Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group,the Neotropical Pristimantis leaf litter frogs

The Neotropical leaf litter frog genus Pristimantis is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in Pristimantis. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 Pristimantis presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of Pristimantis at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in Pristimantis phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within Pristimantis. Diversification rates decrease towards the present following a density-dependent pattern for Pristimantis overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of Pristimantis and thus contributed to the origins of evolutionary independent phylogenetic clusters.     

Prolonged lifespan with enhanced exploratory behavior in mice overexpressing the oxidized nucleoside triphosphatase hMTH1

The contribution that oxidative damage to DNA and/or RNA makes to the aging process remains undefined. In this study, we used the hMTH1‐Tg mouse model to investigate how oxidative damage to nucleic acids affects aging. hMTH1‐Tg mice express high levels of the hMTH1 hydrolase that degrades 8‐oxodGTP and 8‐oxoGTP and excludes 8‐oxoguanine from both DNA and RNA. Compared to wild‐type animals, hMTH1‐overexpressing mice have significantly lower steady‐state levels of 8‐oxoguanine in both nuclear and mitochondrial DNA of several organs, including the brain. hMTH1 overexpression prevents the age‐dependent accumulation of DNA 8‐oxoguanine that occurs in wild‐type mice. These lower levels of oxidized guanines are associated with increased longevity and hMTH1‐Tg animals live significantly longer than their wild‐type littermates. Neither lipid oxidation nor overall antioxidant status is significantly affected by hMTH1 overexpression. At the cellular level, neurospheres derived from adult hMTH1‐Tg neural progenitor cells display increased proliferative capacity and primary fibroblasts from hMTH1‐Tg embryos do not undergo overt senescence in vitro. The significantly lower levels of oxidized DNA/RNA in transgenic animals are associated with behavioral changes. These mice show reduced anxiety and enhanced investigation of environmental and social cues. Longevity conferred by overexpression of a single nucleotide hydrolase in hMTH1‐Tg animals is an example of lifespan extension associated with healthy aging. It provides a link between aging and oxidative damage to nucleic acids.     

M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations

Background

Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to elucidate functional behaviors of proteins on a system level. Gene Ontology (GO) and its annotations are a significant resource for functional characterization of proteins. Because of wide coverage, GO data have often been adopted as a benchmark for protein function prediction on the genomic scale.

Results

We propose a computational approach, called M-Finder, for functional association pattern mining. This method employs semantic analytics to integrate the genome-wide PPIs with GO data. We also introduce an interactive web application tool that visualizes a functional association network linked to a protein specified by a user. The proposed approach comprises two major components. First, the PPIs that have been generated by high-throughput methods are weighted in terms of their functional consistency using GO and its annotations. We assess two advanced semantic similarity metrics which quantify the functional association level of each interacting protein pair. We demonstrate that these measures outperform the other existing methods by evaluating their agreement to other biological features, such as sequence similarity, the presence of common Pfam domains, and core PPIs. Second, the information flow-based algorithm is employed to discover a set of proteins functionally associated with the protein in a query and their links efficiently. This algorithm reconstructs a functional association network of the query protein. The output network size can be flexibly determined by parameters.

Conclusions

M-Finder provides a useful framework to investigate functional association patterns with any protein. This software will also allow users to perform further systematic analysis of a set of proteins for any specific function. It is available online at http://bionet.ecs.baylor.edu/mfinder

     

Systematic revision and molecular phylogeny of the land snail genus Fruticocampylaea (Gastropoda: Hygromiidae) from the Caucasus region

This paper presents a systematic revision and a molecular phylogenetic analysis of the Caucasian land snail genus Fruticocampylaea. The genus is newly delimited based on the reduction of the cavities adjoining the seminal duct in the penial papilla. Shell and genitalia of all five species (F. narzanensis, F. kobensis, F. tushetica sp. nov., F. christophori, F. daghestana) are described and figures provided. All synonyms and all locality records are listed. Maximum likelihood and Bayesian analyses of mitochondrial and nuclear DNA sequences (fragments of cox1, 16S rDNA, ITS2 and 28S rDNA) confirm the monophyly of Fruticocampylaea. The reduction of the dart apparatus and the conical plug, via which the dart apparatus inserts into the vagina, as well as the molecular phylogenetic analyses, suggests a sister group relationship between Fruticocampylaea and Circassina (without Abchasohela). Furthermore, the molecular phylogenetic analyses indicate that the Fruticocampylaea species originated in a rapid radiation. The uplift of the Greater Caucasus in the Late Miocene or Pliocene or climatic changes at the end of the Pliocene or in the early Pleistocene may have caused the radiation of Fruticocampylaea. Low intraspecific variability can be explained by population bottlenecks during Pleistocene glacial periods followed by postglacial population increase.

http://zoobank.org/urn:lsid:zoobank.org:pub:AB15158D-21A3-4945-8D49-F7DE8E406E2B     

High serum sCD163/sTWEAK ratio is associated with lower risk of digital ulcers but more severe skin disease in patients with systemic sclerosis

Introduction

Systemic sclerosis (SSc) is an autoimmune disease characterized by chronic inflammation, vascular injury and excessive fibrosis. CD163 is a scavenger receptor which affects inflammatory response and may contribute to connective tissue remodelling. It has recently been demonstrated that CD163 can bind and neutralize the TNF-like weak inducer of apoptosis (TWEAK), a multifunctional cytokine which regulates inflammation, angiogenesis and tissue remodelling. We aimed to investigate the relationships between serum levels of soluble CD163 (sCD163) and soluble TWEAK (sTWEAK) in relation to disease manifestations in SSc patients.

Methods

This study included 89 patients with SSc who had not received immunosuppressive drugs or steroids for at least 6 months and 48 age- and sex-matched healthy controls (HC) from four European centres. Serum concentrations of sTWEAK and sCD163 were measured using commercially available ELISA kits.

Results

The mean serum concentrations of sTWEAK were comparable between SSc patients (mean +/- SD: 270 +/- 171 pg/mL) and HC (294 +/- 147pg/mL, P >0.05). Concentration of sCD163 and sCD163/sTWEAK ratio were significantly greater in SSc patients (984 +/- 420 ng/mL and 4837 +/- 3103, respectively) as compared to HC (823 +/- 331 ng/mL and 3115 +/- 1346 respectively, P <0.05 for both). High sCD163 levels and a high sCD163/sTWEAK ratio (defined as > mean +2SD of HC) were both associated with a lower risk of digital ulcers in SSc patients (OR, 95%CI: 0.09; 0.01, 0.71, and 0.17; 0.06, 0.51, respectively). Accordingly, patients without digital ulcers had a significantly higher sCD163 concentration and sCD163/sTWEAK ratio as compared to SSc patients with digital ulcers (P <0.01 for both) and HC (P <0.05 for both). A high sCD163/sTWEAK ratio, but not high sCD163 levels, was associated with greater skin involvement.

Conclusions

The results of our study indicate that CD163-TWEAK interactions might play a role in the pathogenesis of SSc and that CD163 may protect against the development of digital ulcers in SSc. Further studies are required to reveal whether targeting of the CD163-TWEAK pathway might be a potential strategy for treating vascular disease and/or skin fibrosis in SSc.     

Systemic sclerosis sera affect fibrillin-1 deposition by dermal blood microvascular endothelial cells: therapeutic implications of cyclophosphamide

Introduction

Systemic sclerosis (SSc) is a connective tissue disorder characterized by endothelial cell injury, autoimmunity and fibrosis. The following three fibrillin-1 alterations have been reported in SSc. (1) Fibrillin-1 microfibrils are disorganized in SSc dermis. (2) Fibrillin-1 microfibrils produced by SSc fibroblasts are unstable. (3) Mutations in the FBN1 gene and anti-fibrillin-1 autoantibodies have been reported in SSc. Fibrillin-1 microfibrils, which are abundantly produced by blood and lymphatic microvascular endothelial cells (B-MVECs and Ly-MVECs, respectively), sequester in the extracellular matrix the latent form of the potent profibrotic cytokine transforming growth factor β (TGF-β). In the present study, we evaluated the effects of SSc sera on the deposition of fibrillin-1 and microfibril-associated glycoprotein 1 (MAGP-1) and the expression of focal adhesion molecules by dermal B-MVECs and Ly-MVECs.

Methods

Dermal B-MVECs and Ly-MVECs were challenged with sera from SSc patients who were treatment-naïve or under cyclophosphamide (CYC) treatment and with sera from healthy controls. Fibrillin-1/MAGP-1 synthesis and deposition and the expression of α_vβ₃ integrin/phosphorylated focal adhesion kinase and vinculin/actin were evaluated by immunofluorescence and quantified by morphometric analysis.

Results

Fibrillin-1 and MAGP-1 colocalized in all experimental conditions, forming a honeycomb pattern in B-MVECs and a dense mesh of short segments in Ly-MVECs. In B-MVECs, fibrillin-1/MAGP-1 production and α_vβ₃ integrin expression significantly decreased upon challenge with sera from naïve SSc patients compared with healthy controls. Upon challenge of B-MVECs with sera from CYC-treated SSc patients, fibrillin-1/MAGP-1 and α_vβ₃ integrin levels were comparable to those of cells treated with healthy sera. Ly-MVECs challenged with SSc sera did not differ from those treated with healthy control sera in the expression of any of the molecules assayed.

Conclusions

Because of the critical role of fibrillin-1 in sequestering the latent form of TGF-β in the extracellular matrix, its decreased deposition by B-MVECs challenged with SSc sera might contribute to dermal fibrosis. In SSc, CYC treatment might limit fibrosis through the maintenance of physiologic fibrillin-1 synthesis and deposition by B-MVECs.     

Volumetric-modulated arc therapy with RapidArc®: An evaluation of treatment delivery efficiency

Aim/background

To evaluate how the use of volumetric-modulated arc therapy (VMAT) with RapidArc^® can improve treatment delivery efficiency based on the analysis of the beam-on times and monitor units (MU) needed to deliver therapy for multiple clinical applications in a large patient population.

Materials and methods

A total of 898 treatment courses were delivered in 745 patients treated from October 2008 to March 2013 using RapidArc® treatment plans generated in Eclipse™ TPS. All patients were treated with curative or palliative intent using different techniques including conventional fractionation (83%) and radiosurgery or SBRT (17%), depending on the clinical indications. Treatment delivery was evaluated based on measured beam-on time and recorded MU values delivered on a Varian Trilogy™ linear accelerator.

Results

For conventional fractionation treatments using RapidArc®, the delivery times ranged from 38 s to 4 min and 40 s (average 2 min and 6 s). For radiosurgical treatments the delivery times ranged from 1 min and 42 s to 9 min and 22 s (average 4 min and 4 s). The average number of MU per Gy was 301 for the entire group, with 285 for the conventional group and 317 for the radiosurgical group.

Conclusions

In this study with a large heterogeneous population, treatments using RapidArc® were delivered with substantially less beam-on time and fewer MUs than conventional fractionation. This was highly advantageous, increasing flexibility of the scheduling allowing treatment of radiosurgery patients during the regular daily work schedule. Additionally, reduction of leakage radiation dose was achieved.     

Intracavitary Immunotherapy and Chemotherapy for Upper Urinary Tract Cancer: Current Evidence

A review of the literature was performed to summarize current evidence regarding the efficacy of topical immunotherapy and chemotherapy for upper urinary tract urothelial cell carcinoma (UUT-UCC) in terms of post-treatment recurrence rates. A Medline database literature search was performed in March 2012 using the terms upper urinary tract, urothelial cancer, bacillus Calmette-Guérin (BCG), and mitomycin C. A total of 22 full-text articles were assessed for eligibility, and 19 studies reporting the outcomes of patients who underwent immunotherapy or chemotherapy with curative or adjuvant intent for UUT-UCC were chosen for quantitative analysis. Overall, the role of immunotherapy and chemotherapy for UUT-UCC is not firmly established. The most established practice is the treatment of carcinoma in situ (CIS) with BCG, even if a significant advantage has not yet been proven. The use of BCG as adjuvant therapy after complete resection of papillary UUT-UCC has been studied less extensively, even if recurrence rates are not significantly different than after the treatment of CIS. Only a few reports describe the use of mitomycin C, making it difficult to obtain significant evidence.Key words: Upper urinary tract, Urothelial cell carcinoma, Bacillus Calmette-Guérin, Mitomycin C, Chemotherapy, ImmunotherapyAccording to the 2011 update of the European Guidelines for the diagnosis and management of upper urinary tract urothelial cell carcinoma (UUT-UCC),¹ urothelial carcinomas are the fourth most common tumors after prostate and breast cancer, lung cancer, and colorectal cancer. Bladder tumors account for 90% to 95% of urothelial carcinomas; UUT-UCC are relatively uncommon and account for only 5% to 10% of urothelial carcinomas. The annual incidence of UUT-UCC in Western countries is approximately one or two new cases per 100,000 inhabitants. Pyelocaliceal tumors are approximately twice as common as ureteral tumors. In 8% to 13% of cases, concurrent bladder cancer is present, and 60% of UUT-UCC are invasive at diagnosis, compared with only 15% of bladder tumors. This kind of carcinoma has a peak incidence in people in their 70s and 80s, with a higher prevalence in men.Radical nephroureterectomy (RNU) with excision of the bladder cuff represents the gold standard treatment for UUT-UCC, regardless of the location of the tumor in the upper urinary tract.¹ Lymph node dissection associated with RNU is of therapeutic interest and allows for optimal staging of the disease.Conservative surgery for low-risk UUT-UCC allows for preservation of the upper urinary renal unit; conservative management can be considered in imperative cases (renal insufficiency, solitary functional kidney) or in elective cases (ie, when the contralateral kidney is functional) for low-grade, low-stage tumors. Endoscopic ablation can be considered if a flexible ureteroscope, laser generator, and pliers (pluck) for biopsies are available, if the patient is informed of the need for closer follow-up, and if a complete resection is advocated.Segmental ureteral resection with wide margins provides adequate pathologic specimens for definitive staging and grade analysis while also preserving the ipsilateral kidney. Segmental resection is possible for the treatment of low- and high-risk tumors of the distal ureter, whereas segmental resection of the iliac and lumbar ureter is associated with a greater failure rate. Open resection of tumors of the renal pelvis or calices has almost disappeared.Percutaneous management can be considered for low-grade or noninvasive UUT-UCC that are inaccessible or difficult to manage by ureteroscopy, even if a theoretical risk of seeding exits in the puncture tract and if perforations occur during the procedure.After conservative treatment of UUT-UCC or for the treatment of carcinoma in situ (CIS), the instillation of bacillus Calmette-Guérin (BCG) or mitomycin C (MMC) is technically feasible by means of a percutaneous nephrostomy or even through a ureteric stent.Different agents have been used for topical therapy, including BCG, MMC, epirubicine, and thiotepa. Topical chemotherapeutic agents can be administered after endoscopic management, whereas instillations of BCG need to be postponed until the urothelium heals to avoid systemic side effects.According to a recent review,² topical therapy appears to be safe, although its efficacy is debatable. Complications from the administration of topical immunotherapy or chemotherapy can be avoided by maintaining low intracavitary pressures during administration. Renal function does not seem to be impaired after instillation of BCG or MMC.³ No systemic side effects result from perfusion with MMC, and persistent fever was reported in 5% of patients in combined major series after BCG administration; therefore, this side effect was resolved with appropriate antimicrobial therapy in all cases. Furthermore, up to 25% of patients may have granulomatous involvement of the urinary tract after BCG.This review summarizes current evidence about the efficacy of topical immunotherapy and chemotherapy in terms of post-treatment recurrence rates.