In situ observation of stress relaxation in epitaxial graphene

Upon cooling, branched line defects develop in epitaxial graphene grown at high temperature on Pt(111) and Ir(111). Using atomically resolved scanning tunneling microscopy we demonstrate that these defects are wrinkles in the graphene layer, i.e. stripes of partially delaminated graphene. With low energy electron microscopy (LEEM) we investigate the wrinkling phenomenon in situ. Upon temperature cycling we observe hysteresis in the appearance and disappearance of the wrinkles. Simultaneously with wrinkle formation a change in bright field imaging intensity of adjacent areas and a shift in the moire spot positions for micro diffraction of such areas takes place. The stress relieved by wrinkle formation results from the mismatch in thermal expansion coefficients of graphene and the substrate. A simple one-dimensional model taking into account the energies related to strain, delamination and bending of graphene is in qualitative agreement with our observations.Comment: Supplementary information: S1: Photo electron emission microscopy and LEEM measurements of rotational domains, STM data of a delaminated bulge around a dislocation. S2: Movie with increasing brightness upon wrinkle formation as in figure 4. v2: Major revision including new experimental dat

Gastroesophageal junction adenocarcinoma displays abnormalities in homologous recombination and nucleotide excision repair

OBJECTIVE: Esophageal adenocarcinoma (EAC) continues to be a disease associated with high mortality. Among the factors leading to poor outcomes are innate resistance to currently available therapies, advanced stage at diagnosis, and complex biology. Platinum and ionizing radiation form the backbone of treatment for the majority of patients with EAC. Of the multiple processes involved in response to platinum chemotherapy or ionizing radiation, deoxyribonucleic acid (DNA) repair has been a major player in cancer sensitivity to these agents. DNA repair defects have been described in various malignancies. The purpose of this study was to determine whether alterations in DNA repair are present in EAC compared with normal gastroesophageal tissues. METHODS: We analyzed the expression of genes involved in homologous recombination (HR), nonhomologous end-joining, and nucleotide excision repair (NER) pathways in 12 EAC tumor samples with their matched normal counterparts. These pathways were chosen because they are the main pathways involved in the repair of platinum- or ionizing-radiation-induced damage. In addition, abnormalities in these pathways have not been well characterized in EAC. RESULTS: We identified increased expression of at least one HR gene in eight of the EAC tumor samples. Alterations in the expression of EME1, a structure-specific endonuclease involved in HR, were the most prevalent, with messenger (m)RNA overexpression in six of the EAC samples. In addition, all EAC samples revealed decreased expression of at least one of numerous NER genes including XPC, XPA, DDB2, XPF, and XPG. CONCLUSION: Our study identified DNA repair dysregulation in EAC involving two critical pathways, HR and NER, and is the first demonstration of EME1 upregulation in any cancer. These DNA repair abnormalities have the potential to affect a number of processes such as genomic instability and therapy response, and the consequences of these defects deserve further study in EAC

Effects of sampling intensity and biomass levels on the precision of acoustic surveys in the Mediterranean Sea

Acoustic surveys represent the standard fishery-independent method worldwide for evaluating the biomass and spatial distribution of small pelagic fish populations. Considering the peculiarities of the spatial behaviour of pelagic fishes, the efficiency of the survey design in determining their biomass and spatial distribution is related to its ability to capture the portion of the patches accounting for larger part of the total biomass. Yet, the spatial structure of the patches could be strongly influenced by ecosystem characteristics as well as by changes in total biomass related to a density-dependent mechanism. This is of particular interest for anchovy and sardine which are known for their wide fluctuations and high sensitivity to the environment. In this study, we analysed the efficiency of acoustic surveys, targeting European anchovy (Engraulis encrasicolus) and European sardine (Sardina pilchardus), in 10 different areas of the Mediterranean Sea across three years of different biomass levels. Using the geostatistical Coefficient of Variation (CVgeo) of the average occurrence probability of high/medium density values, we showed different patterns in terms of survey design efficiency among areas and species. Anchovy usually showed lower CVgeo than sardine, but in the Alboran Sea. In 4 out of 20 cases, CVgeo values showed a consistent decrease with increasing biomass while in the remaining cases the CVgeo did not follow any clear pattern suggesting the presence of important environmental effects. Higher survey design efficiency was found in high productive sectors influenced by river run-off, letting us to hypothesize that higher productivity along with the presence of well-localized enrichment mechanisms could favour a spatially consistent distribution and coherent organization of fish population leading to higher precision estimates with a given transect design. While most surveys displayed CVgeo close to 10% or less even at low biomass, evidencing generally good performances of the survey design, a few areas exhibited higher CVgeo, yielding discussions about a potential need to decrease the inter-transect distance, always keeping in mind that survey should be as synoptic as possible.Versión del edito

The association of aggressive and chronic periodontitis with systemic manifestations and dental anomalies in a jordanian population: a case control study

<p>Abstract</p> <p><b>Background</b></p> <p>The relationship between dental anomalies and periodontitis has not been documented by earlier studies. Although psychological factors have been implicated in the etiopathogenesis of periodontitis, very little information has so far been published about the association of anxiety and depression with aggressive periodontitis. The aim of this study was to investigate the association of chronic periodontitis and aggressive periodontitis with certain systemic manifestations and dental anomalies.</p> <p><b>Methods</b></p> <p>A total of 262 patients (100 chronic periodontitis, 81 aggressive periodontitis and 81 controls), attending the Periodontology clinics at Jordan University of Science and Technology, Dental Teaching Centre) were included. All subjects had a full periodontal and radiographic examination to assess the periodontal condition and to check for the presence of any of the following dental anomalies: dens invaginatus, dens evaginatus, congenitally missing lateral incisors or peg-shaped lateral incisors. Participants were interrogated regarding the following: depressive mood, fatigue, weight loss, or loss of appetite; and their anxiety and depression status was assessed using the Hospital Anxiety and Depression (HAD) scale.</p> <p><b>Results</b></p> <p>Patients with aggressive periodontitis reported more systemic symptoms (51%) than the chronic periodontitis (36%) and control (30%) patients (<it>p </it>< 0.05). Aggressive periodontitis patients had a higher tendency for both anxiety and depression than chronic periodontitis and control patients. Dental anomalies were significantly (<it>p </it>< 0.05) more frequent among both of chronic and aggressive periodontitis patients (15% and 16%, respectively), compared to controls.</p> <p><b>Conclusion</b></p> <p>In this group of Jordanians, systemic symptoms were strongly associated with aggressive periodontitis, and dental anomalies were positively associated with both aggressive and chronic periodontitis.</p

Sequence Homology at the Breakpoint and Clinical Phenotype of Mitochondrial DNA Deletion Syndromes

Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders. Large mtDNA deletions can lead to a broad spectrum of clinical features with different age of onset, ranging from mild mitochondrial myopathies (MM), progressive external ophthalmoplegia (PEO), and Kearns-Sayre syndrome (KSS), to severe Pearson syndrome. The aim of this study is to investigate the molecular signatures surrounding the deletion breakpoints and their association with the clinical phenotype and age at onset. MtDNA deletions in 67 patients were characterized using array comparative genomic hybridization (aCGH) followed by PCR-sequencing of the deletion junctions. Sequence homology including both perfect and imperfect short repeats flanking the deletion regions were analyzed and correlated with clinical features and patients' age group. In all age groups, there was a significant increase in sequence homology flanking the deletion compared to mtDNA background. The youngest patient group (<6 years old) showed a diffused pattern of deletion distribution in size and locations, with a significantly lower sequence homology flanking the deletion, and the highest percentage of deletion mutant heteroplasmy. The older age groups showed rather discrete pattern of deletions with 44% of all patients over 6 years old carrying the most common 5 kb mtDNA deletion, which was found mostly in muscle specimens (22/41). Only 15% (3/20) of the young patients (<6 years old) carry the 5 kb common deletion, which is usually present in blood rather than muscle. This group of patients predominantly (16 out of 17) exhibit multisystem disorder and/or Pearson syndrome, while older patients had predominantly neuromuscular manifestations including KSS, PEO, and MM. In conclusion, sequence homology at the deletion flanking regions is a consistent feature of mtDNA deletions. Decreased levels of sequence homology and increased levels of deletion mutant heteroplasmy appear to correlate with earlier onset and more severe disease with multisystem involvement

A monoclonal antibody raised against bacterially expressed MPV17 sequences shows peroxisomal, endosomal and lysosomal localisation in U2OS cells

Recessive mutations in the MPV17 gene cause mitochondrial DNA depletion syndrome, a fatal infantile genetic liver disease in humans. Loss of function in mice leads to glomerulosclerosis and sensineural deafness accompanied with mitochondrial DNA depletion. Mutations in the yeast homolog Sym1, and in the zebra fish homolog tra cause interesting, but not obviously related phenotypes, although the human gene can complement the yeast Sym1 mutation. The MPV17 protein is a hydrophobic membrane protein of 176 amino acids and unknown function. Initially localised in murine peroxisomes, it was later reported to be a mitochondrial inner membrane protein in humans and in yeast. To resolve this contradiction we tested two new mouse monoclonal antibodies directed against the human MPV17 protein in Western blots and immunohistochemistry on human U2OS cells. One of these monoclonal antibodies showed specific reactivity to a protein of 20 kD absent in MPV17 negative mouse cells. Immunofluorescence studies revealed colocalisation with peroxisomal, endosomal and lysosomal markers, but not with mitochondria. This data reveal a novel connection between a possible peroxisomal/endosomal/lysosomal function and mitochondrial DNA depletion

Ecological indicators to capture the effects of fishing on biodiversityand conservation status of marine ecosystems

IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data avail-ability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii)mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species,and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our under-standing of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses,and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems