Tertiary lymphoid structures and B cells determine clinically relevant T cell phenotypes in ovarian cancer.

Intratumoral tertiary lymphoid structures (TLSs) have been associated with improved outcome in various cohorts of patients with cancer, reflecting their contribution to the development of tumor-targeting immunity. Here, we demonstrate that high-grade serous ovarian carcinoma (HGSOC) contains distinct immune aggregates with varying degrees of organization and maturation. Specifically, mature TLSs (mTLS) as forming only in 16% of HGSOCs with relatively elevated tumor mutational burden (TMB) are associated with an increased intratumoral density of CD8+ effector T (TEFF) cells and TIM3+PD1+, hence poorly immune checkpoint inhibitor (ICI)-sensitive, CD8+ T cells. Conversely, CD8+ T cells from immunologically hot tumors like non-small cell lung carcinoma (NSCLC) are enriched in ICI-responsive TCF1+ PD1+ T cells. Spatial B-cell profiling identifies patterns of in situ maturation and differentiation associated with mTLSs. Moreover, B-cell depletion promotes signs of a dysfunctional CD8+ T cell compartment among tumor-infiltrating lymphocytes from freshly isolated HGSOC and NSCLC biopsies. Taken together, our data demonstrate that - at odds with NSCLC - HGSOC is associated with a low density of follicular helper T cells and thus develops a limited number of mTLS that might be insufficient to preserve a ICI-sensitive TCF1+PD1+ CD8+ T cell phenotype. These findings point to key quantitative and qualitative differences between mTLSs in ICI-responsive vs ICI-irresponsive neoplasms that may guide the development of alternative immunotherapies for patients with HGSOC.

Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction.

While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for molecular residual disease (MRD) detection, its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read level, achieving an error rate of 4.2×10 -7 , which is about two orders of magnitude lower than a read-centric de-noising method. When applied to MRD detection, AccuScan demonstrated analytical sensitivity down to 10 -6 circulating tumor allele fraction at 99% sample level specificity. In colorectal cancer, AccuScan showed 90% landmark sensitivity for predicting relapse. It also showed robust MRD performance with esophageal cancer using samples collected as early as 1 week after surgery, and predictive value for immunotherapy monitoring with melanoma patients. Overall, AccuScan provides a highly accurate WGS solution for MRD, empowering circulating tumor DNA detection at parts per million range without high sample input nor personalized reagents. One Sentence Summary: AccuScan showed remarkable ultra-low limit of detection with a short turnaround time, low sample requirement and a simple workflow for MRD detection.

Investigation of the thermal and physicochemical behavior of two types of gutta-percha cones for back-filling the root canal.

Background: Gutta-percha (Gp) is an inert thermoplastic polymer used as a filling to replace the dental pulp space, which has been reformulated to improve its three-dimensional sealing properties. Therefore, this study aimed to analyze the physical, chemical and thermal properties of two types of gutta-percha filling. As well as measuring the temperature distribution along the cone at the time of cutting through an in-situ test. Material and Methods: Two commercially available brands of gutta-percha point were investigated: Conform Fit TM Gutta-Percha for ProTaper Gold® (PTG) (Dentsply Sirona), and Hygenic Gutta-Percha (Coltene whaledent). Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were selected for the thermal characterization of materials, and Fourier Transform Infrared Spectroscopy (FT-IR) for the chemical analysis of Gp cones. Regarding temperature distribution, it was evaluated using a thermographic camera (FLIR ONE® PRO by MicroUSB P/N 435-0011-01) at 0 to 20 s after the cutting process (n=11/group). Results: Both materials have three fusion endotherms associated with the three crystalline phases of Gp, with similar temperatures but enthalpies that differ by 60%, the fusion enthalpy being higher for Conform Fit. In the chemical characterization, elements such as Zn, C, O, Ba, S and Si were found in both materials but in different proportions. Regarding the content of fillers, the Conform Fit presented around 30% of Gp polymer and 25% for the Hygenic. The morphological characterization shows a microtexturized coating in the form of bars on a micrometric scale for the Conform Fit, which could favor a better three-dimensional seal. In addition to that, in heat transfer studies they showed greater temperature control. Conclusions: The characterization of the materials allowed us to see the variation in terms of their composition and configuration to the Gp cones of two commercial brands. These variations directly modify the thermal behavior of the material. Key words:Gutta-percha, Conform Fit, Infrared thermography, Differential Scanning Calorimetry, Infrared Spectroscopy.

Scalable detection of technically challenging variants through modified next-generation sequencing.

BACKGROUND: Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions). METHODS: We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes. RESULTS: Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats. CONCLUSIONS: NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.

Characterizing storm-induced coastal change hazards along the United States West Coast.

Traditional methods to assess the probability of storm-induced erosion and flooding from extreme water levels have limited use along the U.S. West Coast where swell dominates erosion and storm surge is limited. This effort presents methodology to assess the probability of erosion and flooding for the U.S. West Coast from extreme total water levels (TWLs), but the approach is applicable to coastal settings worldwide. TWLs were derived from 61 years of wave and water level data at shore-perpendicular transects every 100-m along open coast shorelines. At each location, wave data from the Global Ocean Waves model were downscaled to the nearshore and used to empirically calculate wave run-up. Tides were simulated using the Oregon State University's tidal data inversion model and non-tidal residuals were calculated from sea-surface temperature and pressure anomalies. Wave run-up was combined with still water levels to generate hourly TWL estimates and extreme TWLs for multiple return periods. Extremes were compared to onshore morphology to determine erosion hazards and define the probability of collision, overwash, and inundation.

Proteomic analysis of an Enterococcus faecalis mutant generated against the exposure to silver nanoparticles.

INTRODUCTION: Nanoparticles (NPs) have been widely studied as an alternative to antibiotic use due to their antimicrobial properties at lower concentrations. Enterococcus faecalis is a facultative Gram-positive microorganism inhabiting the gastrointestinal tract of humans and animals. It can also be present in other environments such as the oral cavity, water, sewage, soil and food. AIMS: We evaluated whether E. faecalis could develop resistance to silver NPs (AgNPs) after exposure to sublethal concentrations of the NPs. METHODS AND RESULTS: Proteomic analyses revealed that different pathways were activated during the acquired resistance under sublethal concentrations, and selected genes were validated by qPCR. CONCLUSIONS: The results of this study showed that E. faecalis is capable of generating resistance to AgNPs. SIGNIFICANCE AND IMPACT OF THE STUDY: To avoid the generation of resistance against AgNPs, future use of these NPs should be combined with other NPs prepared with different metals to prevent the dissemination of resistant strains.

Type I Interferon acts as a major barrier to the establishment of infectious bursal disease virus (IBDV) persistent infections.

Infectious bursal disease virus (IBDV), the best characterized member of the Birnaviridae family, is a highly relevant avian pathogen causing both acute and persistent infections in different avian hosts. Here, we describe the establishment of clonal, long-term, productive persistent IBDV infections in DF-1 chicken embryonic fibroblasts. Although virus yields in persistently-infected cells are exceedingly lower than those detected in acutely infected cells, the replication fitness of viruses isolated from persistently-infected cells is higher than that of the parental virus. Persistently-infected DF-1 and IBDV-cured cell lines derived from them do not respond to type I interferon (IFN). High-throughput genome sequencing revealed that this defect is due to mutations affecting the IFNα/ß receptor subunit 2 (IFNAR2) gene resulting in the expression of IFNAR2 polypeptides harbouring large C-terminal deletions that abolish the signalling capacity of IFNα/ß receptor complex. Ectopic expression of a recombinant chicken IFNAR2 gene efficiently rescues IFNα responsiveness. IBDV-cured cell lines derived from persistently infected cells exhibit a drastically enhanced susceptibility to establishing new persistent IBDV infections. Additionally, experiments carried out with human HeLa cells lacking the IFNAR2 gene fully recapitulate results obtained with DF-1 cells, exhibiting a highly enhanced capacity to both survive the acute IBDV infection phase and to support the establishment of persistent IBDV infections. Results presented here show that the inactivation of the JAK-STAT signalling pathway significantly reduces the apoptotic response induced by the infection, hence facilitating the establishment and maintenance of IBDV persistent infections.IMPORTANCE Members of the Birnaviridae family, including infectious bursal disease virus (IBDV), exhibit a dual behaviour, causing acute infections that are often followed by the establishment of life-long persistent asymptomatic infections. Indeed, persistently infected specimens might act as efficient virus reservoirs, hence potentially contributing to virus dissemination. Despite the key importance of this biological trait, information about mechanisms triggering IBDV persistency is negligible. Our report evidences the capacity of IBDV, a highly relevant avian pathogen, to establishing long-term, productive, persistent infections in both avian and human cell lines. Data presented here provide novel and direct evidence about the crucial role of type I IFNs on the fate of IBDV-infected cells and their contribution to controlling the establishment of IBDV persistent infections. The use of cell lines unable to respond to type I IFNs opens a promising venue to unveiling additional factors contributing to IBDV persistency.

Biopsy of lung lesions under CT control.

OBJECTIVES: With the increasing number of detected lung nodules and the need for morphological verification, the number of CT- controlled biopsies is increasing. The aim of this study was to assess the risks and benefits of these biopsies. METHODS: This is a prospective and observational study. We evaluated 101 punctures performed on a group of 90 consecutive patients in the Department of Radiology. RESULTS: In patients with a mean age of 66 years, with mostly accidentally detected lung nodules, we observed complications 38 times. The most common were minor pneumothoraxes or insignificant bleedings. In 6 patients, the complications were more serious, 5 times the pneumothoraxes required chest drainage, once massive hemoptysis was recorded. The lesions were successfully biopsied 78 times, the target was missed 23 times. The diagnosis of lung cancer (LC) was confirmed in 60 patients, 49 LCs were verified by puncture under CT control. 42% (25/60) of patients with LC were diagnosed in TNM stages I and II. 23% (14/60) of patients with LC were treated surgically. The remaining 30 patients most often suffered from lung metastazes (13/30), in 8 of them an inflammatory lung disease was diagnosed. 69 patients underwent bronchoscopy, in only 19% (13/69) it contributed to the diagnosis. In a model "screening like" group of 49 patients with only randomly detected lung deposits, we diagnosed LC in 76% (37/49). 49% (18/37) were in TNM stage I and II, 11 were treated surgically. CONCLUSIONS: CT-controlled biopsy of lung lesions is an effective and safe diagnostic method.

Macrophage migration inhibitory factor gene polymorphisms as exacerbating factors of apical periodontitis.

BACKGROUND: Two polymorphisms in the macrophage migration inhibitory factor (MIF) gene have been associated with inflammatory diseases (-794 CATT5-8 and -173G>C); however, so far there are no reports of studies related to oral health. OBJECTIVES: To genotype the -794 CATT5-8 and -173G>C MIF polymorphisms in Mexican patients with apical periodontitis as a genetic risk of exacerbation. MATERIAL AND METHODS: The study involved 120 patients with apical periodontitis: 60 with a diagnosis of acute apical periodontitis (Group A) and 60 without previous episodes of exacerbation (Group B). Allelic discrimination was performed from peripheral blood DNA; the repeat polymorphism -794 CATT5-8 was genotyped with sequencing, while the -173G>C polymorphism was determined using real-time polymerase chain reaction (RT-PCR) using TaqMan probes. The associations between MIF polymorphisms, haplotypes and the risk of exacerbated apical periodontitis were assessed. RESULTS: The allele CATT7 was associated with the risk of a stage of acute inflammation (OR = 4.13; 95% CI = 1.82-9.63; p =< 0.001). Regarding the -173G >C polymorphism, a process of inflammation exacerbation was only associated with the CC genotype (OR = 4.1; 95% CI = 1.02-20.84; p = 0.045). The analysis of the haplotype showed that the combination CATT7/C increases the risk of exacerbation of apical periodontitis (OR = 3.57; 95% CI = 1.038-13.300; p = 0.021). CONCLUSIONS: The polymorphisms -794 CATT5-8 and -173G>C MIF seem to significantly influence the development of a state of exacerbated inflammation in patients with apical periodontitis.

Blind testing of shoreline evolution models.

Beaches around the world continuously adjust to daily and seasonal changes in wave and tide conditions, which are themselves changing over longer time-scales. Different approaches to predict multi-year shoreline evolution have been implemented; however, robust and reliable predictions of shoreline evolution are still problematic even in short-term scenarios (shorter than decadal). Here we show results of a modelling competition, where 19 numerical models (a mix of established shoreline models and machine learning techniques) were tested using data collected for Tairua beach, New Zealand with 18 years of daily averaged alongshore shoreline position and beach rotation (orientation) data obtained from a camera system. In general, traditional shoreline models and machine learning techniques were able to reproduce shoreline changes during the calibration period (1999-2014) for normal conditions but some of the model struggled to predict extreme and fast oscillations. During the forecast period (unseen data, 2014-2017), both approaches showed a decrease in models' capability to predict the shoreline position. This was more evident for some of the machine learning algorithms. A model ensemble performed better than individual models and enables assessment of uncertainties in model architecture. Research-coordinated approaches (e.g., modelling competitions) can fuel advances in predictive capabilities and provide a forum for the discussion about the advantages/disadvantages of available models.

Bacterial Percolation and Sealer Tubular Penetration in a Polymer-based Obturation System Compared with Warm Vertical Condensation Technique: An in Vitro Study.

Introduction: This study compared bacterial percolation and sealer penetration of a novel obturation technique with the ones of warm vertical condensation technique. Methods and Materials: A bacterial percolation test was carried out with 80 single rooted human teeth divided into 5 groups; A (n=20): warm vertical condensation and AH-Plus, B (n=20): CPoint with AH-Plus, C (n= 20): CPoint with EndoSequence BC, +ve Control (n=10): teeth with no canal obturation, -ve Control (n=10): teeth with no access cavity. The samples were inoculated with a multispecies bacterial incoulum. Bacterial percolation was evaluated by turbidity. Confocal laser scanning microscopy (CLSM) was used to observe the presence of gaps and voids. Further 48 extracted human mandibular single-canal premolars were used to determine the sealer penetration. Slices of the samples were observed by CLSM to evaluate tubules penetration of the sealer. Kaplan Meyer survival, ANOVA one way and Tuckey HSD test and a Wilcoxon signed-rank test were utilised. Results: A Kaplan-Meier test showed no significant difference overall (P>0.05) between groups A, B and C. At 43 days, the group B showed a significantly inferior ability to prevent bacterial passage (P<0.05). The group C showed a deeper sealer penetration than group A and B with statistically significant differences (P<0.05) for the total penetration (ANOVA one way and Tukey HSD). A Wilcoxon signed-rank test showed statistically significant differences for the penetration in the middle-and apical third of the 3 groups. Conclusion: Based on this in vitro study, the single polymer-cone obturation technique with a resin based- and bioceramic based-sealer behaved similarly to the warm vertical obturation technique in preventing bacterial passage. The bioceramic sealer showed the deepest penetration but did not fully prevent bacterial leakage.

Antimicrobial activity of endodontic sealers and medications containing chitosan and silver nanoparticles against Enterococcus faecalis.

BACKGROUND: The main microorganism associated with the failure of endodontic treatments is Enterococcus faecalis. Although several endodontic therapeutics have demonstrated antimicrobial activity against E. faecalis, the antimicrobial effectiveness of chitosan (CsNPs) and silver nanoparticles (AgNPs) included into conventional endodontic sealers for endodontic therapies is still unclear. AIM: The objective of this study was to evaluate the antibacterial activity increment (AAI) of endodontic sealers containing CsNPs and AgNPs as well as some chemical components against E. faecalis by direct contact assays. METHODS: CsNPs and AgNPs were synthesized by reduction and ionic gelation methods, respectively. Nanoparticles were characterized by dynamic light scattering and energy dispersive X-ray analysis. The bactericidal activity was tested on monolayers on agar plates and collagen membrane surface assays against E. faecalis. RESULTS: The size of CsNPs was 70.6±14.8 nm and zeta potential was 52.0±5.4 mV; the size of AgNPs was 54.2±8.5 nm, and zeta potential was -48.4±6.9 mV. All materials, single or combined, showed an AAI, especially when CsNPs, chlorhexidine (Chx), and the combination of CsNPs-Chx were added. However, the combination of CsNPs-Chx showed the highest (55%) AAI, followed by Chx (35.5%) and CsNPs (11.1%), respectively. There was a significant statistical difference in all comparisons (p < 0.05). Tubliseal (40%) and AH Plus (32%) sealants showed a higher AAI on E. faecalis in the monolayer test and collagen membrane assay analyzed by scanning electron microscopy. CONCLUSIONS: Tubliseal and AH plus sealers combined with nanoparticles, especially CsNPs-Chx, could be used for conventional endodontic treatments in the control of E. faecalis bacteria.

Molecular Mechanisms of Bacterial Resistance to Metal and Metal Oxide Nanoparticles.

The increase in bacterial resistance to one or several antibiotics has become a global health problem. Recently, nanomaterials have become a tool against multidrug-resistant bacteria. The metal and metal oxide nanoparticles are one of the most studied nanomaterials against multidrug-resistant bacteria. Several in vitro studies report that metal nanoparticles have antimicrobial properties against a broad spectrum of bacterial species. However, until recently, the bacterial resistance mechanisms to the bactericidal action of the nanoparticles had not been investigated. Some of the recently reported resistance mechanisms include electrostatic repulsion, ion efflux pumps, expression of extracellular matrices, and the adaptation of biofilms and mutations. The objective of this review is to summarize the recent findings regarding the mechanisms used by bacteria to counteract the antimicrobial effects of nanoparticles.

A methodology to assess the probability of marine litter accumulation in estuaries.

In this study, a general methodology that is based on numerical models and statistical analysis is developed to assist in the definition of marine litter cleanup and mitigation strategies at an estuarine scale. The methodology includes four main steps: k-means clustering to identify representative metocean scenarios; dynamic downscaling to obtain high-resolution drivers with which to force a transport model; numerical transport modelling to generate a database of potential litter trajectories; and a statistical analysis of this database to obtain probabilities of litter accumulation. The efficacy of this methodology is demonstrated by its application to an estuary along the northern coast of Spain by comparing the numerical results with field data. The necessary criteria to ensure its applicability to any other estuary were provided. As the main conclusion, the developed methodology successfully assesses the litter distribution in estuaries with minimum computational effort.

A recent increase in global wave power as a consequence of oceanic warming.

Wind-generated ocean waves drive important coastal processes that determine flooding and erosion. Ocean warming has been one factor affecting waves globally. Most studies have focused on studying parameters such as wave heights, but a systematic, global and long-term signal of climate change in global wave behavior remains undetermined. Here we show that the global wave power, which is the transport of the energy transferred from the wind into sea-surface motion, has increased globally (0.4% per year) and by ocean basins since 1948. We also find long-term correlations and statistical dependency with sea surface temperatures, globally and by ocean sub-basins, particularly between the tropical Atlantic temperatures and the wave power in high south latitudes, the most energetic region globally. Results indicate the upper-ocean warming, a consequence of anthropogenic global warming, is changing the global wave climate, making waves stronger. This identifies wave power as a potentially valuable climate change indicator.

Treatment strategies after acute exacerbations of chronic obstructive pulmonary disease: Impact on mortality.

INTRODUCTION: Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a common reason for presentation to emergency departments (ED), but the management of these episodes is often heterogeneous regardless of their potential impact on short-term adverse outcomes. METHODS: This was a longitudinal, retrospective study of all patients >40 years old admitted to the ED of two Spanish teaching hospitals for an AECOPD between January 1st and May 31st, 2016. All data were collected from electronic medical records. The primary outcomes were patient treatment at discharge and 90-day mortality. Logistic regression was used to model the determinants of 90-day mortality. RESULTS: Of the 465 included patients, 56% were prescribed a 3-drug combination at hospital discharge, 22% a 2-drug combination, 19% a single drug, and 4% other or no treatment. Approximately 8% of patients died within 90 days after an AECOPD. Multivariate logistic models revealed that having more than 2 severe exacerbations within the last 12 months (OR (95% CI): 15.12 (4.22-54.22)) and being prescribed a single drug at discharge (OR (95% CI): 7.23 (2.44-21.38)) were the main determinants of 90-day mortality after an AECOPD. CONCLUSIONS: This study reflects the real-life heterogeneity in the pharmacological treatments prescribed after an ED admission for an AECOPD and suggests the potential impact of suboptimal inhaled treatment strategies on 90-day mortality rates.

Lung function impairment is not associated with the severity of acute coronary syndrome but is associated with a shorter stay in the coronary care unit.

BACKGROUND: Previous population-based studies have suggested that lung function impairment (LFI) could be associated with an increase in the mortality of cardiovascular events. METHODS: We evaluated the association between LFI and the severity and short-term prognosis of acute coronary syndrome (ACS). LFI was established through presence of a forced expiratory volume in one second (FEV1) and/or a forced vital capacity (FVC) less than 80% of predicted. RESULTS: Seventy-one LFI subjects (61.45±10.70 years, 83.10% males) and 247 non-LFI subjects (58.98±11.18 years, 80.57% males) with ACS were included. Subjects with LFI exhibited a higher prevalence of systemic hypertension (57.75% vs. 40.89%, P=0.02) and tobacco exposure (28.50±26.67 vs. 18.21±19.83 pack-years, P=0.007). No significant differences between groups were found regarding the severity of ACS (ejection fraction, Killip class, number of affected vessels, and peak plasma troponin). However, in comparison to non-LFI subjects, a significantly shorter length of stay in the coronary care unit (CCU) was observed in the LFI group (1.83±1.10 vs. 2.24±1.21 days, P=0.01) and this was even shorter in subjects with obstructive LFI (1.62±1.17 days, P=0.009). When considering obstructive sleep apnea (OSA), an interaction with length of stay was found, revealing that OSA subjects with obstructive LFI had the shortest length of stay in the CCU (0.60±0.89 days, P=0.05) also in comparison to non-LFI. CONCLUSIONS: This study indicates a possible association between LFI and a shorter length of stay in the CCU but does not show a significant association with ACS severity.

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin Leontopithecus chrysopygus (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family.

We describe the complete mitochondrial genome sequence of the Black Lion Tamarin, an endangered primate species endemic to the Atlantic Rainforest of Brazil. We assembled the Leontopithecus chrysopygus mitogenome, through analysis of 523M base pairs (bp) of short reads produced by next-generation sequencing (NGS) on the Illumina Platform, and investigated the presence of nuclear mitochondrial pseudogenes and heteroplasmic sites. Additionally, we conducted phylogenetic analyses using all complete mitogenomes available for primates until June 2017. The single circular mitogenome of BLT showed organization and arrangement that are typical for other vertebrate species, with a total of 16618 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region (D-loop region). Our full phylogenetic tree is based on the most comprehensive mitogenomic dataset for Callitrichidae species to date, adding new data for the Leontopithecus genus, and discussing previous studies performed on primates. Moreover, the mitochondrial genome reported here consists of a robust mitogenome with 3000X coverage, which certainly will be useful for further phylogenetic and evolutionary analyses of Callitrichidae and higher taxa.

Ecological typologies of large areas. An application in the Mediterranean Sea.

One approach to identifying and mapping the state of marine biophysical conditions is the identification of large-scale ecological units for which conditions are similar and the strategies of management may also be similar. Because biological processes are difficult to directly record over large areas, abiotic characteristics are used as surrogate parameters. In this work, the Mediterranean Sea was classified into homogeneous spatial areas based on abiotic variables. Eight parameters were selected based on salinity, sea surface temperature, photosynthetically active radiation, sea-wave heights and depth variables. The parameters were gathered in grid points of 0.5° spatial resolution in the open sea and 0.125° in coastal areas. The typologies were obtained by data mining the eight parameters throughout the Mediterranean and combining two clustering techniques: self-organizing maps and the k-means algorithm. The result is a division of the Mediterranean Sea into seven typologies. For these typologies, the classification recognizes differences in temperature, salinity and radiation. In addition, it separates coastal from deep areas. The influence of river discharges and the entrance of water from other seas are also reflected. These results are consistent with the ecological requirements of the five studied seagrasses (Posidonia oceanica, Zostera marina, Zostera noltei, Cymodocea nodosa, Halophila stipulacea), supporting the suitability of the resulting classification and the proposed methodology. The approach thus provides a tool for the sustainable management of large marine areas and the ability to address not only present threats but also future conditions, such as climate change.