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Radon (222Rn) is a naturally occurring gas that represents a health threat due to its causal relationship with lung cancer. Despite its potential health impacts, several regions have not conducted studies, mainly due to data scarcity and/or economic constraints. This study aims to bridge the baseline information gap by building an interactive dashboard (http://ircmodelingdashboard.eu.pythonanywhere.com/, last access: 17 April 2024) that uses inferential statistical methods to estimate the spatial distribution of indoor radon concentration (IRC) for a target area. We demonstrate the functionality of the dashboard by modeling IRC in the city of Bogotá, Colombia, using 30 in situ measurements. IRC measured was the highest reported in the country, with a geometric mean of 91±14 Bq m−3 and a maximum concentration of 407 Bq m−3. In 57 % of the residences, RC exceeded the WHO's recommendation of 100 Bq m−3. A prediction map for houses registered in Bogotá's cadaster was built in the dashboard by using a log-linear regression model fitted with the in situ measurements, together with meteorological, geologic and building-specific variables. The model showed a cross-validation root mean squared error of 57 Bq m−3. Furthermore, the model showed that the age of the house presented a statistically significant positive association with RC. According to the model, IRC measured in houses built before 1980 presents a statistically significant increase of 72 % compared to IRC of those built after 1980 (p value = 0.045). The prediction map exhibited higher IRC in older buildings most likely related to cracks in the structure that could enhance gas migration in older houses. This study highlights the importance of expanding 222Rn studies in countries with a lack of baseline values and provides a cost-effective alternative that could help deal with the scarcity of IRC data and get a better understanding of place-specific variables that affect IRC spatial distribution.

The combined application of the MBT (degree of methylation) and CBT (degree of cyclization) indices, based on the distribution of branched glycerol dialkyl glycerol tetraethers (brGDGTs) in soils, has been proposed as a paleoproxy to estimate mean annual temperature (MAT). CBT quantifies the degree of cyclization of brGDGTs and relates to soil pH. MBT and the simplified version MBT' quantify the degree of methylation of brGDGTs and relate to MAT and soil pH. However, other factors such as soil water availability have also been suggested to influence MBT' and possibly restrict the combined application of the MBT' and CBT indices as a paleotemperature proxy. To assess the effect of hydrological conditions on MBT' and CBT, a set of 23 Iberian Peninsula soil samples, covering a MAT range from 10 to 18 °C and a mean annual precipitation (MAP) range of 405 mm to 1455 mm, was analyzed. We found that the CBT was indeed significantly correlated with soil pH in our sample set. In contrast, MBT' was not correlated with MAT but had a significant correlation with the aridity index (AI), a parameter related to water availability in soils. The AI can explain 50% of the variation of the MBT', and 70% of the residuals of MAT estimated with the MBT/CBT proxy as compared to instrumentally measured MAT. We propose that, in arid settings, where water may be an ecologically limiting factor, MBT' is influenced by hydrological conditions rather than temperature. Thus, our results suggest that the combination of MBT' and CBT indices should be applied with caution in paleotemperature reconstructions in soils from dry subhumid to hyperarid environments.

The present paper is the result of a workshop sponsored by the DFG Research Center/Cluster of Excellence MARUM "The Ocean in the Earth System", the International Graduate College EUROPROX, and the Alfred Wegener Institute for Polar and Marine Research. The workshop brought together specialists on organic matter degradation and on proxy-based environmental reconstruction. The paper deals with the main theme of the workshop, understanding the impact of selective degradation/preservation of organic matter (OM) in marine sediments on the interpretation of the fossil record. Special attention is paid to (A) the influence of the molecular composition of OM in relation to the biological and physical depositional environment, including new methods for determining complex organic biomolecules, (B) the impact of selective OM preservation on the interpretation of proxies for marine palaeoceanographic and palaeoclimatic reconstruction, and (C) past marine productivity and selective preservation in sediments. It appears that most of the factors influencing OM preservation have been identified, but many of the mechanisms by which they operate are partly, or even fragmentarily, understood. Some factors have not even been taken carefully into consideration. This incomplete understanding of OM breakdown hampers proper assessment of the present and past carbon cycle as well as the interpretation of OM based proxies and proxies affected by OM breakdown. To arrive at better proxy-based reconstructions "deformation functions" are needed, taking into account the transport and diagenesis-related molecular and atomic modifications following proxy formation. Some emerging proxies for OM degradation may shed light on such deformation functions. The use of palynomorph concentrations and selective changes in assemblage composition as models for production and preservation of OM may correct for bias due to selective degradation. Such quantitative assessment of OM degradation may lead to more accurate reconstruction of past productivity and bottom water oxygenation. Given the cost and effort associated with programs to recover sediment cores for paleoclimatological studies, as well as with generating proxy records, it would seem wise to develop a detailed sedimentological and diagenetic context for interpretation of these records. With respect to the latter, parallel acquisition of data that inform on the fidelity of the proxy signatures and reveal potential diagenetic biases would be of clear value.

Abstract Background Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. Results Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. Conclusions Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.

Due to the error-prone nature of viral RNA-dependent RNA polymerases, the replication of RNA viruses results in a diversity of viral genomes harboring point mutations, deletions, insertions, and genome rearrangements. Citrus tristeza virus (CTV), a causal agent of diseases of economically important citrus species, shows intrinsic genetic stability. While the virus appears to have some mechanism that limits the accumulation of single-nucleotide variants, the production of defective viral genomes (DVGs) during virus infection has been reported for certain variants of CTV. The intra-host diversity generated during plant infection with variant T36 (CTV-T36) remains unclear. To address this, we analyzed the RNA species accumulated in the initially infected and systemic leaves of Nicotiana benthamiana plants inoculated with an infectious cDNA clone of CTV-T36, which warranted that infection was initiated by a known, well-defined sequence variant of the virus. CTV-T36 limited the accumulation of single-nucleotide mutants during infection. With that, four types of DVGs—deletions, insertions, and copy- and snap-backs—were found in all the samples, with deletions and insertions being the most common types. Hot-spots across the genome for DVG recombination and short direct sequence repeats suggest that sequence complementarity could mediate DVG formation. In conclusion, our study illustrates the formation of diverse DVGs during CTV-T36 infection. To the best of our knowledge, this is the first study that has analyzed the genetic variability and recombination of a well-defined sequence variant of CTV in an herbaceous host.

Pitch canker, caused by the fungal pathogen Fusarium circinatum, is a global disease affecting many Pinus spp. Often fatal, this disease causes significant mortality in both commercially grown and natural pine forests and is an issue of current and growing concern. F. circinatum isolates collected from three locations in the U.S. state of Florida were shown to be virulent on both slash and loblolly pine, with two of the isolates causing equivalent and significantly larger lesions than those caused by the third isolate during pathogenicity trials. In addition, significant genetic variation in lesion length in the pedigreed slash pine population was evident and rankings of parents for lesion length were similar across isolates. Experimental data demonstrate that both host and pathogen genetics contribute to disease severity. High-quality genomic assemblies of all three isolates were created and compared for structural differences and gene content. No major structural differences were observed among the isolates; however, missing or altered genes do contribute to genomic variation in the pathogen population. This work evaluates in planta virulence among three isolates of F. circinatum, provides genomic resources to facilitate study of this organism, and details comparative genomic methods that may be used to explore the pathogen’s contribution to disease development.[Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract Objective ‘Candidatus Liberibacter asiaticus’ (CLas) is associated with the devastating citrus ‘greening’ disease. All attempts to achieve axenic growth and complete Koch’s postulates with CLas have failed to date, at best yielding complex cocultures with very low CLas titers detectable only by PCR. Reductive genome evolution has rendered all pathogenic ‘Ca. Liberibacter’ spp. deficient in multiple key biosynthetic, metabolic and structural pathways that are highly unlikely to be rescued in vitro by media supplementation alone. By contrast, Liberibacter crescens (Lcr) is axenically cultured and its genome is both syntenic and highly similar to CLas. Our objective is to achieve replicative axenic growth of CLas via addition of missing culturability-related Lcr genes. Results Bioinformatic analyses identified 405 unique ORFs in Lcr but missing (or truncated) in all 24 sequenced CLas strains. Site-directed mutagenesis confirmed and extended published EZ-Tn5 mutagenesis data, allowing elimination of 310 of these 405 genes as nonessential, leaving 95 experimentally validated Lcr genes as essential for CLas growth in axenic culture. Experimental conditions for conjugation of large GFP-expressing plasmids from Escherichia coli to Lcr were successfully established for the first time, providing a practical method for transfer of large groups of ‘essential’ Lcr genes to CLas.

Citrus tristeza virus (CTV, family Closteroviridae) is an economically important pathogen of citrus. CTV resides in the phloem of the infected plants and induces a range of disease phenotypes, including stem pitting and quick decline as well as a number of other deleterious syndromes. To uncover the biological processes underlying the poorly understood damaging symptoms of CTV, we profiled the transcriptome of sweet orange (Citrus sinensis) phloem-rich bark tissues of non-infected, mock-inoculated trees and trees singly infected with two distinct variants of CTV, T36 or T68-1. The T36 and T68-1 variants accumulated in the infected plants at similar titers. With that, young trees infected with T68-1 were markedly repressed in growth, while the growth rate of the trees infected with T36 was comparable to the mock-inoculated trees. Only a small number of differentially expressed genes (DEGs) were identified in the nearly asymptomatic T36-infected trees, whereas almost fourfold the number of DEGs were identified with the growth-restricting T68-1 infection. DEGs were validated using quantitative reverse transcription-PCR. While T36 did not induce many noteworthy changes, T68-1 altered the expression of numerous host mRNAs encoding proteins within significant biological pathways, including immunity and stress response proteins, papain-like cysteine proteases (PLCPs), cell-wall modifying enzymes, vascular development proteins and others. The transcriptomic alterations in the T68-1-infected trees, in particular, the strong and persistent increase in the expression levels of PLCPs, appear to contribute to the observed stem growth repression. On the other hand, analysis of the viral small interfering RNAs revealed that the host RNA silencing-based response to the infection by T36 and that by T68-1 was comparable, and thus, the induction of this antiviral mechanism may not contribute to the difference in the observed symptoms. The DEGs identified in this study promote our understanding of the underlying mechanisms of the yet unexplained growth repression induced by severe CTV isolates in sweet orange trees.

Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), is a soilborne disease that significantly limits yield in watermelon (Citrullus lanatus) and occasionally causes the loss of an entire year's harvest. Reference-quality de novo genomic assemblies of pathogenic and nonpathogenic strains were generated using a combination of next-generation and third-generation sequencing technologies. Chromosomal-level genomes were produced with representatives from three Fon races, facilitating comparative genomic analysis and the identification of chromosomal structural variation. Syntenic analysis between isolates allowed for differentiation of the core and lineage-specific portions of their genomes. This research will support future efforts to refine the scientific understanding of the molecular and genetic factors underpinning the Fon host range, develop diagnostic assays for each of the four races, and decipher the evolutionary history of race 3. [Figure: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 h post inoculation and 5521 genes were differentially expressed at 48 h post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.

Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.

Abstract Background Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains. Results We utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs. Due to the intriguing nature of this pathogenicity plasmid with Tn3-like transposon association, repetitive elements and multiple putative sites for origins of replication, we might expect alternative structures of this plasmid in nature, illustrating the strong adaptive potential of X. citri strains. Analysis of the pathogenicity plasmid among completely sequenced X. citri strains, coupled with Southern hybridization of the pathogenicity plasmids, revealed clues to rearrangements of plasmids and resulting reshuffling of TALEs among strains. Conclusions We demonstrate in this study the importance of long-read sequencing for obtaining intact sequences of TALEs and plasmids, as well as for identifying rearrangement events including plasmid reshuffling. Rearrangement events, such as the hybrid plasmid in this case, could be a frequent phenomenon in the evolution of X. citri strains, although so far it is undetected due to the inability to obtain complete plasmid sequences with short-read sequencing methods.

Approximately 10 Streptomyces species cause disease on underground plant structures. The most economically important of these is potato scab, and the most studied of these pathogens is Streptomyces scabiei (syn. S. scabies). The main pathogenicity determinant of scab-causing Streptomyces species is a nitrated diketopiperazine, known as thaxtomin A (ThxA). In the pathogenic species Streptomyces turgidiscabies, ThxA biosynthetic genes reside on a mobile pathogenicity island (PAI). However, the mobilization of PAIs in other Streptomyces species remains uncharacterized. Here, we investigated the mobilization of the PAI of S. scabiei 87-22. Based on whole genome sequences, we inferred the evolutionary relationships of pathogenic Streptomyces species and discovered that Streptomyces sp. strain 96-12, a novel pathogenic species isolated from potatoes in Egypt, was phylogenetically grouped with nonpathogenic species rather than with known pathogenic species. We also found that Streptomyces sp. strain 96-12 contains a PAI that is almost identical to the PAI in S. scabiei 87-22, despite significant differences in their genome sequences. This suggested direct or indirect in vivo mobilization of the PAI between S. scabiei and nonpathogenic Streptomyces species. To test whether the S. scabiei 87-22 PAI could, indeed, be mobilized, S. scabiei 87-22 deletion mutants containing antibiotic resistance markers in the PAI were mated with Streptomyces diastatochromogenes, a nonpathogenic species. The PAI of S. scabiei was site-specifically inserted into the aviX1 gene of S. diastatochromogenes and conferred pathogenicity in radish seedling assays. Our results demonstrated that S. scabiei, the earliest described Streptomyces pathogen, could be the source of a PAI responsible for the emergence of novel pathogenic species.

Pseudomonas syringae sensu stricto (phylogroup 2; referred to as P. syringae) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several P. syringae lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six P. syringae strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of P. syringae stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the P. syringae core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT). This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of P. syringae sensu lato genomes.

Strains of the Ralstonia solanacearum species complex in the phylotype IIB group are capable of causing Bacterial Wilt disease in potato and tomato at temperatures lower than 24°C. The capability of these strains to survive and to incite infection at temperatures colder than their normally tropical boundaries represents a threat to United States agriculture in temperate regions. In this work, we used a comparative genomics approach to identify orthologous genes linked to the lower temperature virulence phenotype. Six R. solanacearum cool virulent (CV) strains were compared to six strains non-pathogenic at low temperature (NPLT). CV strains can cause Bacterial Wilt symptoms at temperatures below 24°C, while NPLT cannot. Four R. solanacearum strains were sequenced for this work in order to complete the comparison. An orthologous genes comparison identified 44 genes present only in CV strains and 19 genes present only in NPLT strains. Gene annotation revealed a high percentage of genes compared with whole genomes in the transcriptional regulator and transport categories. A single nucleotide polymorphism (SNP) analysis identified 265 genes containing conserved non-synonymous SNPs in CV strains. Ten genes in the pathogenicity category were identified in this group. Comparisons of type 3 secretion system, type 6 secretion system (T6SS) clusters, and associated effectors did not indicate a correlation with the CV phenotype except for one T6SS VGR effector potentially associated with the CV phenotype. This is the first R. solanacearum genomic comparative analysis of multiple strains with different temperature related virulence. The candidate genes identified by this comparison are potential factors involved in virulence at low temperatures that need to be investigated. The high percentage of transcriptional regulators among the genes present only in CV strains supports the hypothesis that temperature dependent regulation of virulence genes explains the differential virulence phenotype at low temperatures. This comparison contributes to find new possible connections of temperature dependent virulence to the previously described complex regulatory system involving quorum-sensing, phenotype conversion (phcA), acyl-HSL production and responses to SA. It also added novel candidate T6SS effectors and useful detailed information about the T6SS in R. solanacearum.

Plant-pathogenic Streptomyces spp. cause scab disease on economically important root and tuber crops, the most important of which is potato. Key virulence determinants produced by these species include the cellulose synthesis inhibitor, thaxtomin A, and the secreted Nec1 protein that is required for colonization of the plant host. Recently, the genome sequence of Streptomyces scabies 87-22 was completed, and a biosynthetic cluster was identified that is predicted to synthesize a novel compound similar to coronafacic acid (CFA), a component of the virulence-associated coronatine phytotoxin produced by the plant-pathogenic bacterium Pseudomonas syringae. Southern analysis indicated that the cfa-like cluster in S. scabies 87-22 is likely conserved in other strains of S. scabies but is absent from two other pathogenic streptomycetes, S. turgidiscabies and S. acidiscabies. Transcriptional analyses demonstrated that the cluster is expressed during plant–microbe interactions and that expression requires a transcriptional regulator embedded in the cluster as well as the bldA tRNA. A knockout strain of the biosynthetic cluster displayed a reduced virulence phenotype on tobacco seedlings compared with the wild-type strain. Thus, the cfa-like biosynthetic cluster is a newly discovered locus in S. scabies that contributes to host–pathogen interactions.

Pythium insidiosum ATCC 200269 strain CDC-B5653, an isolate from necrotizing lesions on the mouth and eye of a 2-year-old boy in Memphis, Tennessee, USA, was sequenced using a combination of Illumina MiSeq (300 bp paired-end, 14 millions reads) and PacBio (10 Kb fragment library, 356,001 reads). The sequencing data were assembled using SPAdes version 3.1.0, yielding a total genome size of 45.6 Mb contained in 8992 contigs, N50 of 13 Kb, 57% G + C content, and 17,867 putative protein-coding genes. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRHR00000000. Keywords: Oomycete, Pythium insidiosum, Pythiosis, Human emerging pathogen, Genome sequencing

PAISt is a large genomic island located in the chromosome of the plant pathogen Streptomyces turgidiscabies Car8. The island carries clustered virulence genes, transfers to other Streptomyces species, and integrates by site-specific recombination at the 8 bp palindrome TTCATGAA. The palindrome is located at the 3' end of the bacitracin resistance gene (bacA). We demonstrate that PAISt is able to excise in modules by recombination of one internal and two flanking palindromic direct repeats. The gene intSt located at the 3( end of PAISt encodes a tyrosine recombinase. Site-specific recombination activity of intSt was tested and confirmed by heterologous expression in Streptomyces coelicolor. Comparative analysis of PAISt homologues in Streptomyces scabies 87-22 and Streptomyces acidiscabies 84-104 indicates that these islands have been fixed by sequence erosion of intSt and the recombination sites.

Five patients fitted with a biliary T-tube after cholecystectomy were given orally a tracer dose of [14C]hyodeoxycholic acid and 500 mg of the same unlabeled acid. Intestinal absorption and biotransformation, liver metabolism, bile secretion, fecal and urinary excretions of this acid or of its metabolites were studied. Hyodeoxycholic acid was well absorbed by the human intestine. It was not subjected to intestinal transformations and, particularly, did not produce a significant amount of lithocholic acid, which does not support the existence of intestinal bacterial 6 alpha-dehydroxylases. The percentage of hyodeoxycholic acid and of its metabolites recovered in bile varied from 11.5 to 31%. Two major metabolites were isolated from bile: glycohyodeoxycholic acid and hyodeoxycholic acid glucuronide. Analysis of urinary bile acids showed that a large proportion (30-84%) of the administered hyodeoxycholic acid was excreted by the kidney as a glucuronide. The large extent of both glucuronidation and urinary excretion of hyodeoxycholic acid is a unique example of bile acid metabolism and excretion in man.

Paramos, unique and biodiverse ecosystems found solely in the high mountain regions of the tropics, are under threat. Despite their crucial role as primary water sources and significant carbon repositories in Colombia, they are deteriorating rapidly and garner less attention than other vulnerable ecosystems like the Amazon rainforest. Their fertile soil and unique climate make them prime locations for agriculture and cattle grazing, often coinciding with economically critical deposits such as coal which has led to a steady decline in paramo area. Anthropic impact was evaluated using multispectral images from Landsat and Sentinel over 37 years, on the Guerrero and Rabanal paramos in central Colombia which have experienced rapid expansion of mining and agriculture. Our analysis revealed that since 1984, the Rabanal and Guerrero paramos have lost 47.96% and 59.96% of their native vegetation respectively, replaced primarily by crops, pastures, and planted forests. We detected alterations in the spectral signatures of native vegetation near coal coking ovens, indicating a deterioration of paramo health and potential impact on ecosystem services. Consequently, human activity is reducing the extent of paramos and their efficiency as water sources and carbon sinks, potentially leading to severe regional and even global consequences., (© 2024. The Author(s).)

Arming oncolytic viruses with transgenes encoding immunomodulators improves their therapeutic efficacy by enhancing and/or sustaining the innate and adaptive anti-tumoral immune responses. We report here the isolation, selection, and vectorization of a blocking anti-human PDL1 single-domain antibody (sdAb) isolated from PDL1-immunized alpacas. Several formats of this sdAb were vectorized into the vaccinia virus (VV) and evaluated for their programmed cell death protein 1 (PD1)/PD1 ligand (PDL1) blocking activity in the culture medium of tumor cells infected in vitro . In those conditions, VV-encoded homodimeric sdAb generated superior PDL1 blocking activity compared to a benchmark virus encoding full-length avelumab. The sdAb was further used to design simple, secreted, and small tumor necrosis factor superfamily (TNFSF) fusions with the ability to engage their cognate receptors (TNFRSF) only in the presence of PDL1-positive cells. Finally, PDL1-independent alternatives of TNFRSF agonists were also constructed by fusing different variants of surfactant protein-D (SP-D) oligomerization domains with TNFSF ectodomains. An optimal SP-D-CD40L fusion with an SP-D collagen domain reduced by 80% was identified by screening with a transfection/infection method where poxvirus transfer plasmids and vaccinia virus were successively introduced into the same cell. However, once vectorized in VV, this construct had a much lower CD40 agonist activity compared to the SP-D-CD40L construct, which is completely devoid of the collagen domain that was finally selected. This latest result highlights the importance of working with recombinant viruses early in the payload selection process. Altogether, these results bring several complementary solutions to arm oncolytic vectors with powerful immunomodulators to improve their immune-based anti-tumoral activity., Competing Interests: Authors CR, EP, PK, HR, LF, RB, MG, CR, DS, EW, NS, EQ, and J-BM were employed by the company Transgene SA. MD, SS, CH, and PF were employed by the company Randox Laboratories Ltd., (Copyright © 2023 Remy, Pintado, Dunlop, Schön, Kleinpeter, Rozanes, Fend, Brandely, Geist, Suhner, Winter, Silvestre, Huguet, Fitzgerald, Quéméneur and Marchand.)

Despite compelling evidence that stress or stress-related hormones influence fear memory consolidation processes, the understanding of molecular mechanisms underlying the effects of stress is still fragmentary. The release of corticosterone in response to pre-learning stress exposure has been demonstrated to modulate positively or negatively memory encoding and/or consolidation according to many variables such as stress intensity, the emotional valence of the learned material or the interval between stressful episode and learning experience. Here, we report that contextual but not cued fear memory consolidation was selectively impaired in male mice exposed to a 50 min-period of restraint stress just before the unpaired fear conditioning session. In addition to behavioral impairment, acute stress down-regulated activated/phosphorylated ERK1/2 (pERK1/2) in dorsal hippocampal area CA1 in mice sacrificed 60 min and 9 h after unpaired conditioning. In lateral amygdala, although acute stress by itself increased the level of pERK1/2 it nevertheless blocked the peak of pERK1/2 that was normally observed 15 min after unpaired conditioning. To examine whether stress-induced corticosterone overflow was responsible of these detrimental effects, the corticosterone synthesis inhibitor, metyrapone, was administered 30 min before stress exposure. Metyrapone abrogated the stress-induced contextual fear memory deficits but did not alleviate the effects of stress on pERK1/2 and its downstream target phosphorylated CREB (pCREB) in hippocampus CA1 and lateral amygdala. Collectively, our observations suggest that consolidation of hippocampus-dependent memory and the associated signaling pathway are particularly sensitive to stress. However, behavioral normalization by preventive metyrapone treatment was not accompanied by renormalization of the canonical signaling pathway. A new avenue would be to consider surrogate mechanisms involving proper metyrapone influence on both nongenomic and genomic actions of glucocorticoid receptors., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Inhibition of hydroxy acid oxidase 1 (HAO1) is a strategy to mitigate the accumulation of toxic oxalate that results from reduced activity of alanine-glyoxylate aminotransferase (AGXT) in primary hyperoxaluria 1 (PH1) patients. DNA-Encoded Chemical Library (DECL) screening provided two novel chemical series of potent HAO1 inhibitors, represented by compounds 3 - 6 . Compound 5 was further optimized via various structure-activity relationship (SAR) exploration methods to 29 , a compound with improved potency and absorption, distribution, metabolism, and excretion (ADME)/pharmacokinetic (PK) properties. Since carboxylic acid-containing compounds are often poorly permeable and have potential active glucuronide metabolites, we undertook a brief, initial exploration of acid replacements with the aim of identifying non-acid-containing HAO1 inhibitors. Structure-based drug design initiated with Compound 5 led to the identification of a nonacid inhibitor of HAO1, 31 , which has weaker potency and increased permeability.

Bispecific degraders (PROTACs) of ERα are expected to be advantageous over current inhibitors of ERα signaling (aromatase inhibitors/SERMs/SERDs) used to treat ER+ breast cancer. Information from DNA-encoded chemical library (DECL) screening provides a method to identify novel PROTAC binding features as the linker positioning, and binding elements are determined directly from the screen. After screening ∼120 billion DNA-encoded molecules with ERα WT and 3 gain-of-function (GOF) mutants, with and without estradiol to identify features that enrich ERα competitively, the off-DNA synthesized small molecule exemplar 7 exhibited nanomolar ERα binding, antagonism, and degradation. Click chemistry synthesis on an alkyne E3 ligase engagers panel and an azide variant of 7 rapidly generated bispecific nanomolar degraders of ERα, with PROTACs 18 and 21 inhibiting ER+ MCF7 tumor growth in a mouse xenograft model of breast cancer. This study validates this approach toward identifying novel bispecific degrader leads from DECL screening with minimal optimization.

Infectious diseases are among the greatest threats to global health in the 21st century, and one critical concern is due to antibiotic resistance developed by an increasing number of bacterial strains. New resistance mechanisms are emerging with many infections becoming more and more difficult if not impossible to treat. This growing phenomenon not only is associated with increased mortality but also with longer hospital stays and higher medical costs. For these reasons, there is an urgent need to find new antibiotics targeting pathogenic microorganisms such as ESKAPEE bacteria. Most of currently approved antibiotics are derived from microorganisms, but higher fungi could constitute an alternative and remarkable reservoir of anti-infectious compounds. For instance, pleuromutilins constitute the first class of antibiotics derived from mushrooms. However, macromycetes still represent a largely unexplored source. Publications reporting the antibacterial potential of mushroom extracts are emerging, but few purified compounds have been evaluated for their bioactivity on pathogenic bacterial strains. Therefore, the aim of this review is to compile up-to-date data about natural products isolated from fruiting body fungi, which significantly inhibit the growth of ESKAPEE pathogenic bacteria. When available, data regarding modes of action and cytotoxicity, mandatory when considering a possible drug development, have been discussed in order to highlight the most promising compounds., Competing Interests: The authors declare that they have no conflict of interest., (Thieme. All rights reserved.)

DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value. We demonstrate a new approach applying machine learning to DEL selection data by identifying active molecules from large libraries of commercial and easily synthesizable compounds. We train models using only DEL selection data and apply automated or automatable filters to the predictions. We perform a large prospective study (∼2000 compounds) across three diverse protein targets: sEH (a hydrolase), ERα (a nuclear receptor), and c-KIT (a kinase). The approach is effective, with an overall hit rate of ∼30% at 30 μM and discovery of potent compounds (IC 50 < 10 nM) for every target. The system makes useful predictions even for molecules dissimilar to the original DEL, and the compounds identified are diverse, predominantly drug-like, and different from known ligands. This work demonstrates a powerful new approach to hit-finding.

Large tropical river dam projects are expected to accelerate over the forthcoming decades to satisfy growing demand for energy, irrigation and flood control. When tropical rivers are dammed the immediate impacts are relatively well studied, but the long-term (decades-centuries) consequences of impoundment remain poorly known. We combined historical records of water quality, river flow and climate with a multi-proxy (macrofossils, diatoms, biomarkers and trace elements) palaeoecological approach to reconstruct the limnological evolution of a shallow basin in Gatun Lake (Panama Canal, Panama) and assess the effects of multiple linked factors (river damming, forest flooding, deforestation, invasive species, pollution and hydro-climate) on the study area. Results show that a century after dam construction, species invasion, deforestation and salt intrusions have forced a gradual change in the study basin from a swamp-type environment towards a more saline lake-governed system of benthic-littoral production likely associated with the expansion of macrophyte stands. Hydrology still remains the most important long-term (decades) structural factor stimulating salinity intrusions, primary productivity, deposition of minerals, and reduction of water transparency during wet periods. During dry periods, physical-chemical conditions are in turn linked to clear water and aerobic conditions while nutrients shift to available forms for the aquatic biota in the detrital-rich reductive sediments. Our study suggests that to preserve the natural riverine system functioning of this area of the Panama Canal, management activities must address long-term ecosystem structural drivers such as river flow, runoff patterns and physical-chemical conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

High-resolution paleoclimate data on stable isotopes in a stalagmite were coupled to glycerol dialkyl glycerol tetraethers (GDGTs). The Indian Summer Monsoon (ISM) transitioned from limited rainfall during the Last Glacial Maximum (LGM) to intense precipitation during early Holocene (22 to 6 ka). This was associated with changes in stalagmite growth, abundance of branched (br) and isoprenoid (iso) GDGTs, as well as δ 18 O, δ 13 C, Sr/Ca and GDGT-derived signals providing both temperature and moisture information. The reconstructed mean annual air temperature (MAAT) of the most modern stalagmite sample at ~19 °C, matches the surface and cave MAAT, but was ~4 °C lower during LGM. Warming at the end of LGM occurred before ISM strengthened and indicate 6 ka lag consistent with sea surface temperature records. The isotope records during the Younger Dryas show rapid progressions to dry conditions and weak monsoons, but these shifts are not coupled to TEX 86 . Moreover, change to wetter and stronger ISM, along with warmer Holocene conditions are not continuous indicating a decoupling of local temperatures from ISM.

Archaeal tetraether membrane lipids span the whole membrane width and present two C 40 isoprenoid chains bound by two glycerol groups (or one glycerol and calditol). These lipids confer stability and maintain the membrane fluidity in mesophile to extremophile environments, making them very attractive for biotechnological applications. The isoprenoid lipid composition in archaeal membranes varies with temperature, which has placed these lipids in the focus of paleo-climatological studies for over a decade. Non-hydroxylated isoprenoid archaeal lipids are typically used as paleo-thermometry proxies, but recently identified hydroxylated (OH) derivatives have also been proposed as temperature proxies. The relative abundance of hydroxylated lipids increases at lower temperatures, but the physiological function of the OH moiety remains unknown. Here we present molecular dynamics simulations of membranes formed by the acyclic glycerol-dialkyl-glycerol-tetraether caldarchaeol (GDGT-0), the most widespread archaeal core lipid, and its mono-hydroxylated variant (OH-GDGT-0) to better understand the physico-chemical properties conferred to the membrane by this additional moiety. The molecular dynamics simulations indicate that the additional OH group forms hydrogen bonds mainly with the sugar moieties of neighbouring lipids and with water molecules, effectively increasing the size of the polar headgroups. The hydroxylation also introduces local disorder that propagates along the entire alkyl chains, resulting in a slightly more fluid membrane. These changes would help to maintain trans-membrane transport in cold environments, explaining why the relative abundance of hydroxylated Archaea lipids increases at lower temperatures. The in silico approach aids to understand the underlying physiological mechanisms behind the hydroxylated lipid based paleo-thermometer recently proposed., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Purpose: To assess the prevalence of vitreoretinal interface abnormalities in a general population of healthy adults ≥45 years of age., Design: Cross-sectional study carried out at 17 ophthalmology services throughout Spain., Participants: Between September 2015 and March 2016, all consecutive healthy persons aged ≥45 years who were accompanying patients to ophthalmology services were invited to take part in the study. Exclusion criteria were known retinal disease, uveitis, history of ocular trauma or previous intraocular surgery (including cataract surgery and intravitreal injections), severe myopia (>-6 dioptres), and poor ocular media transparency., Methods: Spectral-domain OCT or swept-source OCT was performed on all participants. Diseases of the vitreomacular interface were classified according to the OCT-based anatomic classification system of the International Vitreomacular Traction Study Group. All pathologic and borderline images as well as doubtful cases were evaluated blindly in a central reading center., Main Outcome Measures: Prevalence of vitreomacular interface abnormalities (vitreomacular traction epiretinal membrane, lamellar hole)., Results: The study included 2257 participants with a mean age of 59.5 years (range 45-90), and a total of 4490 eyes (right eyes 2242, left eyes 2248). Vitreoretinal interface abnormalities were detected in 70 eyes, with a prevalence of 1.6%. Vitreomacular adhesion was observed in 1317 eyes (29.3%). Results of spectral-domain OCT or swept-source OCT examination were unrevealing in 3103 eyes. Vitreoretinal interface abnormalities were found in 61 participants, with a prevalence in the study population of 2.7%. Vitreomacular traction was observed in 14 participants (0.6%), epiretinal membrane in 44 (1.9%), and lamellar macular hole in 3 (0.1%). The prevalence of both vitreomacular traction and epiretinal membrane increased significantly with age. The presence of vitreoretinal interface abnormalities was unrelated to concomitant diabetes mellitus or hypertension., Conclusions: An important percentage of healthy participants from the general population ≥45 years of age showed vitreoretinal interface abnormalities. Screening with OCT is advisable at any first routine consultation or preoperative assessment, particularly in older participants., (Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.)

The infection caused by the zoonotic opportunistic pathogen Mycobacterium avium subsp. hominissuis (Mah) was reported for the first time in a pet ferret. Both owners were HIV-positive. Euthanasia of the pet was recommended due to medical reasons and as a preventive action. Disseminated and open tuberculosis lesions were observed in the gastrointestinal and respiratory systems of the ferret. Ecographic and radiographic surveys showed a severe generalized lymphadenopathy, strong thickening of the gastric wall and peritoneum layer. The histopathological findings revealed a disseminated, granulomatous, chronic inflammation affecting the gastrointestinal tract, lungs, lymphoid tissues (spleen, tonsils and lymph nodes) and liver. Ziehl-Neelsen staining displayed the presence of positive acid-fast bacilli within these granulomas. Bacteriology and sequencing of the isolates yielded Mah sequevar code 3. Ferrets can act as reservoirs of mycobacteria exposing their owners to the infection, which is of major concern in immunodeficient individuals, as those HIV-infected., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

We have recently shown that post-extinction retraining of rats, with a shock intensity that is too weak to induce by itself significant fear acquisition, impairs the recall of fear extinction memory. Tetanic stimulation (TS) of the medial prefrontal cortex (mPFC), applied before or following this retraining, facilitates extinction recall. Here we investigated whether mPFC TS can also facilitate expression of fear extinction when rats are retrained with the same shock intensity as during the initial fear acquisition. Rats were implanted with stimulating electrodes in the mPFC and were trained to acquire freezing to a conditioning chamber, in which they had to enter freely. In Experiment 1, extinction of this response was followed by reconditioning and then another extinction training. Acquired freezing was extinguished successfully, while reacquired freezing, which was associated with increased chamber entry latencies, was resistant to subsequent extinction. Both reacquired freezing and increased chamber entry latencies were absent in rats that received post-reconditioning mPFC TS. In Experiment 2, post-conditioning mPFC TS had no effect on initially acquired freezing. In Experiment 3, rats were submitted to reconditioning without experiencing extinction training. In this condition, both reacquired freezing and increased chamber entry latencies were still present in rats that received post-reconditioning mPFC TS. These findings provide additional evidence for the fundamental role of the mPFC in maintaining expression of fear extinction., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Lake Van in Turkey is the world's largest soda lake (607 km(3)). The lake's catchment area is estimated to be ∼12,500 km(2), and the terrestrial input is carried through eolian, riverine, snowmelt and anthropogenic paths. Extent and seasonality of the terrestrial inputs to the lake have not been studied, but it is essential to evaluate its environmental status and to assess the use of environmental proxies to estimate the lake's response to climate changes. This study aims to measure seasonal changes in terrestrial input of natural and anthropogenic origin as recorded by the fluxes of pollen and biomarkers of soil bacteria and vascular or higher plants, as well as petrogenic biomarkers in monthly resolved sediment traps from August 2006 to July 2007. Fluxes of pollen, soil and higher plant biomarkers seem to be related to precipitation and snowmelt in autumn and spring. In addition, dust storms, which are common during the summer months, may have resulted in long-distance transport. Anthropogenic biomarker fluxes indicate year-round petrogenic contamination although some mature biomarker fluxes are higher in summer and in late winter-spring. The relative changes between petrogenic markers indicate variations in the pollutant sources.

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10(3)-10(5) cells cm(-3)). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance., (© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

There is great interest in the membrane lipids of archaea (glycerol dialkyl glycerol tetraethers [GDGTs]) as tracers of archaeal biomass because of their utility as paleoproxies and because of the biogeochemical importance of archaea. While core GDGTs (formed by hydrolysis of polar head groups of intact GDGTs after cell death) are appropriate for paleostudies, they have also been used to trace archaeal populations. Also, despite the small size (0.2 by 0.7 μm) of cultivated marine archaea, 0.7-μm glass-fiber filters (GFFs) are typically used to collect GDGTs from natural waters. We quantified both core and intact GDGTs in free-living (0.2- to 0.7-μm), suspended (0.7- to 60-μm), and aggregate (>60-μm) particle size fractions in Puget Sound (Washington State). On average, the free-living fraction contained 36% of total GDGTs, 90% of which were intact. The intermediate-size fraction contained 62% of GDGTs, and 29% of these were intact. The aggregate fraction contained 2% of the total GDGT pool, and 29% of these were intact. Our results demonstrate that intact GDGTs are largely in the free-living fraction. Because only intact GDGTs are present in living cells, protocols that target this size fraction and analyze the intact GDGT pool are necessary to track living populations in marine waters. Core GDGT enrichment in larger-size fractions indicates that archaeal biomass may quickly become attached or entrained in particles once the archaea are dead or dying. While the concentrations of the two pools were generally not correlated, the similar sizes of the core and intact GDGT pools suggest that core GDGTs are removed from the water column on timescales similar to those of cell replication, on timescales of days to weeks.

Dynamic modelling of hydrochemistry is a valuable tool to study and predict the recovery of surface waters from acidification, and to assess the effects of confounding factors (such as delayed soil response and changing climate) that cause hysteresis during reversal from acidification. The availability of soil data is often a limitation for the regional application of dynamic models. Here we present a method to upscale site-specific soil properties to a regional scale in order to circumvent that problem. The method proposed for upscaling relied on multiple regression models between soil properties and a suite of environmental variables used as predictors. Soil measurements were made during a field survey in 13 catchments in the Pyrenees (NW Spain). The environmental variables were derived from mapped or remotely sensed topographic, lithological, land-cover, and climatic information. Regression models were then used to model soil parameters, which were supplied as input for the biogeochemical model MAGIC (Model for Acidification of Groundwater In Catchments) in order to reconstruct the history of acidification in Pyrenean lakes and forecast the recovery under a scenario of reduced acid deposition. The resulting simulations were then compared with model runs using field measurements as input parameters. These comparisons showed that regional averages for the key water and soil chemistry variables were suitably reproduced when using the modelled parameters. Simulations of water chemistry at the catchment scale also showed good results, whereas simulated soil parameters reflected uncertainty in the initial modelled estimates.

Institutions should normally have an integrative influence. The family, for example, has the task of protecting and giving socio-emotional support to children, and schools should prepare young people for their future. Ideally the common goal of all of society's institutions is to secure the integration of youth and prevent or intervene against deviant behavior. But sometimes institutions provoke or even cause juvenile delinquency. The article discusses institutional influences and the role of the police in the criminal and violent situation in the favelas of Rio de Janeiro.Starting with an overview of the origins and the development of violence, crime, and drug trafficking in the favelas, the authors show how these slums arose. Their analysis examines the lack of a state presence with an integration policy to avoid social disintegration. Instead of social integration policy, there is a dual approach that both controls and produces violence. The article also presents the first results of a government attempt in 2000 to introduce a new police unit to stop the violence and improve the social opportunity structure of the residents of the favelas, especially young people.

The TEX86 is a recently proposed paleothermometer through which ancient seawater temperatures of up to 120 My ago can be reconstructed. It is based on the relative distribution of glycerol dibiphytanyl glycerol tetraethers as measured by high-performance liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry (HPLC/APCI-MS). The aim of this study was to examine and improve several analytical aspects in the determination of this important proxy in environmental matrices. Comparison of TEX86 analysis using single ion mode (SIM) and mass scanning (m/z 950 to 1450) detection, respectively, revealed that SIM is up to 2 orders of magnitude more sensitive and that the TEX86 can be determined with a reproducibility of +/-0.004 or +/-0.3 degrees C using this method. Comparison of TEX86 values obtained with two different HPLC/APCI-MS set-ups revealed no significant differences. In addition, analysis of TEX86 of extracts obtained by Soxhlet, ultrasonic, and accelerated high-pressure extraction techniques also showed no significant differences between the methods. Our results suggest that TEX86 analysis by HPLC/APCI-MS is robust and can be determined with analytical errors comparable to those of other temperature proxies.

Aim: The treatment of common bile duct stones has changed with the new therapeutic techniques, that have replaced the conventional therapy, represented by surgery. Anyway, they could cause some problems, that must be regarded. Therefore, we wish to confirm the importance of the conventional surgery in the management of patients with common bile duct stones., Methods: A total of 147 patients were operated for common bile duct stones (73 in emergency and 74 in election). The intraoperative cholangiography was carried out in 141 patients and a choledocoscopy in 130 patients. A drain of Kehr was positioned in 120 patients, a bilio-digestive anastomosis in 26 cases and in 1 case there was a direct suture of the common bile duct without drain. All patients were treated with a short-term antibioticotherapy, protracted to 5 days in the emergency cases. In the patients with the drain of Kehr there was a control cholangiography after 7 days from operation and it was removed after 25 days. The analysis of the results was done dividing the patients according to the age: <75 years old and >75 years old., Results: Nobody died during the operation. Complications were 17.4% in the patients >75 years old and 2,6% in the patients <75 years old. There were 2 death, in the postoperative period, for the group >75 years old. Cases operated in emergency were 68.1% of "old" patients and 37.2% of "young" patients. The postoperative period was 14.9+/-9.2 days for the "old" group and 10.9+/-5.2 days for the "young" group., Conclusions: The treatment of common bile duct stones is still a surgical treatment, particularly for "old" patients.

Duodenal cystic dystrophy due to ectopic pancreas deposit is an uncommon pathology. Diagnosis is made by modern imaging techniques, mainly endoscopic ultrasound which localizes precisely cysts in duodenal wall. The most frequent clinical symptoms are pain, duodenal obstruction, and weight loss. We report the case of a 40 year-old man with cystic dystrophy of the 2nd part of the duodenum, without chronic pancreatitis, treated by a conservative surgical procedure including segmental duodenal resection. This original approach is an alternative to the Whipple procedure.

Liver metastasis of carcinoid tumors from the digestive tract are rare entities, with characteristic symptoms and slow evolution. Symptomatic metastases may justify surgical resection. Herein, we report a series of nine patients, who underwent 14 hepatic resections (6 major and 8 minor), which was radically operated in 71%. The postoperative mortality was zero and the morbidity was 7%. Mean follow-up was 82 month (median 75 months) and global survival rate was 89%. Two patients are in complete remission. Our experience suggest that surgical hepatic resection, when feasible, is efficient and associated with prolonged survival despite a high recurrence rate.

Superficial lipomas are very common benign adipose tissue tumors. In contrast, deep-seated lipomas such as retroperitoneal lipomas, are extremely rare and have to be carefully distinguished from well-differentiated liposarcomas for appropriate treatment and follow-up. We report to, our knowledge, the first cytogenetic analysis of a retroperitoneal lipoma occurring in an adult, which showed a complex rearrangement interpreted as t(1;8)(q32;q22-q23) followed by a pericentric inversion of der(8). There was no detectable rearrangement of chromosome 12, and in particular no 12q14-q15 amplification. Because rearrangements of the 8q11-q13 region involving the PLAG1 gene have been described in lipoblastoma-another kind of benign adipose tumor--we used fluorescence in situ hybridization analysis to determine in the present case the chromosomal breakpoint on 8q was located between the ETO (8q22) and COX6C (8q22-q23) genes at a great distance from PLAG1. Karyotypic analysis of additional cases of retroperitoneal lipomas will be required to assess the significance of chromosome 1 and 8 rearrangements in a continuous effort to attain a better classification of adipose tissue tumors. Of great importance is the determination of such genetic markers as additional tools for the differential diagnosis between benign and malignant forms of adipose tumors, and to avoid erroneous diagnoses.

Unlabelled: Suicide gene therapy consists of transferring into tumor cells a viral or bacterial gene encoding for an enzyme which converts a non-toxic product into a lethal drug., Study Aim: To analyze the therapeutic potential of vaccination with tumor cells expressing the bacterial cytosine deaminase (CD) gene and 5-fluorocytosine (5-FC) treatment in a rat liver metastasis model., Material and Method: We used a rat colon carcinoma cell line which, after subcapsular or intraportal injection in syngenic animals, generates single or multiple experimental liver metastases, respectively. We have shown that introduction of a vector expressing the CD gene in this colon carcinoma cell line results in 5-FC sensitivity (PRObCD)., Results: Intrahepatic subcapsular injection of PRObCD tumor cells, followed by 5-FC treatment, induces total regression of a wild-type tumor pre-established in the contralateral liver lobe in 45% of animals with a 96% decrease in mean volume (p < 0.0001), demonstrating the existence of a distant bystander effect. This vaccination significantly increased the survival of rats with single (log-rank p < 0.0001) or multiple (log-rank p = 0.01) liver metastasis, Conclusions: These results suggest that suicide gene-modified tumor cells can act as potent therapeutic vaccines against liver metastasis from colon carcinoma.

We previously reported that the Ets1 transcription factor is expressed in endothelial cells during angiogenesis both in normal and pathological development. We analyse here the effects of the stable expression of an Ets transdominant negative mutant (Ets1-DB), consisting in an Ets1 protein lacking its transactivation domain. A retrovirus containing the Ets1-DB sequence fused to an IRES-Neo sequence was designed and used to infect brain capillary (IBE) and aorta (MAE) mouse endothelial cell lines. Cells expressing this Ets1 mutant were examined for proliferation, migration and adhesion. Consistent changes were observed on cell morphology, with increased spreading and modifications in the organization of the cytoskeleton, and increased cell adhesion. We investigated the ability of endothelial cells to organise into capillary-like structures using three-dimensional gels. On Matrigel, all endothelial cell lines formed a cord-like network within 24 h, with an increased ability of Ets1-DB cells to spread on this substrate. In long term cultures, IBE cells expressing Ets1-DB showed a higher capacity to form branched structures; this effect was potentiated by FGF2. These results demonstrate a role of the Ets transcription factors in the regulation of the adhesive and morphogenetic properties of endothelial cells.

Giant diverticulum of the colon is a rare complication of the colonic diverticulosis. It generally involves the sigmoid colon. In the chronic form, without symptoms or with only a few non-specific symptoms, an abdominal mass is frequently palpable. A plain abdominal radiogram, showing a gas-filled cyst, can suggest the diagnosis. If needed, an abdominal CT scan is appropriate and seems to be more accurate than a barium enema. The treatment of choice is a segmental resection of the colon involving the giant diverticulum, followed by a direct anastomosis. Despite the old age of these patients, both postoperative morbidity and mortality are low and justify such a radical approach. The acute clinical presentation (about 20%) is generally due to a peritonitis by perforation of the giant diverticulum and requires an emergency colectomy.

Adrenal medullary hyperplasia is often misdiagnosed. The clinical features may resemble those of pheochromocytoma, with paroxysmal hypertension and elevated urinary catecholamine and metanephrine levels. Pathologic study shows diffuse or nodular adrenal medullary hyperplasia, determined by morphometric analysis: increased adrenal gland weight, increased relative medullary volume, increased relative medullary weight, decreased cortico-medullary ratio. Adrenal medullary hyperplasia may be primary or sporadic, but is often associated with multiple endocrine neoplasia (MEN) type II.