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.     

Photoreceptor topography in the duplex retina of the paddlefish (Polyodon spathula)

Retinal whole-mount preparations from the eyes of the North American paddlefish, Polyodon spathula, were examined with a combination of bright field and differential interference contrast microscopy. The entire retina was mapped and population counts of rod and cone photoreceptors were made at regular intervals throughout the retina. The retina is dominated by rods, but a significant percentage (ca. 38%) of the photoreceptors are cones. Mean cone packing density for the entire retina is 6,402+/-1,216 cones/mm2. There is a small (16%) but statistically significant difference between cone packing density in the dorsal retina (6,674+/-1,168 cones/mm2) and the ventral retina (5,745+/-1,076 cones/mm2). There is no region of unusually high cone concentration that might be construed as a fovea or a visual streak. Mean rod packing density for the entire retina is 10,271+/-1,205 rods/mm2. Except in the far periphery, where rods are less numerous, the density of rods is fairly uniform throughout the retina. The data are discussed with regard to paddlefish habitat and behavior.     

Food, audience and sex effects on pinyon jay (Gymnorhinus cyanocephalus) communication

Pinyon jays (Gymnorhinus cyanocephalus) have a complex social system that may require a complex communication system. They need to interact with multiple flock members, and they form life-long pair-bonds. We researched whether pinyon jays would selectively vocalize depending on the presence or absence of food and certain flock members. We recorded the vocalizations of nine pinyon jays (four pair-bonds and one single male) in response to different audience types. The calls of the test bird were recorded after it was given either an empty food cup or one containing 50 pinyon pine (Pinus edulis) seeds, and the bird was in the presence of one of the following audience types: (1) two males and two females including subject's mate; (2) two males and two females excluding subject's mate; (3) four males excluding mate; (4) three females excluding mate; and (5) no audience. Birds gave fewer calls when there was food. When alone, birds called in a manner that may maximize long-distance transmission. Trends indicate that birds call differently to their mate. A sex effect was also found in that males and females called in a distinct manner, possibly reflecting differences in dominance status. Overall, birds responded to the presence or absence of an audience.     

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily

Protein-interaction domains can create unique macromolecular complexes that drive evolutionary innovation. By combining bioinformatic and phylogenetic analyses with structural approaches, we have discovered that the docking and dimerization (D/D) domain of the PKA regulatory subunit is an ancient and conserved protein fold. An archetypal function of this module is to interact with A-kinase-anchoring proteins (AKAPs) that facilitate compartmentalization of this key cell-signaling enzyme. Homology searching reveals that D/D domain proteins comprise a superfamily with 18 members that function in a variety of molecular and cellular contexts. Further in silico analyses indicate that D/D domains segregate into subgroups on the basis of their similarity to type I or type II PKA regulatory subunits. The sperm autoantigenic protein 17 (SPA17) is a prototype of the type II or R2D2 subgroup that is conserved across metazoan phyla. We determined the crystal structure of an extended D/D domain from SPA17 (amino acids 1–75) at 1.72 Å resolution. This revealed a four-helix bundle-like configuration featuring terminal β-strands that can mediate higher order oligomerization. In solution, SPA17 forms both homodimers and tetramers and displays a weak affinity for AKAP18. Quantitative approaches reveal that AKAP18 binding occurs at nanomolar affinity when SPA17 heterodimerizes with the ropporin-1-like D/D protein. These findings expand the role of the D/D fold as a versatile protein-interaction element that maintains the integrity of macromolecular architectures within organelles such as motile cilia.     

PXL01 in Sodium Hyaluronate for Improvement of Hand Recovery after Flexor Tendon Repair Surgery: Randomized Controlled Trial

Background

Postoperative adhesions constitute a substantial clinical problem in hand surgery. Fexor tendon injury and repair result in adhesion formation around the tendon, which restricts the gliding function of the tendon, leading to decreased digit mobility and impaired hand recovery. This study evaluated the efficacy and safety of the peptide PXL01 in preventing adhesions, and correspondingly improving hand function, in flexor tendon repair surgery.

Methods

This prospective, randomised, double-blind trial included 138 patients admitted for flexor tendon repair surgery. PXL01 in carrier sodium hyaluronate or placebo was administered around the repaired tendon. Efficacy was assessed by total active motion of the injured finger, tip-to-crease distance, sensory function, tenolysis rate and grip strength, and safety parameters were followed, for 12 months post-surgery.

Results

The most pronounced difference between the treatment groups was observed at 6 months post-surgery. At this timepoint, the total active motion of the distal finger joint was improved in the PXL01 group (60 vs. 41 degrees for PXL01 vs. placebo group, p = 0.016 in PPAS). The proportion of patients with excellent/good digit mobility was higher in the PXL01 group (61% vs. 38%, p = 0.0499 in PPAS). Consistently, the PXL01 group presented improved tip-to-crease distance (5.0 vs. 15.5 mm for PXL01 vs. placebo group, p = 0.048 in PPAS). Sensory evaluation showed that more patients in the PXL01 group felt the thinnest monofilaments (FAS: 74% vs. 35%, p = 0.021; PPAS: 76% vs. 35%, p = 0.016). At 12 months post-surgery, more patients in the placebo group were considered to benefit from tenolysis (30% vs. 12%, p = 0.086 in PPAS). The treatment was safe, well tolerated, and did not increase the rate of tendon rupture.

Conclusions

Treatment with PXL01 in sodium hyaluronate improves hand recovery after flexor tendon repair surgery. Further clinical trials are warranted to determine the most efficient dose and health economic benefits.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01022242","term_id":"NCT01022242"}}NCT01022242; EU Clinical Trials 2009-012703-25.     

Issue Information

The population of Yellow‐naped Amazons (Amazona auropalliata) declined by an estimated 50% between 1980 and 2000, and the current population is estimated to be between 10,000 and 50,000. Poaching of young has been a persistent problem, but the species is also threatened by habitat loss and degradation. Because most aspects of their life history, behavior, and ecology have not been examined in wild populations, we studied Yellow‐naped Amazons with the following objectives: (1) identify the species of trees used for nesting, (2) determine the size and potential function of breeding territories, (3) determine nesting success, and (4) examine their duetting behavior. We located nests at 16 sites on the Pacific Slope of Costa Rica from 1999 to 2008. We searched for nests from January to May. Every nest was visited at least once and some nests were visited every 2–3 weeks throughout the breeding season. We also collected territory and duetting data at one site (Ahogados). The breeding season of Yellow‐naped Amazons was during the dry season (January–May). Yellow‐naped Amazons nested in 21 species of trees, but 68% of nests were located in only five species, and cavities in dead coyols (Acrocomia aculeata) were used most often. We found no association between breeding success and the species of tree in which birds nested. Mean territory size was 25,578 m², and these small areas generally consisted of several trees surrounding a nest tree. Pairs continued to duet throughout the breeding season, suggesting that duetting is important for territory defense. The nest failure rate in our study was 89%, and most nest failures (64%) were due to poaching for the pet trade. We recommend immediate population management and conservation actions, including increased law enforcement to reduce nest poaching, protection of key nesting areas, educational programs, and habitat conservation.