The human gene SLC25A29, of solute carrier family 25, encodes a mitochondrial transporter of basic amino acids

The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport carboxylates, amino acids, nucleotides, and cofactors across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. In this work, a member of this family, SLC25A29, previously reported to be a mitochondrial carnitine/acylcarnitine- or ornithine-like carrier, has been thoroughly characterized biochemically. The SLC25A29 gene was overexpressed in Escherichia coli, and the gene product was purified and reconstituted in phospholipid vesicles. Its transport properties and kinetic parameters demonstrate that SLC25A29 transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Carnitine and acylcarnitines were not transported by SLC25A29. This carrier catalyzed substantial uniport besides a counter-exchange transport, exhibited a high transport affinity for arginine and lysine, and was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation

Potential predictive role of chemotherapy-induced changes of soluble CD40 ligand in untreated advanced pancreatic ductal adenocarcinoma

Pancreas ductal adenocarcinoma lacks predictive biomarkers. CD40 is a member of the tumor necrosis factor superfamily. CD40-sCD40L interaction is considered to contribute to the promotion of tumor cell growth and angiogenesis. The aim of the present study was to investigate the role of serum sCD40L as a predictor in metastatic pancreatic cancer. We evaluated 27 consecutive pancreatic cancer patients treated with FOLFIRINOX (21 patients) or gemcitabine plus nab-paclitaxel combination (six patients). The sCD40L level was measured in serum by enzyme-linked immunosorbent assay at baseline, at first evaluation (all patients), and at time to progression (18 patients). The radiological response was evaluated according to the Response Evaluation Criteria in Solid Tumors, Version 1.1. The Wilcoxon signed-rank test was used to compare pre-post treatment sCD40L levels with respect to clinical response, while Pearson's correlation coefficient was used for the correlation between sCD40L and CA19.9 pre- and post-treatment. The Kruskal-Wallis test was also conducted for further comparisons. We observed a statistically significant reduction in the sCD40L level after 3 months of treatment in patients with partial response (11,718.05\ub17,097.13 pg/mL vs 4,689.42\ub15,409.96 pg/mL; P<0.01). Conversely, in patients with progressive disease, the biomarker statistically increased in the same time (9,351.51\ub17,356.91 pg/mL vs 22,282.92\ub111,629.35 pg/mL; P<0.01). This trend of sCD40L was confirmed in 18 patients at time to progression after the first evaluation. No differences were recorded within the stable disease group. Moreover, there was a positive correlation between the sCD40L and CA19.9 pre-post treatment variation percentage (Pearson's correlation coefficient =0.52; P<0.05). Our data suggest a possible predictive role of sCD40L in pancreatic cancer patients, similar to CA19.9

Mutations in the Mitochondrial Citrate Carrier SLC25A1 are Associated with Impaired Neuromuscular Transmission.

BACKGROUND AND OBJECTIVE: Congenital myasthenic syndromes are rare inherited disorders characterized by fatigable weakness caused by malfunction of the neuromuscular junction. We performed whole exome sequencing to unravel the genetic aetiology in an English sib pair with clinical features suggestive of congenital myasthenia. METHODS: We used homozygosity mapping and whole exome sequencing to identify the candidate gene variants. Mutant protein expression and function were assessed in vitro and a knockdown zebrafish model was generated to assess neuromuscular junction development. RESULTS: We identified a novel homozygous missense mutation in the SLC25A1 gene, encoding the mitochondrial citrate carrier. Mutant SLC25A1 showed abnormal carrier function. SLC25A1 has recently been linked to a severe, often lethal clinical phenotype. Our patients had a milder phenotype presenting primarily as a neuromuscular (NMJ) junction defect. Of note, a previously reported patient with different compound heterozygous missense mutations of SLC25A1 has since been shown to suffer from a neuromuscular transmission defect. Using knockdown of SLC25A1 expression in zebrafish, we were able to mirror the human disease in terms of variable brain, eye and cardiac involvement. Importantly, we show clear abnormalities in the neuromuscular junction, regardless of the severity of the phenotype. CONCLUSIONS: Based on the axonal outgrowth defects seen in SLC25A1 knockdown zebrafish, we hypothesize that the neuromuscular junction impairment may be related to pre-synaptic nerve terminal abnormalities. Our findings highlight the complex machinery required to ensure efficient neuromuscular function, beyond the proteomes exclusive to the neuromuscular synapse

Increasing contextual information by merging existing archaeological data with the state of the art laser scanning in the prehistoric funerary deposit of Pastora Cave, Eastern Spain

In this paper we present a virtual reconstruction of prehistoric funerary practices in Pastora Cave,a collective burial site in Eastern Spain that dates from the Late Neolithic, Chalcolithic and Bronze Age. Modern data of the cave was captured by 3D laser scanning techniques and added to recorded archaeological data and 3D graphic information. The combination of these data sets allowed us to create a hypothetical reconstruction to analyze the material excavated in the 1940s and 50s in greater spatial context. A 3D model of the current cave was created in order to serve as a basis for modeling the relative stratigraphic information available. We present the methodology employed and the results and implications of the analysis for Pastora Cave with particular emphasis on the spatial and chronological data

Update on the Combined Analysis of Muon Measurements from Nine Air Shower Experiments

Over the last two decades, various experiments have measured muon densities in extensive air showers over several orders of magnitude in primary energy. While some experiments observed differences in the muon densities between simulated and experimentally measured air showers, others reported no discrepancies. We will present an update of the meta-analysis of muon measurements from nine air shower experiments, covering shower energies between a few PeV and tens of EeV and muon threshold energies from a few 100 MeV to about 10GeV. In order to compare measurements from different experiments, their energy scale was cross-calibrated and the experimental data has been compared using a universal reference scale based on air shower simulations. Above 10 PeV, we find a muon excess with respect to simulations for all hadronic interaction models, which is increasing with shower energy. For EPOS-LHC and QGSJet-II.04 the significance of the slope of the increase is analyzed in detail under different assumptions of the individual experimental uncertainties

Search for Spatial Correlations of Neutrinos with Ultra-high-energy Cosmic Rays

For several decades, the origin of ultra-high-energy cosmic rays (UHECRs) has been an unsolved question of high-energy astrophysics. One approach for solving this puzzle is to correlate UHECRs with high-energy neutrinos, since neutrinos are a direct probe of hadronic interactions of cosmic rays and are not deflected by magnetic fields. In this paper, we present three different approaches for correlating the arrival directions of neutrinos with the arrival directions of UHECRs. The neutrino data are provided by the IceCube Neutrino Observatory and ANTARES, while the UHECR data with energies above ∼50 EeV are provided by the Pierre Auger Observatory and the Telescope Array. All experiments provide increased statistics and improved reconstructions with respect to our previous results reported in 2015. The first analysis uses a high-statistics neutrino sample optimized for point-source searches to search for excesses of neutrino clustering in the vicinity of UHECR directions. The second analysis searches for an excess of UHECRs in the direction of the highest-energy neutrinos. The third analysis searches for an excess of pairs of UHECRs and highest-energy neutrinos on different angular scales. None of the analyses have found a significant excess, and previously reported overfluctuations are reduced in significance. Based on these results, we further constrain the neutrino flux spatially correlated with UHECRs

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The mitochondrial aspartate/glutamate carrier AGC1 and calcium homeostasis: Physiological links and abnormalities in autism

Autism spectrum disorder (ASD) is a severe, complex neurodevelopmental disorder characterized by impairments in reciprocal social interaction and communication, and restricted and stereotyped patterns of interests and behaviors. Recent evidence has unveiled an important role for calcium (Ca2+) signaling in the pathogenesis of ASD. Postmortem studies of autistic brains have pointed toward abnormalities in mitochondrial function as possible downstream consequences of altered Ca2+ signaling, abnormal synapse formation, and dysreactive immunity. SLC25A12, an ASD susceptibility gene, encodes the Ca2+-regulated mitochondrial aspartate–glutamate carrier, isoform 1 (AGC1). AGC1 is an important component of the malate/aspartate shuttle, a crucial system supporting oxidative phosphorylation and adenosine triphosphate (ATP) production. Here, we review the physiological roles of AGC1, its links to calcium homeostasis, and its involvement in autism pathogenesis

Mitochondrial Carriers for Aspartate, Glutamate and Other Amino Acids: A Review

Members of the mitochondrial carrier (MC) protein family transport various molecules across the mitochondrial inner membrane to interlink steps of metabolic pathways and biochemical processes that take place in different compartments; i.e., are localized partly inside and outside the mitochondrial matrix. MC substrates consist of metabolites, inorganic anions (such as phosphate and sulfate), nucleotides, cofactors and amino acids. These compounds have been identified by in vitro transport assays based on the uptake of radioactively labeled substrates into liposomes reconstituted with recombinant purified MCs. By using this approach, 18 human, plant and yeast MCs for amino acids have been characterized and shown to transport aspartate, glutamate, ornithine, arginine, lysine, histidine, citrulline and glycine with varying substrate specificities, kinetics, influences of the pH gradient, and capacities for the antiport and uniport mode of transport. Aside from providing amino acids for mitochondrial translation, the transport reactions catalyzed by these MCs are crucial in energy, nitrogen, nucleotide and amino acid metabolism. In this review we dissect the transport properties, phylogeny, regulation and expression levels in different tissues of MCs for amino acids, and summarize the main structural aspects known until now about MCs. The effects of their disease-causing mutations and manipulation of their expression levels in cells are also considered as clues for understanding their physiological functions

Role of mitochondria in the regulation of apoptosis and autophagy: molecular mechanisms and effects of pathogenic mutations\u201d.

L'apoptosi \ue8 un meccanismo di morte cellulare che pu\uf2 esplicarsi mediante vie diverse che convergono a livello dei mitocondri. Alterazioni delle vie apoptotiche sono associate a numerose malattie tra cui il cancro. La crescita tumorale \ue8 un processo molto complesso che coinvolge alterazioni nelle vie di segnalazione che inducono l'attivazione della proliferazione e/o l'inibizione della morte cellulare. Questo progetto si propone di studiare la regolazione dell'apoptosi in modelli cellulari di due differenti tumori, gli oncocitomi della tiroide, caratterizzati da iperplasia mitocondriale, e tumori midollari della tiroide, causati da alterazioni funzionali del proto-oncogene RET. Recentemente, il nostro gruppo di ricerca ha riportato una significativa frequenza di mutazioni "disruptive" nei geni mitocondriali che codificano alcune subunit\ue0 del complesso I nei tumori oncocitici. Negli stessi tumori, abbiamo identificato anche mutazioni nei geni nucleari che codificano altre subunit\ue0 dello stesso complesso respiratorio, che potrebbe quindi rappresentare un "hotspot" di potenziali mutazioni patogene. Tuttavia, non \ue8 ancora stato chiarito se e come queste mutazioni contribuiscano allo sviluppo del tumore. Il primo scopo di questo progetto \ue8 dimostrare che la mancanza del complesso I promuove la tumorigenesi e che la crescita tumorale \ue8 associata all'inibizione dell'apoptosi, come suggerito da nostri esperimenti preliminari. Inoltre, intendiamo analizzare quali meccanismi molecolari sono coinvolti nella resistenza all'apoptosi. A questo proposito, \ue8 possibile che il difetto nel complesso I attivi la biogenesi mitocondriale come risposta al deficit energetico, favorendo la proliferazione cellulare. Per verificare questa ipotesi analizzeremo il coinvolgimento di vari regolatori della biogenesi mitocondriale, focalizzando la nostra attenzione su PGC1-a. Come ipotesi alternativa, \ue8 possibile che la disfunzione energetica mitocondriale causi una riduzione del contenuto intracellulare di calcio, che \ue8 stata associata con la resistenza all'apoptosi. L'omeostasi del calcio intracellulare sar\ue0 studiata in collaborazione con l'Unit\ue0 1, utilizzando proteine ricombinanti indirizzate ai diversi depositi di calcio intracellulari. Le disfunzioni mitocondriali potrebbero anche indurre l'attivazione del processo autofagico, che \ue8 noto essere utilizzato dalle cellule tumorali per la sopravvivenza. Si valuter\ue0 pertanto il coinvolgimento di tale processo. L'altro tumore di cui ci occupiamo \ue8 quello midollare della tiroide, caratterizzato da mutazioni nel proto-oncogene RET, un recettore tirosin-chinasico che appartiene alla famiglia dei "dependence receptors". Tali recettori possono generare segnali intracellulari opposti. In presenza del ligando, attivano la sopravvivenza, il differenziamento e la migrazione cellulare, mentre in sua assenza, innescano il processo apoptotico. Infatti, in assenza del ligando GDNF e dei fattori di crescita correlati, RET viene tagliato producendo un frammento intracellulare pro-apoptotico. I meccanismi che inducono la morte cellulare in presenza del frammento di RET sono poco noti. Intendiamo pertanto, analizzare l'effetto di tale frammento sulla funzione energetica mitocondriale. Inoltre, valuteremo se RET trasloca sui mitocondri e se interagisce con proteine della membrana esterna. In particolare, in collaborazione con l'Unit\ue0 2, si determiner\ue0 la sua interazione con VDAC-2 e il suo coinvolgimento nel processo di morte. Dato che il frammento pro-apoptotico di RET si lega ad AIP, che a sua volta interagisce con Tom20, un'altra proteina della membrana esterna, si indagher\ue0 il ruolo funzionale di questa interazione sul processo apoptotico. Infine, \ue8 stato riportato che il taglio di RET \ue8 accompagnato da un aumento dei livelli proteici di p53. Analizzeremo se l'aumento di questa proteina \ue8 associato alla sua traslocazione sui mitocondri e ad un suo coinvolgimento nella morte cellulare