Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort.

BACKGROUND: Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS: Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS: The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS: Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.

Comparison of the distraction index and Norberg angle with radiographic grading of canine hip dysplasia.

The Orthopedic Foundation for Animals (OFA) radiographic grading system stands as a well-established benchmark for categorizing hip dysplasia in canines. Although more objective techniques to quantify early hip laxity in young dogs, such as the Norberg angle (NA) and distraction index (DI), have been documented, there is a scarcity of published studies that directly compare these radiographic measures. The primary objectives of this prospective, analytical study were to assess and compare the NA and DI measures with OFA grades within a cohort of dogs. Thirty dogs (57 hip joints) were evaluated, with a mean age of 5.4 ± 2.9 years and a mean body weight of 34.3 ± 7.1 kg. The discriminative power of hip dysplasia for DI and NA used OFA as a reference were compared by multivariate discriminant analysis test. Using the DI (≤0.3) 12 joints were classified as normal, using NA (≥105°) 24 joints and using OFA (≤3) 29. When comparing the discriminant power of NA with OFA resulting similar (P = .8324) with correct classifications of 81% using cross validation, however, the discriminant power of dysplasia of the DI resulted significantly greater (P = .0034) than OFA with correct classifications of only 59% using cross-validation, consequently it was possible determined that of 29 patients with OFA ≤ 3, 20 had DI > 0.3. These findings demonstrated that phenotypic healthy dogs according to OFA grading can present passive hip joint laxity, as demonstrated by radiographic evaluation with distraction. Furthermore, DI can contribute to the screening of CHD when evaluated in conjunction with OFA grading.

Oxygen transfer and gas holdup in airlift bioreactors assembled with helical flow promoters.

Bioreactors can perform biochemical conversions mediated by biocatalysts, such as enzymes, animal cells, plants, and microorganisms. Among several existing models, airlift bioreactors are devices with the low shear environment and good mass transfer with low energy consumption, employed in several biochemical processes. The fluid flow is enabled through air injection by the sparger located at the bioreactor base. Despite its simple geometry compared with the conventional bioreactors, airlift performance can be optimized via geometrical modifications. Therefore, the objective of this work was to evaluate the effects of the addition of helical flow promoters, positioned in the riser and/or downcomer regions of an airlift of concentric tubes measuring the volumetric oxygen coefficient (kLa) and gas holdup. The results obtained by varying the gas flow rate from 1.0 to 4.0 vvm allowed the system evaluation of oxygen transfer and gas holdup. The inclusion of helical flow promoters increased the kLa, reaching up to 23% in oxygen transfer compared to tests without helicoids and up to 14% increase in the gas holdup. The inclusion of helical flow promotors was beneficial for all gas flow rates. Thus, including these flow promoters is an effective strategy to increase the oxygen transfer rate for bioprocess optimization.

Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia.

PURPOSE: Ataxia-Telangiectasia Mutated (ATM) has been implicated in the risk of several cancers, but establishing a causal relationship is often challenging. Although ATM single-nucleotide polymorphisms have been linked to melanoma, few functional alleles have been identified. Therefore, ATM impact on melanoma predisposition is unclear. METHODS: From 22 American, Australian, and European sites, we collected 2,104 familial, multiple primary (MPM), and sporadic melanoma cases who underwent ATM genotyping via panel, exome, or genome sequencing, and compared the allele frequency (AF) of selected ATM variants classified as loss-of-function (LOF) and variants of uncertain significance (VUS) between this cohort and the gnomAD non-Finnish European (NFE) data set. RESULTS: LOF variants were more represented in our study cohort than in gnomAD NFE, both in all (AF = 0.005 and 0.002, OR = 2.6, 95% CI = 1.56-4.11, p < 0.01), and familial + MPM cases (AF = 0.0054 and 0.002, OR = 2.97, p < 0.01). Similarly, VUS were enriched in all (AF = 0.046 and 0.033, OR = 1.41, 95% CI = 1.6-5.09, p < 0.01) and familial + MPM cases (AF = 0.053 and 0.033, OR = 1.63, p < 0.01). In a case-control comparison of two centers that provided 1,446 controls, LOF and VUS were enriched in familial + MPM cases (p = 0.027, p = 0.018). CONCLUSION: This study, describing the largest multicenter melanoma cohort investigated for ATM germline variants, supports the role of ATM as a melanoma predisposition gene, with LOF variants suggesting a moderate-risk.

Amazonian deforestation and soil biodiversity.

Clearance and perturbation of Amazonian forests are one of the greatest threats to tropical biodiversity conservation of our times. A better understanding of how soil communities respond to Amazonian deforestation is crucially needed to inform policy interventions that effectively protect biodiversity and the essential ecosystem services it provides. We assessed the impact of deforestation and ecosystem conversion to arable land on Amazonian soil biodiversity through a meta-analysis. We analyzed 274 pairwise comparisons of soil biodiversity in Amazonian primary forests and sites under different stages of deforestation and land-use conversion: disturbed (wildfire and selective logging) and slash-and-burnt forests, pastures, and cropping systems. Overall, 60% and 51% of responses of soil macrofauna and microbial community attributes (i.e., abundance, biomass, richness, and diversity indexes) to deforestation were negative, respectively. We found few studies on mesofauna (e.g., microarthropods) and microfauna (e.g., protozoa and nematodes), so those groups could not be analyzed. Macrofauna abundance and biomass were more vulnerable to the displacement of forests by pastures than by agricultural fields, whereas microbes showed the opposite pattern. Effects of Amazonian deforestation on macrofauna were more detrimental at sites with mean annual precipitation >1900 mm, and higher losses of microbes occurred in highly acidic soils (pH < 4.5). Limited geographic coverage, omission of meso- and microfauna, and low taxonomic resolution were main factors impairing generalizations from the data set. Few studies assessed the impacts of within-forest disturbance (wildfires and selective logging) on soil species in Amazonia, where logging operations rapidly expand across public lands and more frequent severe dry seasons are increasing the prevalence of wildfires.

Deforestación en el Amazonas y Biodiversidad del Suelo Resumen Actualmente, el despeje y la perturbación de los bosques del Amazonas son las principales amenazas para la conservación de la biodiversidad tropical. Se requiere urgentemente de un mejor entendimiento sobre cómo las comunidades del suelo responden a la deforestación amazónica para informar a las intervenciones políticas que protegen efectivamente a la biodiversidad y a los servicios ambientales esenciales que proporciona. Evaluamos el impacto de la deforestación y la conversión del ecosistema a suelo arable sobre la biodiversidad del suelo amazónico por medio de un meta-análisis. Analizamos 274 comparaciones por pares de la biodiversidad del suelo amazónico en bosques primarios y sitios bajo diferentes etapas de deforestación y conversión de uso de suelo: bosques perturbados (incendios forestales y tala selectiva) y de corte-y-quema, pasturas, y sistemas agrícolas. En general, el 60% y el 51% de las respuestas de los atributos (es decir, abundancia, biomasa, riqueza, e índices de biodiversidad) de la macrofauna del suelo y de las comunidades microbianas ante la deforestación fueron negativas, respectivamente. Encontramos pocos estudios sobre la mesofauna (p. ej.: microartrópodos) y la microfauna (p. ej.: protozoarios y nematodos), así que estos grupos no pudieron ser analizados. La abundancia de la macrofauna y la biomasa fueron más vulnerables al desplazamiento de bosques por las pasturas que por los campos agrícolas, mientras que los microbios mostraron el patrón opuesto. Los efectos de la deforestación amazónica sobre la macrofauna fueron más dañinos en sitios con una precipitación anual media mayor a los 1,900 mm, y ocurrieron pérdidas más elevadas de microbios en suelos con una acidez alta (pH < 4.5). La cobertura geográfica limitada, la omisión de la mesofauna y la microfauna, y la baja resolución taxonómica fueron los factores principales que obstaculizaron las generalizaciones del conjunto de datos. Pocos estudios evaluaron los impactos de las perturbaciones internas del bosque (incendios forestales y tala selectiva) sobre las especies del suelo amazónico, a la vez que las operaciones de tala se expanden rápidamente en los terrenos públicos y la ocurrencia con mayor frecuencia de temporadas con sequía grave aumentan la prevalencia de los incendios forestales.

Bioactive Aliphatic Sulfates from Marine Invertebrates.

The occurrence of sulfated steroids and phenolics in marine organisms is quite widespread, being typically reported from Echinoderms. In contrast, alkane and alkene aliphatic sulfates are considerably rarer with examples being reported from a diverse array of organisms including echinoderms, sponges and ascidians. While no ecological roles for these metabolites have been proposed, they do exhibit a diverse array of biological activities including thrombin inhibition; the ability to induce metamorphosis in larvae; antiproliferative, antibacterial and antifungal properties; and metalloproteinase inhibition. Of particular interest and an avenue for future development is the finding of antifouling properties with low or nontoxic effects to the environment. This review focuses on alkyl sulfates and related sulfamates, their structures and biological activities. Spectroscopic and spectrometric techniques that can be used to recognize the presence of sulfate groups are also discussed, data for which will enhance the ability of researchers to recognize this class of chemically- and biologically-interesting marine natural products.

Curation, integration and visualization of bacterial virulence factors in PATRIC.

MOTIVATION: We've developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity. RESULTS: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A-C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein-protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC. AVAILABILITY AND IMPLEMENTATION: All tools and data are freely available at PATRIC (http://patricbrc.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PATRIC, the bacterial bioinformatics database and analysis resource.

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

The condition-dependent transcriptional landscape of Burkholderia pseudomallei.

Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes--Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes--quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an "accidental pathogen", where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.

Spontaneously hypertensive rats have more orexin neurons in their medial hypothalamus than normotensive rats.

NEW FINDINGS: What is the central question of this study? Blockade of orexin receptors reduces blood pressure in spontaneously hypertensive rats (SHRs) but not in normotensive Wistar-Kyoto (WKY) rats, suggesting that upregulation of orexin signalling underlies the hypertensive phenotype of the SHR. However, it is not known what causes this upregulation. What is the main finding and its importance? Using orexin immunolabelling, we show that SHRs have 20% more orexin neurons than normotensive WKY and Wistar rats in the medial hypothalamus, which is a good match to their blood pressure phenotype. In contrast, there is no such match for the orexin neurons of the lateral hypothalamus. Essential hypertension may be linked to an increase in orexin neurons in the medial hypothalamus. The neuropeptide orexin contributes to the regulation of blood pressure as part of its role in the control of arousal during wakefulness and motivated behaviour (including responses to psychological stress). Recent work shows that pharmacological blockade of orexin receptors reduces blood pressure in spontaneously hypertensive rats (SHRs) but not in normotensive Wistar-Kyoto (WKY) rats. It is not clear why orexin signalling is upregulated in the SHR, but one possibility is that these animals have more orexin neurons than their normotensive WKY and Wistar relatives. To test this possibility, SHRs, WKY and Wistar male rats (6-16 weeks old) were killed, perfused and their brains sectioned and immunolabelled for orexin A. Labelled neurons were plotted and counted in the six best labelled hemisections (120 µm apart) of each brain. There were significantly more orexin neurons (+20%) in the medial hypothalamus (medial to fornix) of SHRs compared with WKY and Wistar rats (126 ± 4 versus 106 ± 5 and 104 ± 5 per hemisection, respectively, P < 0.05), which matches well the blood pressure phenotypes. In contrast, counts in the lateral hypothalamus did not match the blood pressure phenotypes (69 ± 2 versus 50 ± 3 and 76 ± 4, respectively). The results support the idea that orexin signalling is upregulated in the SHR and suggest that this is due, at least in part, to a greater number of orexin neurons in the medial hypothalamus. These medial orexin neurons, which are also involved in hyperarousal and stress responses, may contribute to the development of essential hypertension.

Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.

Brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family Brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens. Phylogenetic analysis split the genus into two groups: recently identified and early-dividing "atypical" strains and a highly conserved "classical" core clade containing the major pathogenic species. Lateral gene transfer events brought unique genomic regions into Brucella that differentiated them from Ochrobactrum and allowed the stepwise acquisition of virulence factors that include a type IV secretion system, a perosamine-based O antigen, and systems for sequestering metal ions that are absent in progenitors. Subsequent radiation within the core Brucella resulted in lineages that appear to have evolved within their preferred mammalian hosts, restricting their virulence to become stealth pathogens capable of causing long-term chronic infections.

Kinematic analysis of forelimb and hind limb joints in clinically healthy sheep.

BACKGROUND: Variations associated with sex, age, velocity, breed and body geometry should be considered in the determination of kinematic parameters for a gait considered normal. Therefore, this study aimed to evaluate kinematic patterns of forelimbs and hind limbs in clinically normal sheep from two different age groups walking at a constant velocity. The hypothesis was that the age may influence sagittal plane kinematic patterns. Fourteen clinically healthy female sheep were divided into Group 1--seven animals aged from 8 to 12 months, and Group 2--seven animals aged above 5 years. Before starting data collection, the sheep were trained to be conducted for walking in a pre-determined space at constant velocity. A minimum of 5 valid trials were obtained from the right and left sides of each sheep. Data were analyzed by use of a motion-analysis program. Flexion and extension joint angles (maximum, minimum, displacement), and angular velocity (maximum, minimum) were determined for the shoulder, elbow, carpal, hip, stifle, and tarsal joints. RESULTS: Within each group, no significant differences were observed between the right and left limbs in all kinematic variables. Significant differences were observed in the following kinematic parameters between G1 and G2: minimum angle (G1 < G2), angular displacement (G1 > G2), maximum angular velocity (G1 > G2), minimum angular velocity (G1 > G2) of the carpus; angular displacement (G1 > G2), minimum angular velocity (G1 > G2) of the shoulder; minimum angle (G1 > G2), angular displacement (G1 < G2) of the tarsus; maximum angular velocity (G1 < G2) of the stifle; maximum angular velocity G1 > G2 of the hip. The lengths of both forelimbs and hind limbs differed between groups (G1 < G2). The Froude number differed between groups for forelimbs and hind limbs. CONCLUSIONS: In conclusion, sheep of two different ages walking at a constant velocity present, within the same group, similar kinematic data between sides, and exhibit some differences in kinematic variables that may be age-related or body size. Further studies using sheep walking at similar Froude numbers are necessary to exclude the body size.

Early Surgical Management of Medial Patellar Luxation in Juvenile Dogs.

The aim of this study was to analyse a series of five cases of early surgical treatment in juvenile canine patients with high-grade medial patellar luxation. Canine patients, with immature skeleton, affected by grade III or IV medial patellar luxation and treated by multimodal surgical techniques were selected. Five dogs of different breeds, mean age 7.2 ± 3.0 months, met the inclusion criteria. Simultaneous distal femoral varus and external tibial torsion were identified in three of the five cases, whereas in the others, femoral varus with associated tibial valgus and isolated external tibial torsion were observed. Four of the five patients were treated surgically with closing wedge osteotomy of the distal femur, and three of them underwent tibial tuberosity transposition simultaneously. Only two animals required trochleoplasty. Mean time to beginning of weight bearing was 9.8 ± 5.5 days, whereas time to bone healing was 55 ± 24 days. Bone realignment of the extensor apparatus and return to limb support were achieved in all cases. Postoperative reintervention was needed in one patient; however, it was not linked to the initial surgery. Patients were followed up to 1 year postoperatively, with maintenance of extensor alignment and no late complications. The early surgical approach has been shown to be effective in the definitive treatment of juvenile dogs affected by high-grade medial patellar luxation.

The tale of an endemic shrimp's exceptional osmoregulation and the ancient Athalassic mangrove oasis.

The hyperarid mangrove in the Middle East is characterised by the absence of rivers or freshwater inputs and is one of the most extreme settings of this ecosystem on Earth. Endemic to Qatar's hyperarid mangroves, a Palaemon shrimp is uniquely confined to a sole mangrove site in the Arabian Gulf. Within these mangrove channels, we unveiled brine groundwater sources exceeding 70 ppt salinity, contrasting the local marine standard of 42 ppt. Concurrently, a mysid species typically linked to salt pans and groundwater coexists. Stable isotopic analysis implied the existence of a predator-prey dynamic between this mysid species and the studied shrimp. Then, investigating the endemic shrimp's adaptation to extreme salinity, we conducted osmolarity experiments and phylogenetic studies. Our findings demonstrate that this shrimp transitions from hypo- to hyper-osmoregulation, tolerating salinities from 18 to 68 ppt-an unprecedented osmoregulatory capacity among caridean shrimps. This speciation pattern likely arises from the species osmolarity adaptation, as suggested for other Palaemon congeners. Phylogenetic analysis of the studied Palaemon, along with the mangrove's geological history, suggests a profound evolutionary interplay between the ecosystem and the shrimp since the Eocene. This study proposes the hyperarid mangrove enclave as an Athalassic mangrove oasis-a distinctive, isolated ecosystem within the desert landscape.

Effects of Human Observer Presence on Pain Assessment Using Facial Expressions in Rabbits.

The goal of this study was to evaluate the effect of a human observer on Rabbit Grimace Scale (RbtGS) scores. The study scored video footage taken of 28 rabbits before and after orthopedic surgery, as follows: 24 h before surgery ( baseline), 1 h after surgery ( pain), 3 h after analgesia administration ( analgesia), and 24 h after surgery ( 24h) in the presence and absence of an observer. Videos were assessed twice in random order by 3 evaluators who were blind to the collection time and the presence or absence of an observer. Responses to pain and analgesia were evaluated by comparing the 4 time points using the Friedman test, followed by the Dunn test. The influence of the presence or absence of the observer at each time point was evaluated using the Wilcoxon test. Intra- and interrater reliabilities were estimated using the intraclass correlation coefficient. The scale was responsive to pain, as the scores increased after surgery and had decreased by 24 h after surgery. The presence of the observer reduced significantly the RbtGS scores (median and range) at pain (present, 0.75, 0 to 1.75; absent, 1, 0 to 2) and increased the scores at baseline (present, 0.2, 0 to 2; absent, 0, 0 to 2) and 24h after surgery (present, 0.33, 0 to 1.75; absent, 0.2, 0 to 1.5). The intrarater reliability was good (0.69) to very good (0.82) and interrater reliability was moderate (0.49) to good (0.67). Thus, the RbtGS appeared to detect pain when scored from video footage of rabbits before and after orthopedic surgery. In the presence of the observer, the pain scores were underestimated at the time considered to be associated with the greatest pain and overestimated at the times of little or no pain.

Expanding ocean protection and peace: a window for science diplomacy in the Gulf.

The ecological state of the Persian or Arabian Gulf (hereafter 'Gulf') is in sharp decline. Calls for comprehensive ecosystem-based management approaches and transboundary conservation have gone largely unanswered, despite mounting marine threats made worse by climate change. The region's long-standing political tensions add additional complexity, especially now as some Gulf countries will soon adopt ambitious goals to protect their marine environments as part of new global environmental commitments. The recent interest in global commitments comes at a time when diplomatic relations among all Gulf countries are improving. There is a window of opportunity for Gulf countries to meet global marine biodiversity conservation commitments, but only if scientists engage in peer-to-peer diplomacy to build trust, share knowledge and strategize marine conservation options across boundaries. The Gulf region needs more ocean diplomacy and coordination; just as critically, it needs actors at its science-policy interface to find better ways of adapting cooperative models to fit its unique marine environment, political context and culture. We propose a practical agenda for scientist-led diplomacy in the short term and lines of research from which to draw (e.g. co-production, knowledge exchange) to better design future science diplomacy practices and processes suited to the Gulf's setting.

A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle.

We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ~35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity.

Abscisic acid regulates inflammation via ligand-binding domain-independent activation of peroxisome proliferator-activated receptor gamma.

Abscisic acid (ABA) has shown efficacy in the treatment of diabetes and inflammation; however, its molecular targets and the mechanisms of action underlying its immunomodulatory effects remain unclear. This study investigates the role of peroxisome proliferator-activated receptor γ (PPAR γ) and lanthionine synthetase C-like 2 (LANCL2) as molecular targets for ABA. We demonstrate that ABA increases PPAR γ reporter activity in RAW 264.7 macrophages and increases ppar γ expression in vivo, although it does not bind to the ligand-binding domain of PPAR γ. LANCL2 knockdown studies provide evidence that ABA-mediated activation of macrophage PPAR γ is dependent on lancl2 expression. Consistent with the association of LANCL2 with G proteins, we provide evidence that ABA increases cAMP accumulation in immune cells. ABA suppresses LPS-induced prostaglandin E(2) and MCP-1 production via a PPAR γ-dependent mechanism possibly involving activation of PPAR γ and suppression of NF-κB and nuclear factor of activated T cells. LPS challenge studies in PPAR γ-expressing and immune cell-specific PPAR γ null mice demonstrate that ABA down-regulates toll-like receptor 4 expression in macrophages and T cells in vivo through a PPAR γ-dependent mechanism. Global transcriptomic profiling and confirmatory quantitative RT-PCR suggest novel candidate targets and demonstrate that ABA treatment mitigates the effect of LPS on the expression of genes involved in inflammation, metabolism, and cell signaling, in part, through PPAR γ. In conclusion, ABA decreases LPS-mediated inflammation and regulates innate immune responses through a bifurcating pathway involving LANCL2 and an alternative, ligand-binding domain-independent mechanism of PPAR γ activation.

Integration and visualization of host-pathogen data related to infectious diseases.

MOTIVATION: Infectious disease research is generating an increasing amount of disparate data on pathogenic systems. There is a growing need for resources that effectively integrate, analyze, deliver and visualize these data, both to improve our understanding of infectious diseases and to facilitate the development of strategies for disease control and prevention. RESULTS: We have developed Disease View, an online host-pathogen resource that enables infectious disease-centric access, analysis and visualization of host-pathogen interactions. In this resource, we associate infectious diseases with corresponding pathogens, provide information on pathogens, pathogen virulence genes and the genetic and chemical evidences for the human genes that are associated with the diseases. We also deliver the relationships between pathogens, genes and diseases in an interactive graph and provide the geolocation reports of associated diseases around the globe in real time. Unlike many other resources, we have applied an iterative, user-centered design process to the entire resource development, including data acquisition, analysis and visualization. AVAILABILITY AND IMPLEMENTATION: Freely available at http://www.patricbrc.org; all major web browsers supported. CONTACT: cmao@vbi.vt.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effect of intraperitoneal or incisional bupivacaine on pain and the analgesic requirement after ovariohysterectomy in dogs.

OBJECTIVE: To compare the effect of intraperitoneal (IP) or incisional (INC) bupivacaine on pain and the analgesic requirement after ovariohysterectomy in dogs. STUDY DESIGN: Prospective, randomized clinical study. ANIMALS: Thirty female dogs undergoing ovariohysterectomy (OHE). METHODS: Dogs admitted for elective OHE were anesthetized with acepromazine, butorphanol, thiopental and halothane. Animals were randomly assigned to one of three groups (n = 10 per group). The treatments consisted of preincisional infiltration with saline solution (NaCl 0.9%) or bupivacaine with epinephrine and/or IP administration of the same solutions, as follows: INC and IP 0.9% NaCl (control group); INC 0.9% NaCl and IP bupivacaine (5 mg kg(-1), IP group); INC bupivacaine (1 mg kg(-1)) and IP 0.9% NaCl (INC group). Postoperative pain was evaluated by a blinded observer for 24 hours after extubation by means of a visual analog scale (VAS) and a numeric rating scale (NRS). Rescue analgesia (morphine, 0.5 mg kg(-1) , IM) was administered if the VAS was >5/10 or the NRS >10/29. RESULTS: At 1 hour after anesthesia, VAS pain scores were [medians (interquartile range)]: 6.4 (3.1-7.9), 0.3 (0.0-2.6) and 0.0 (0.0-7.0) in control, IP and INC groups, respectively. VAS pain scores were lower in the IP compared to the control group. Over the first 24 hours, rescue analgesia was administered to 7/10, 5/10 and 3/10 dogs of the control, INC and IP groups, respectively. Total number of dogs given rescue analgesia over the first 24 hours did not differ significantly among groups. CONCLUSIONS AND CLINICAL RELEVANCE: Intraperitoneal bupivacaine resulted in lower pain scores during the first hour of the postoperative period and there was a trend towards a decreased need for rescue analgesia after OHE in dogs.