A DNA barcoding approach for identification of hidden diversity in Parmeliaceae (Ascomycota): Parmelia sensu stricto as a case study

Accurate specimen identification is challenging in groups with subtle or scarce taxonomically diagnostic characters, and the use of DNA barcodes can provide an effective means for consistent identification. Here, we investigate the utility of DNA barcode identification of species in a cosmopolitan genus of lichen‐forming fungi, Parmelia (Parmeliaceae). Two hundred and two internal transcribed spacer (ITS) sequences generated from specimens collected from all continents, including Antarctica, were analysed, and DNA barcodes of 14 species of Parmelia s.s. are reported. Almost all species show a barcode gap. Overall, intraspecific divergence values were lower than the threshold previously established for Parmeliaceae. However, the mean and range were elevated by deep barcode divergences in three species, indicating the likely occurrence of overlooked species‐level lineages. Here, we provide a DNA barcode reference library with well‐identified specimens sampled worldwide and sequences from most of the type material to enable easy and fast accurate sample identification and to assist in uncovering overlooked species in Parmelia s.s. Further, our results confirm the efficiency of the ITS region in the identification of species of Parmelia s.s. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 21–29.     

A new species of Plesiodimylus (Dimylidae,Eulipotyphla, Mammalia) from the Early Miocene of Spain

Abstract

We report a new dimylid species, Plesiodimylus ilercavonicus sp. nov., from the Early Miocene locality of Mas d’Antolino B-5 (Ribesalbes-Alcora, Castelló, Spain). This new species of Plesiodimylus is an amblyodont form of the genus and exhibits some primitive characters. The phylogenetic and palaeoenvironmental implications of this southern occurrence of Plesiodimylus in Lower Miocene sediments are discussed.

http://zoobank.org/lsid:zoobank.org:pub:E78DB979-6552-4BE2-BEC9-FA2EA05B7B39     

Buttermilk and Krill Oil Phospholipids Improve Hippocampal Insulin Resistance and Synaptic Signaling in Aged Rats

Impaired glucose metabolism and mitochondrial decay greatly increase with age, when cognitive decline becomes rampant. No pharmacological or dietary intervention has proven effective, but proper diet and lifestyle do postpone the onset of neurodegeneration and some nutrients are being investigated. We studied insulin signaling, mitochondrial activity and biogenesis, and synaptic signaling in the hippocampus and cortex following dietary supplementation with bioactive phospholipid concentrates of krill oil (KOC), buttermilk fat globule membranes (BMFC), and a combination of both in aged rats. After 3 months of supplementation, although all groups of animals showed clear signs of peripheral insulin resistance, the combination of KOC and BMFC was able to improve peripheral insulin sensitivity. We also explored brain energy balance. Interestingly, the hippocampus of supplemented rats—mainly when supplemented with BMFC or the combination of KOC and BMFC—showed an increase in intracellular adenosine triphosphate (ATP) levels, whereas no difference was observed in the cerebral cortex. Moreover, we found a significant increase of brain-derived neurotrophic factor (BDNF) in the hippocampus of BMFC+KO animals. In summary, dietary supplementation with KOC and/or BMFC improves peripheral and central insulin resistance, suggesting that their administration could delay the onset of these phenomena. Moreover, n-3 fatty acids (FAs) ingested as phospholipids increase BDNF levels favoring an improvement in energy state within neurons and facilitating both mitochondrial and protein synthesis, which are necessary for synaptic plasticity. Thus, dietary supplementation with n-3 FAs could protect local protein synthesis and energy balance within dendrites, favoring neuronal health and delaying cognitive decline associated to age-related disrepair.     

Prazosin induced lysosomal tubulation interferes with cytokinesis and the endocytic sorting of the tumour antigen CD98hc

The quinazoline based drug prazosin (PRZ) is a potent inducer of apoptosis in human cancer cells. We recently reported that PRZ enters cells via endocytosis and induces tubulation of the endolysosomal system. In a proteomics approach aimed at identifying potential membrane proteins with binding affinity to quinazolines, we detected the oncoprotein CD98hc. We confirmed shuttling of CD98hc towards lysosomes and upregulation of CD98hc expression in PRZ treated cells. Gene knockout (KO) experiments revealed that endocytosis of PRZ still occurs in the absence of CD98hc - suggesting that PRZ does not enter the cell via CD98hc but misroutes the protein towards tubular lysosomes. Lysosomal tubulation interfered with completion of cytokinesis and provoked endoreplication. CD98hc KO cells showed reduced endoreplication capacity and lower sensitivity towards PRZ induced apoptosis than wild type cells. Thus, loss of CD98hc does not affect endocytosis of PRZ and lysosomal tubulation, but the ability for endoreplication and survival of cells. Furthermore, we found that glutamine, lysomototropic agents – namely chloroquine and NH₄Cl – as well as inhibition of v-ATPase, interfere with the intracellular transport of CD98hc. In summary, our study further emphasizes lysosomes as target organelles to inhibit proliferation and to induce cell death in cancer. Most importantly, we demonstrate for the first time that the intracellular trafficking of CD98hc can be modulated by small molecules. Since CD98hc is considered as a potential drug target in several types of human malignancies, our study possesses translational significance suggesting, that old drugs are able to act on a novel target.     

Unique antibiotic sensitivity of an in vitro polypeptide synthesis system from the archaebacterium Thermoplasma acidophilum. Phylogenetic implications

Summary The susceptibility of Thermoplasma acidophilum (an extremely acidophilic, moderately thermophilic, wall-less sulphur-oxidizing archaebacterium) to 50 ribosome-specific inhibitors of polypeptide elongation was surveyed using efficient poly(U)-and poly(UG)-directed cell-free systems and comparable reference systems derived from eubacterial (Bacillus stearothermophilus, Escherichia coli) and eukaryotic (Saccharomyces cerevisiae) species. Under optimum temperature (58° C) and ionic conditions for polypeptide synthesis Thermoplasma ribosomes are only sensitive to the 70 S/80 S ribosome-directed aminoglycoside neomycin, and to five 80 S ribosome-directed inhibitors all of which (-sarcin, mitogillin, restrictocin, dianthin and gelonin) impair the functioning of the large (60 S) ribosomal subunit. Sensitivity of the three structurally related compounds -sarcin, mitogillin and restrictocin and susceptibility to neomycin place Thermoplasma ribosomes between those of Sulfolobus solfataricus (only sensitive to -sarcin) and Methanococcus vannielli (sensitive to -sarcin, mitogillin, restrictocin and neomycin but also affected by a variety of 70 S ribosome-directed drugs). The phylogenetic significance of the greatly diversified antibiotic sensitivity spectra displayed by archaebacteria in general, as opposed to the uniform ones exhibited by eubacteria and eukaryotes, is discussed.     

Intralineage diversity of archaebacterial ribosomes: A dichotomy of ribosome features separates sulfur-dependent archaebacteria and methanococcaceae from other archaebacterial taxa

Summary The aggregate masses and relative protein contents of eubacterial and archaebacterial ribosomes have been estimated from the buoyant densities of the ribosomal subunits and the anhydrous weights of the rRNA species. In contrast to the situation in eubacteria, archaebacterial ribosomes fall into two size classes that differ only in the relative abundances of their protein moieties. One class comprises eubacterial-sized particles (2.3-megadalton (Mdal) monomer; 1.5-Mdal and 0.8-Mdal large and small subunits, respectively) having a eubacterial composition of roughly one-third protein and two-thirds RNA. The other class comprises ribosomes heavier than those of eubacteria (3-Mdal monomer; 1.8-Mdal and 1.2-Mdal subunits) and having the same protein/RNA ratio as eukaryotic ribosomes (55% and 50% protein for the small and large subunits, respectively). Eubacterialsized ribosomes are harbored by extreme halophiles and all methanogens but the Methanococcaceae. Ribosomes heavier than those of eubacteria are found in the Methanococcaceae and all sulfur-dependent thermophiles. The data indicate that a change in ribosome structure occurred within the methanogen branch; therefore, although ribosome composition is distributed in archaebacteria, its distribution does not break them into two separate kingdoms: The Methanococcaceae and Methanobacteriaceae are related to each other far more closely than either is to the sulfur-dependent thermophiles, and the root of the archaebacterial tree definitely does not lie betweenMethanobacterium andMethanococcus. We surmise that ribosomes larger than those of eubacteria represent a more rudimentary organelle structure that became fixed owing to nonparallel evolution of the translational machinery in archaebacteria.     

Estimation of muscle forces in gait using a simulation of the electromyographic activity and numerical optimization

Clinical gait analysis provides great contributions to the understanding of gait patterns. However, a complete distribution of muscle forces throughout the gait cycle is a current challenge for many researchers. Two techniques are often used to estimate muscle forces: inverse dynamics with static optimization and computer muscle control that uses forward dynamics to minimize tracking. The first method often involves limitations due to changing muscle dynamics and possible signal artefacts that depend on day-to-day variation in the position of electromyographic (EMG) electrodes. Nevertheless, in clinical gait analysis, the method of inverse dynamics is a fundamental and commonly used computational procedure to calculate the force and torque reactions at various body joints. Our aim was to develop a generic musculoskeletal model that could be able to be applied in the clinical setting. The musculoskeletal model of the lower limb presents a simulation for the EMG data to address the common limitations of these techniques. This model presents a new point of view from the inverse dynamics used on clinical gait analysis, including the EMG information, and shows a similar performance to another model available in the OpenSim software. The main problem of these methods to achieve a correct muscle coordination is the lack of complete EMG data for all muscles modelled. We present a technique that simulates the EMG activity and presents a good correlation with the muscle forces throughout the gait cycle. Also, this method showed great similarities whit the real EMG data recorded from the subjects doing the same movement.     

Connexins and their channels in inflammation

Inflammation may be caused by a variety of factors and is a hallmark of a plethora of acute and chronic diseases. The purpose of inflammation is to eliminate the initial cell injury trigger, to clear out dead cells from damaged tissue and to initiate tissue regeneration. Despite the wealth of knowledge regarding the involvement of cellular communication in inflammation, studies on the role of connexin-based channels in this process have only begun to emerge in the last few years. In this paper, a state-of-the-art overview of the effects of inflammation on connexin signaling is provided. Vice versa, the involvement of connexins and their channels in inflammation will be discussed by relying on studies that use a variety of experimental tools, such as genetically modified animals, small interfering RNA and connexin-based channel blockers. A better understanding of the importance of connexin signaling in inflammation may open up towards clinical perspectives.