Skeletal Muscle for Endomyocardial Biopsy: Comparable Stress Response in Doxorubicin Cardio-myopathy

In the present study, we compared the cell damage response in skeletal and cardiac muscle tissue when exposed to doxorubicin. This was carried out by means of a less invasive informative substitute to endomyocardiac biopsy based on Hsp70 immunodetection and a subcellular analysis of the nucleolus. Male Sprague Dawley rats (62 g body weight) were randomly distributed into 3 group, the control and doxorubicin I and doxorubicin II groups, in which 15 and 25 mg/kg body weight of doxorubicin (0.1 ml, i.v.) was administered, respectively. After 15, 30, 45 and 60 minutes, portions of the left and right ventricle wall and interventricle wall, together with skeletal muscle from the posterior and anterior member, were prepared for Hsp70 immunodetection by Western blot analysis and ultrastructural study using the thin cut technique. Differential cell response between the control and treated groups was observed in Hsp70 immunodetection and at the subcellular level. In the control group, the Hsp70 recognition levels and typical normal nucleolar morphology were similar, while the treated groups showed variable-dependent Hsp70 recognition and segregation of nucleolar components, forming ring-like figures of a variable-independent nature. Comparison of cardiac and skeletal muscle tissue cell response to doxorubicin toxic aggression revealed parallelism in terms of Hsp70 accumulation in certain regions of both tissues (15 mg/kg body weight of doxorubicin), which suggests that replacing endomyocardiac biopsy analysis with skeletal muscle analysis may be a safe option

Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids

A series of thiophene-2-carboxylic acids and thiophene-3-carboxylic acids were identified as a new class of DAO inhibitors. Structure-activity relationship (SAR) studies revealed that small substituents are well-tolerated on the thiophene ring of both the 2-carboxylic acid and 3-carboxylic acid scaffolds. Crystal structures of human DAO in complex with potent thiophene carboxylic acids revealed that Tyr224 was tightly stacked with the thiophene ring of the inhibitors, resulting in the disappearance of the secondary pocket observed with other DAO inhibitors. Molecular dynamics simulations of the complex revealed that Tyr224 preferred the stacked conformation irrespective of whether Tyr224 was stacked or not in the initial state of the simulations. MM/GBSA indicated a substantial hydrophobic interaction between Tyr244 and the thiophene-based inhibitor. In addition, the active site was tightly closed with an extensive network of hydrogen bonds including those from Tyr224 in the stacked conformation. The introduction of a large branched side chain to the thiophene ring markedly decreased potency. These results are in marked contrast to other DAO inhibitors that can gain potency with a branched side chain extending to the secondary pocket due to Tyr224 repositioning. These insights should be of particular importance in future efforts to optimize DAO inhibitors with novel scaffolds

Thermal expansion, heat capacity and magnetostriction of RAl3_3 (R = Tm, Yb, Lu) single crystals

We present thermal expansion and longitudinal magnetostriction data for cubic RAl3 (R = Tm, Yb, Lu) single crystals. The thermal expansion coefficient for YbAl3 is consistent with an intermediate valence of the Yb ion, whereas the data for TmAl3 show crystal electric field contributions and have strong magnetic field dependencies. de Haas-van Alphen-like oscillations were observed in the magnetostriction data of YbAl3 and LuAl3, several new extreme orbits were measured and their effective masses were estimated. Zero and 140 kOe specific heat data taken on both LuAl3 and TmAl3 for T < 200 K allow for the determination of a CEF splitting scheme for TmAl3

Percutaneous Trans-Thoracic Procedures in Children With Tumors of Thoracic Wall, Mediastinum and Lung. The Experience of a Single Institution

Background While percutaneous trans-thoracic procedures (PTTP) are commonly performed in adults with tumors of thoracic wall, mediastinum and lung, the experience is limited in children, in whom however less invasive methods should be the choice for the diagnosis or the identification of small pulmonary nodules that need to be removed, sparing lung tissue. The results of the PTTP performed by the interventional radiologists in our Pediatric Surgery Department are analyzed. Methods CT-guided biopsies, utilizing a 64-slice CTscanner, with low-radiation dose, were performed applying the coaxial technique with 16-18G needles with a single tissue path. For localization of lung nodules before surgery, two 20G-hook wires were positioned beyond the nodule. CT images after each manipulation of the needles were obtained. US-guided biopsies were performed either with or without coaxial technique through a needle bracket. Younger patients required sedation. All patients underwent a chest radiogram two hours after the procedure and remained under observation for 24 hours. Results From January 2015 to March 2019, 23 procedures were performed in 22 patients (Age:16M- 19Y): 6 patients underwent CT-guided biopsy (4 lung nodules, 2 mediastinal mass); 3 underwent 4 CT-guided hook-wire localization of pulmonary nodules, just before surgery; 13 underwent US-guided biopsy (posterior mediastinum 2; anterior mediastinum 5, thoracic/intrathoracic mass 5). Adequate core biopsies were obtained in all patients, except three, who underwent thoracoscopy/thoracotomy. The hook-wires were successfully positioned in all cases, as confirmed by histology. After the procedure, two patients presented perilesional hemorrhage and one pneumothorax, but they did not required treatment. Conclusion PTTP were successful in most patients, without significant complications. These techniques should be encouraged to avoid diagnostic aggressive surgical approaches in children with cancer. For all cases a multidisciplinary team is essential to discuss the indications and planning the procedures

Re-evaluating the resource potential of lomas fog oasis environments for Preceramic hunter-gatherers under past ENSO modes on the south coast of Peru

Lomas – ephemeral seasonal oases sustained by ocean fogs – were critical to ancient human ecology on the desert Pacific coast of Peru: one of humanity’s few independent hearths of agriculture and “pristine” civilisation. The role of climate change since the Late Pleistocene in determining productivity and extent of past lomas ecosystems has been much debated. Here we reassess the resource potential of the poorly studied lomas of the south coast of Peru during the long Middle Pre-ceramic period (c. 8,000 – 4,500 BP): a period critical in the transition to agriculture, the onset of modern El Niño Southern Oscillation (‘ENSO’) conditions, and eustatic sea-level rise and stabilisation and beach progradation. Our method combines vegetation survey and herbarium collection with archaeological survey and excavation to make inferences about both Preceramic hunter-gatherer ecology and the changed palaeoenvironments in which it took place. Our analysis of newly discovered archaeological sites – and their resource context – show how lomas formations defined human ecology until the end of the Middle Preceramic Period, thereby corroborating recent reconstructions of ENSO history based on other data. Together, these suggest that a five millennia period of significantly colder seas on the south coast induced conditions of abundance and seasonal predictability in lomas and maritime ecosystems, that enabled Middle Preceramic hunter-gatherers to reduce mobility by settling in strategic locations at the confluence of multiple eco-zones at the river estuaries. Here the foundations of agriculture lay in a Broad Spectrum Revolution that unfolded, not through population pressure in deteriorating environments, but rather as an outcome of resource abundance.We thank the Ministerio de Cultural del Perú for granting permission for archaeological fieldwork (Resolución Directoral Nº 933-2012-DGPC-VMPCIC/MC, 19 December 2012 and Nº 386-2014-DGPA-VMPCIC/MC, 22 August 2014) and the export of samples for dating; Don Alberto Benavides Ganoza and the people of Samaca for facilitating fieldwork; the Leverhulme Trust (grant number RPG-117) and the late Don Alberto Benavides de la Quintana (grant number RG69428) and the McDonald Institute for Archaeological Research for funding Cambridge University’s One River Archaeological Project, and the NERC Radiocarbon facility (grant number NF/2013/2/2) for funding radiocarbon dating. We also thank the Servicio Nacional Forestal y de Fauna Silvestre (SERFOR) and the Servicio Nacional de Áreas Naturales Protegidas por el Estado (SERNANP), Peru for permits for the Proyecto Kew Perú to carry out botanical and ecological survey, and Delsy Trujillo, Eric Ramírez, Consuelo Borda and other participants of the Proyecto Kew Perú: Conservación, Restauración de Hábitats y Medios de Vida Útiles, Ica, Peru.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.quascirev.2015.10.02

ATP-Dependent Unwinding of U4/U6 snRNAs by the Brr2 Helicase Requires the C Terminus of Prp8

The spliceosome is a highly dynamic machine requiring multiple RNA-dependent ATPases of the DExD/H-box family. A fundamental unanswered question is how their activities are regulated. Brr2 function is necessary for unwinding the U4/U6 duplex, a step essential for catalytic activation of the spliceosome. Here we show that Brr2-dependent dissociation of U4/U6 snRNAs in vitro is activated by a fragment from the C terminus of the U5 snRNP protein Prp8. In contrast to its helicase-stimulating activity, this fragment inhibits Brr2 U4/U6-dependent ATPase activity. Notably, U4/U6 unwinding activity is not stimulated by fragments carrying alleles of prp8 that in humans confers an autosomal dominant form of retinitis pigmentosa. Because Brr2 activity must be restricted to prevent premature catalytic activation, our results have important implications for fidelity maintenance in the spliceosome

Temporal and Tissue Specific Regulation of RP-Associated Splicing Factor Genes PRPF3, PRPF31 and PRPC8—Implications in the Pathogenesis of RP

Genetic mutations in several ubiquitously expressed RNA splicing genes such as PRPF3, PRP31 and PRPC8, have been found to cause retina-specific diseases in humans. To understand this intriguing phenomenon, most studies have been focused on testing two major hypotheses. One hypothesis assumes that these mutations interrupt retina-specific interactions that are important for RNA splicing, implying that there are specific components in the retina interacting with these splicing factors. The second hypothesis suggests that these mutations have only a mild effect on the protein function and thus affect only the metabolically highly active cells such as retinal photoreceptors.We examined the second hypothesis using the PRPF3 gene as an example. We analyzed the spatial and temporal expression of the PRPF3 gene in mice and found that it is highly expressed in retinal cells relative to other tissues and its expression is developmentally regulated. In addition, we also found that PRP31 and PRPC8 as well as snRNAs are highly expressed in retinal cells.Our data suggest that the retina requires a relatively high level of RNA splicing activity for optimal tissue-specific physiological function. Because the RP18 mutation has neither a debilitating nor acute effect on protein function, we suggest that retinal degeneration is the accumulative effect of decades of suboptimal RNA splicing due to the mildly impaired protein

Exploiting protein flexibility to predict the location of allosteric sites

Background: Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results: By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity), by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing that this simple coarse-grained methodology is able to capture the effects triggered by allosteric ligands already described in the literature. Conclusions: We introduce a simple computational approach to predict the presence and position of allosteric sites in a protein based on the analysis of changes in protein normal modes upon the binding of a coarse-grained ligand at predicted cavities. Its performance has been demonstrated using a newly curated non-redundant set of 91 proteins with reported allosteric properties. The software developed in this work is available upon request from the authors