fruit: compared to the models built with the DLP NIR Scan Nano (the worst individual block) where SO-PLS showed an increase in R2p up to 56% and a corresponding 47% decrease in RMSEP. Differences were less pronounced to the use of Felix data alone, but still the R2p was increased by 2.5% and the RMSEP was reduced by 6.5%. Sequential data fusion is not limited to NIR data but it can be considered as a general tool for integrating information from multiple sensors