Mitochondrial introgressions into the nuclear genome of the domestic cat

Translocation of mtDNA into the nuclear genome, also referred to as numt, was first reported in the domestic cat (Felis catus) by Lopez et al. (1994). The Lopez-numt consisted of a translocation of 7.9 kbp of mtDNA that inserted into the domestic cat chromosome D2 around 1.8 million years ago. More than a decade later, the release of the domestic cat whole-genome shotgun sequences (1.9x coverage) provides the resource to obtain more comprehensive insight into the extent of mtDNA transfer over time in the domestic cat genome. MegaBLAST searches revealed that the cat genome harbors a wide variety of numts (298 320 bp), one-third of which likely correspond to the Lopez-numt tandem repeat, whereas the remaining numts are probably derived from multiple independent insertions, which in some cases were followed by segmental duplication after insertion in the nucleus. Numts were detected across most cat chromosomes, but the number of numts assigned to chromosomes is underestimated due to the relatively high number of numt sequences with insufficient flanking sequence to map. The catalog of cat numts provides a valuable resource for future studies in Felidae species, including its use as a tool to avoid numt contaminations that may confound population genetics and phylogenetic studies.     

Biochemical characterization of ecto-nucleotide pyrophosphatase/phosphodiesterase (E-NPP, E.C. 3.1.4.1) from rat heart left ventricle

In the present study we investigate the biochemical properties of the members of NPP family in synaptosomes prepared from rat heart left ventricles. Using p-nitrophenyl-5′-thymidine monophosphate (p-Nph-5′-TMP) as substrate for E-NPPs in rat cardiac synaptosomes, we observed an alkaline pH dependence, divalent cation dependence and the K _M value corresponded to 91.42 ± 13.97 μM and the maximal velocity (V _max ) value calculated was 63.79 ± 3.59 nmol p-nitrophenol released/min/mg of protein (mean ± SD, n = 4). Levamisole (1 mM), was ineffective as inhibitor of p-Nph-5′-TMP hydrolysis in pH 8.9 (optimum pH for the enzyme characterized). Suramin (0.25 mM) strongly reduced the hydrolysis of p-Nph-5′-TMP by about 46%. Sodium azide (10 and 20 mM) and gadolinium chloride (0.3 and 0.5 mM), E-NTPases inhibitors, had no effects on p-Nph-5′-TMP hydrolysis. RT-PCR analysis of left ventricle demonstrated the expression of NPP2 and NPP3 enzymes, but excluded the presence of NPP1 member. By quantitative real-time PCR we identified the NPP3 as the enzyme with the highest expression in rat left ventricle. The demonstration of the presence of the E-NPP family in cardiac system, suggest that these enzymes could contribute with the fine-tuning control of the nucleotide levels at the nerve terminal endings of left ventricles that are involved in several cardiac pathologies.     

A neurobiological model of the recovery strategies from perturbed walking

This paper proposes a human mimetic neuro-musculo-skeletal model to simulate the recovery reactions from perturbations during walking. The computational model incorporates nonlinear viscoelastic muscular mechanics, supraspinal control of the center-of-mass, spinal pattern generator including muscle synergy network, spinal reflexes, and long-loop reflexes. Especially the long-loop reflexes specify recovery strategies based on the experimental observations [Schillings, A.M., van Wezel, B.M.H., Mulder, T.H., Duysen, J., 2000. Muscular responses and movement strategies during stumbling over obstacles. J. Neurophysiol. 83, 2093–2102; Eng, J.J., Winter, D.A., Patla, A.E., 1994. Strategies for recovery from a trip in early and late swing during human walking. Exp. Brain Res. 102, 339–349]. The model demonstrates two typical recovery strategies, i.e., elevating and lowering strategies against pulling over a swing leg. Sensed perturbation triggers a simple tonic pulse from the cortex. Depending on the swing phase, the tonic pulse activates a different compound of muscles over lower limbs. The compound induces corresponding recovery strategies. The reproduction of principal recovery behaviors may support the model's proposed functional and/or anatomical correspondence.     

No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males

The first complete mitochondrial DNA (mtDNA) sequences (approximately 16,569 bp) in 20 patients with asthenozoospermia and a comparison with 23 new complete mtDNA sequences in teratoasthenozoospermic individuals, confirmed no sharing of specific polymorphisms or specific mitochondrial lineages between these individuals. This is strong evidence against the accepted claim of a major role played by mtDNA in male fertility, once supported by haplogroup association studies based on the screening of hypervariable region I. The hypothesis of maternally driven selection acting in male reproductive success must thus be treated with caution.     

Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns

Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme.     

Silicon fertigation with appropriate source reduces water requirement of maize under water deficit

Plant and Soil - The objective was to evaluate soluble sources of silicon (Si) applied through fertigation in mitigating water deficit in maize plants. Another objective was to determine the...     

Focus on Chromatin/Epigenetics: Flowering Locus C’s Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation

Analysis of how seasonal cues influence the timing of the floral transition has revealed many important principles for how epigenetic regulation can integrate a variety of environmental cues with developmental signals. The study of the pathways that necessitate overwintering in plants and their ability to respond to prolonged cold (the vernalization requirement and response pathways) has elaborated different chromatin regulatory pathways and the involvement of noncoding RNAs. The major target of these vernalization pathways in Arabidopsis (Arabidopsis thaliana) is Flowering Locus C (FLC). A relatively simple picture of FLC regulation is emerging of a few core complexes and mechanisms that antagonize each other’s actions. This balance provides a fine degree of control that has nevertheless permitted evolution of a wide range of natural variation in vernalization in Arabidopsis. Similar simple routes of adaptation may underlie life history variation between species.The time at which different species flower is an important marker of seasonal and climatic changes and is ecologically and economically important. The sessile nature of plants means that they experience the full range of environmental changes over the seasons. Flowering time control in many species is highly responsive to environmental cues and therefore very sensitive to local climate conditions. The impact of this on many ecosystem and agricultural processes has made understanding flowering time control an important objective.Many genetic pathways influence flowering time, either as part of seasonal (photoperiod and past and present temperature), developmental (developmental phase and age), or stress response (overcrowding and nutrient stress). Despite the variety of competing inputs, these many and various mechanisms are integrated at the action of a small number of nodes in Arabidopsis (Arabidopsis thaliana) termed floral pathway integrators (Simpson and Dean, 2002). Analyses of the genes identified by flowering time mutants have shown many have roles as chromatin modifiers (Andrés and Coupland, 2012; Pajoro et al., 2014). Timing of flowering seems particularly sensitive to chromatin regulation, potentially due to the necessity for long-term storage of seasonal information.In this review, we focus on vernalization in Arabidopsis and summarize our understanding of how chromatin modifiers interact with other proteins and noncoding RNAs to integrate developmental and temperature cues into chromatin changes at the key integrating locus Flowering Locus C (FLC). Further, we explore how changes in these mechanisms underlie different life history strategies and vernalization responses in different accessions and species. A key observation we wish to convey is that the complexity of these systems at the molecular level belies simplicity in balancing forces that enable a fine degree of control and adaptive responses at the phenotypic level.     

Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.