Automatically extracting functionally equivalent proteins from SwissProt

Background  

There is a frequent need to obtain sets of functionally equivalent homologous proteins (FEPs) from different species. While it is usually the case that orthology implies functional equivalence, this is not always true; therefore datasets of orthologous proteins are not appropriate. The information relevant to extracting FEPs is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEPs to be extracted on a one-off basis. However there has been no resource allowing the easy, automatic extraction of groups of FEPs – for example, all instances of protein C.     

Fetal microchimerism in kidney biopsies of lupus nephritis patients may be associated with a beneficial effect

IntroductionMicrochimeric male fetal cells (MFCs) have been associated with systemic lupus erythematosus, and published studies have further correlated MFC with lupus nephritis (LN). In the present study, we evaluated the frequency of MFC in the renal tissue of patients with LN.MethodsTwenty-seven renal biopsies were evaluated: Fourteen were from women with clinical and laboratory findings of LN, and thirteen were from controls. Genomic DNA was extracted from kidney biopsies, and the male fetal DNA was quantified using real-time quantitative polymerase chain reactions for the detection of specific Y chromosome sequences.ResultsMFCs were detected in 9 (64%) of 14 of patients with LN, whereas no MFCs were found in the control group (P = 0.0006). No differences in pregnancy history were found between patients with LN and the control group. Significantly higher amounts of MFCs were found in patients with LN with serum creatinine ≤1.5 mg/dl. Furthermore, women with MFCs had significantly better renal function at the time of biopsy (P = 0.03). In contrast, patients with LN without MFCs presented with more severe forms of glomerulonephritis (World Health Organization class IV = 60% and class V = 40%).ConclusionsOur data indicate a high prevalence of MFCs in renal biopsy specimens from women with LN, suggesting a role for MFCs in the etiology of LN. The present report also provides some evidence that MFCs could have a beneficial effect in this disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0615-4) contains supplementary material, which is available to authorized users.     

Synthesis and mass spectroscopy kinetics of a novel ternary copper(II) complex with cytotoxic activity against cancer cells

The X-ray structure of the [Cu(I-hip)(phen)2](+).(I-hip-).(H2O)7 complex (1) (where I-hipH is referred to o-iodohippuric acid and phen is 1,10-phenanthroline) and its binary synthetic intermediate [Cu(I-hip)2(H2O)3].(H2O)2 (2) have been solved and characterized by different techniques. This ternary [Cu(I-hip)(phen)2]+.(I-hip-).7H2O complex generates the copper(I) complex [Cu(phen)2]+ in aqueous solution without the addition of any external reductant, possibly by an intramolecular red-ox process in the presence of oxygen; the ESI-HRMS spectra (electrospray ionization-high resolution mass spectroscopy) detect these species and 24h after the solution, [Cu(phen)2]+ is the main product. The complex 1 is capable of cleaving DNA. To evaluate the biological properties, we carried out: cell culture, cell proliferation assays, cell cycle analysis, and electrophoresis (SDS-PAGE) and immunoblotting. Complex 1 induced apoptosis of A549 cells at low nanomolar and induced marked decreases of cancer cells at concentrations that did not change adipocyte survival. These data indicate that the parent complex is a potential anticancer drug.     

Aclidinium bromide and formoterol fumarate as a fixed-dose combination in COPD: pooled analysis of symptoms and exacerbations from two six-month,multicentre, randomised studies (ACLIFORM and AUGMENT)

Background

The combination of aclidinium bromide, a long-acting anticholinergic, and formoterol fumarate, a long-acting beta₂-agonist (400/12 μg twice daily) achieves improvements in lung function greater than either monotherapy in patients with chronic obstructive pulmonary disease (COPD), and is approved in the European Union as a maintenance treatment. The effect of this combination on symptoms of COPD and exacerbations is less well established. We examined these outcomes in a pre-specified analysis of pooled data from two 24-week, double-blind, parallel-group, active- and placebo-controlled, multicentre, randomised Phase III studies (ACLIFORM and AUGMENT).

Methods

Patients ≥40 years with moderate to severe COPD (post-bronchodilator forced expiratory volume in 1 s [FEV₁]/forced vital capacity <70 % and FEV₁ ≥30 % but <80 % predicted normal) were randomised (ACLIFORM: 2:2:2:2:1; AUGMENT: 1:1:1:1:1) to twice-daily aclidinium/formoterol 400/12 μg or 400/6 μg, aclidinium 400 μg, formoterol 12 μg or placebo via Genuair™/Pressair®. Dyspnoea (Transition Dyspnoea Index; TDI), daily symptoms (EXAcerbations of Chronic pulmonary disease Tool [EXACT]-Respiratory Symptoms [E-RS] questionnaire), night-time and early-morning symptoms, exacerbations (Healthcare Resource Utilisation [HCRU] and EXACT definitions) and relief-medication use were assessed.

Results

The pooled intent-to-treat population included 3394 patients. Aclidinium/formoterol 400/12 μg significantly improved TDI focal score versus placebo and both monotherapies at Week 24 (all p < 0.05). Over 24 weeks, significant improvements in E-RS total score, overall night-time and early-morning symptom severity and limitation of early-morning activities were observed with aclidinium/formoterol 400/12 μg versus placebo and both monotherapies (all p < 0.05). The rate of moderate or severe HCRU exacerbations was significantly reduced with aclidinium/formoterol 400/12 μg compared with placebo (p < 0.05) but not monotherapies; the rate of EXACT-defined exacerbations was significantly reduced with aclidinium/formoterol 400/12 μg versus placebo (p < 0.01) and aclidinium (p < 0.05). Time to first HCRU or EXACT exacerbation was longer with aclidinium/formoterol 400/12 μg compared with placebo (all p < 0.05) but not the monotherapies. Relief-medication use was reduced with aclidinium/formoterol 400/12 μg versus placebo and aclidinium (p < 0.01).

Conclusions

Aclidinium/formoterol 400/12 μg significantly improves 24-hour symptom control compared with placebo, aclidinium and formoterol in patients with moderate to severe COPD. Furthermore, aclidinium/formoterol 400/12 μg reduces the frequency of exacerbations compared with placebo.

Trial registration

{"type":"clinical-trial","attrs":{"text":"NCT01462942","term_id":"NCT01462942"}}NCT01462942 and {"type":"clinical-trial","attrs":{"text":"NCT01437397","term_id":"NCT01437397"}}NCT01437397 (ClinicalTrials.gov)

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0250-2) contains supplementary material, which is available to authorized users.     

Regional Speciation or Taxonomic Inflation? The Status of Several Narrowly Distributed and Endangered Species of Narcissus Using ISSR and Nuclear Ribosomal ITS Markers

The mountains of the southeast Iberian Peninsula harbor several narrowly endemic species belonging to Narcissus section Pseudonarcissi (N. alcaracensis, N. bugei, N. enemeritoi, N. longispathus, N. nevadensis, N. segurensis, and N. yepesii) that are protected by regional Spanish laws. Most of these trumpet daffodils show a very similar overall morphology, and the correct identification of species is difficult unless the geographical origins of the accessions are known. ISSR (Inter-Simple Sequence Repeat) and nuclear ribosomal ITS sequences were used to assess patterns of genetic discontinuities present among the members of this section from southeast Spain. Species-specific ISSR bands were found in N. bugei, N. longispathus and N. nevadensis, but were absent in the other species. The multivariate ordination of the 288 ISSR-genotyped accessions showed that only N. longispathus and N. bugei were clearly differentiated, while the other species formed an unresolved group. ITS sequences of N. bugei were highly divergent from those retrieved from the remaining species, which were placed in a single largely unresolved clade in phylogenetic analysis. In conclusion, ISSR and ITS markers support the taxonomic distinction of N. bugei and N. longispathus. However, N. alcaracensis, N. segurensis, N. yepesii, N. enemeritoi, and N. nevadensis could be merged within a single species (N. nevadensis for nomenclatural priority).     

Ternary complexes metal [Co(II), Ni(II), Cu(II) and Zn(II)]--ortho-iodohippurate (I-hip)--acyclovir. X-ray characterization of isostructural [(Co, Ni or Zn)(I-hip)(2)(ACV)(H(2)O)(3)] with stacking as a recognition factor

Four ternary metal--ortho-iodohippurate (I-hip)--acyclovir (ACV) complexes, [M(I-hip)(2)(ACV)(H(2)O)(3)] where M is Co(II) (1), Ni(II) (2), Cu (3) and Zn(II) have been obtained by reaction between the corresponding binary complexes M(II)(I-hip)(2)xnH(2)O and ACV. Three ternary complexes (M=Co, Ni and Zn) and the corresponding Zn(II)--ortho-iodohippurate binary derivative have been structurally characterized by X-ray diffraction: The studies show these three ternary complexes are isostructural and present, in solid state, an interesting stacking between the nucleobase and the aryl ring of the hippurate moiety, which probably promotes the formation of ternary complexes. Moreover, the two different ligands interact between them by means of ancillary hydrogen bonds with water molecules coordinated to the metal ion. It must be mentioned that these two recognition factors, hydrogen bonds plus stacking, could explain the reason for the isostructurality of these ternary derivatives with so different three metal ions, with diverses trends in coordination numbers and geometries. In solid state, there are two enantiomeric molecules that are related by an inversion center as the crystal-building unit (as a translational motif) for the ternary complexes.     

Use of Temperature for Standardizing the Progression of Francisella tularensis in Mice

The study of infectious agents, their pathogenesis, the host response and the evaluation of newly developed countermeasures often requires the use of a living system. Murine models are frequently used to undertake such investigations with the caveat that non-biased measurements to assess the progression of infection are underutilized. Instead, murine models predominantly rely on symptomology exhibited by the animal to evaluate the state of the animal''s health and to determine when euthanasia should be performed. In this study, we used subcutaneous temperature as a non-subjective measurement to follow and compare infection in mice inoculated with Francisella tularensis, a Gram-negative pathogen that produces an acute and fatal illness in mice. A reproducible temperature pattern defined by three temperature phases (normal, febrile and hypothermic) was identified in all mice infected with F. tularensis, regardless of the infecting strain. More importantly and for the first time a non-subjective, ethical, and easily determined surrogate endpoint for death based on a temperature, termed drop point, was identified and validated with statistical models. In comparative survival curve analyses for F. tularensis strains with differing virulence, the drop point temperature yielded the same results as those obtained using observed time to death. Incorporation of temperature measurements to evaluate F. tularensis was standardized based on statistical models to provide a new level of robustness for comparative analyses in mice. These findings should be generally applicable to other pathogens that produce acute febrile disease in animal models and offers an important tool for understanding and following the infection process.