Simplified and still meaningful: assessing butterfly habitat quality in grasslands with data collected by pupils

Public participation in scientific research, now commonly referred to as citizen science, is increasingly promoted as a possibility to overcome the large-scale data limitations related to biodiversity and conservation research. Furthermore, public data-collection projects can stimulate public engagement and provide transformative learning situations. However, biodiversity monitoring depends on sound data collection and warranted data quality. Therefore, we investigated if and how trained and supervised pupils are able to systematically collect data about the occurrence of diurnal butterflies, and how this data could contribute to a permanent butterfly monitoring system. We developed a specific assessment scheme suitable for laypeople and applied it at 35 sampling sites in Tyrol, Austria. Data quality and its explanatory power to predict butterfly habitat quality was investigated comparing data collected by pupils with independent assessments of professional butterfly experts. Despite substantial identification uncertainties for some species or species groups, the data collected by pupils was successfully used to predict the general habitat quality for butterflies using a linear regression model (r²?=?0.73, p?<0.001). Applying the proposed method in a citizen science context with laypeople could support both the long term monitoring of butterfly habitat quality, as well as the efficient selection of sites for professional in-depth assessments.     

Suggested guidelines for the diagnosis and management of urea cycle disorders

ABSTRACT: Urea cycle disorders (UCDs) are inborn errors of ammonia detoxification/arginine synthesis due to defects affecting the catalysts of the Krebs-Henseleit cycle (five core enzymes, one activating enzyme and one mitochondrial ornithine/citrulline antiporter) with an estimated incidence of 1:8.000. Patients present with hyperammonemia either shortly after birth (~50%) or, later at any age, leading to death or to severe neurological handicap in many survivors. Despite the existence of effective therapy with alternative pathway therapy and liver transplantation, outcomes remain poor. This may be related to underrecognition and delayed diagnosis due to the nonspecific clinical presentation and insufficient awareness of health care professionals because of disease rarity. These guidelines aim at providing a trans-European consensus to: guide practitioners, set standards of care and help awareness campaigns. To achieve these goals, the guidelines were developed using a Delphi methodology, by having professionals on UCDs across seven European countries to gather all the existing evidence, score it according to the SIGN evidence level system and draw a series of statements supported by an associated level of evidence. The guidelines were revised by external specialist consultants, unrelated authorities in the field of UCDs and practicing pediatricians in training. Although the evidence degree did not exceed level C (evidence from non-analytical studies like case reports and series), it was sufficient to guide practice on both acute and chronic presentations, address diagnosis, management, monitoring, outcomes, and psychosocial and ethical issues. Also, it identified knowledge voids that must be filled by future research. We believe these guidelines will help to: harmonise practice, set common standards and spread good practices with a positive impact on the outcomes of UCD patients.     

Characterization of monoclonal antibodies to human immunodefiency virus type 1 gp41 by HIV-1 polypeptides expressed in Escherichia coli

Abstract Two monoclonal antibodies (MAbs) were produced in Balb/c mice by immunization with recombinant gp41 derived from expression of λ-BH10 cDNA of the human immunowdeficiency virus-1 (HIV-1) in the prokaryotic expression vector pEX-41 [1, 2]. Characterization of the epitopes recognized by these MAbs was done with HIV-1 envelope (env) fusion proteins expressed in Escherochia coli encoding ten distinct segments of the env proteins [3]. In comparison, another mouse MAb, M25 [4], a human MAb directed against gp41, which was produced by the xeno hydridoma line 3D6 [5, 6] and a pool of human patient sera containing antibodies to HIV-1 were tested. We were able to demonstrate that the epitopes recognized by our MAbs are located betweeni arg732 and ser759 [7] of the HIV-1 env glycoprotein gp160 of HTLV-III strain B. M25 reacted with epitopes between ser647 and pro731, which includes the hydrophobic transmembrane region of gp41 [4]. The human MAb against gp41, 3D6 [5, 6] reacts with epitopes between ile474 and trp646, a polypeptide stretch consisting of gp120 and gp41 specific amino acids. The human serum pool, positive for HIV-1 antibodies, reacted predominantly with antigenic determinants locatedp between ile474 and leu863. The recombinant env fusion proteins were initially produced to test the immunoreactivity with patient sera and to characterize epitopes which are relevant for immunodiagnostic purposes [3]. In this study, we showed that the set of recombinant evr proteins is also a simple and accurate tool for the characterization of MAbs directed to the HIV envelope proteins.     

Left handed �� helix models for mammalian prion fibrils

We propose models for in vitro grown mammalian prion protein fibrils based upon left handed beta helices formed both from the N-terminal and C-terminal regions of the proteinase resistant infectious prion core. The C-terminal threading onto a β-helical structure is almost uniquely determined by fixing the cysteine disulfide bond on a helix corner. In comparison to known left handed helical peptides, the resulting model structures have similar stability attributes including relatively low root mean square deviations in all atom molecular dynamics, substantial side-chain-to-side-chain hydrogen bonding, good volume packing fraction, and low hydrophilic/hydrophobic frustration. For the N-terminus, we propose a new threading of slightly more than two turns, which improves upon the above characteristics relative to existing three turn β-helical models. The N-terminal and C-terminal beta helices can be assembled into eight candidate models for the fibril repeat units, held together by large hinge (order 30 residues) domain swapping, with three amenable to fibril promoting domain swapping via a small (five residue) hinge on the N-terminal side. Small concentrations of the metastable C-terminal β helix in vivo might play a significant role in templating the infectious conformation and in enhancing conversion kinetics for inherited forms of the disease and explain resistance (for canines) involving hypothesized coupling to the methionine 129 sulfur known to play a role in human disease.Key words: prion, amyloid fibril, domain swap, beta helix, computational biology     

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

Background  

Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets.     

Effects of dopamine on human retinal vessel diameter and its modulation during flicker stimulation

We performed a randomized, subject-blinded, placebo and time-controlled, two-way crossover study in 12 healthy male subjects. Placebo or dopamine was administered on two separate study days. After saline infusion, dopamine hydrochloride was infused in three consecutive doses (5, 10, and 15 microg x kg(-1) x min(-1)). Plasma levels of dopamine were determined at each perfusion step. Arterial and venous retinal vessel diameters were measured with the use of a Zeiss retinal vessel analyzer. Diffuse luminance flicker stimuli of 8 Hz were applied for 60 s. Blood pressure and pulse rate were monitored continuously. Flicker stimulation (8 Hz) increased retinal vessel diameters under basal conditions. The response to 8-Hz flicker light was significantly reduced by dopamine administration. In addition, dopamine slightly but significantly increased retinal vessel diameters. Dopamine hydrochloride significantly increased systolic but not diastolic or mean arterial pressure. The present study indicates that dopamine has a distinct effect on retinal vessel diameters also attenuating the flicker-induced response reactivity of retinal vessels. This implies a role of dopamine in retinal blood flow hemodynamics.     

Analysis of publications in three plastic surgery journals for the year 2002

The goal of this study was to analyze the publications in the plastic surgery literature for the year 2002. Contents of these articles, authors' information (such as nationality affiliation of the first author), type of institution, presence of grant support, and previous presentation were analyzed. For inclusion in this study, the publications had to be original articles from the three most frequently read general plastic surgery journals: Annals of Plastic Surgery, British Journal of Plastic Surgery, and Plastic and Reconstructive Surgery. With this approach, 533 articles were included in the study. To give a cross-sectional analysis of the content of all articles, 11 distinct categories were created in which all the articles were subsummarized. The categories were based on anatomical regions and specific plastic surgical areas. A summary is given for each of the categories to provide an overview of the field in which most of the research in plastic surgery was taking place in 2002 and which topics were focused on. The authors found that only 7 percent of all articles had grant support, whereas 36 percent of articles were presented previously during a scientific meeting. Most of the articles came from university-based institutions (68 percent), followed by non-university-based institutions (29 percent) and private practice (3 percent). Regarding nationality affiliation, most of the articles came from the United States (n = 229) and Europe (n = 128); in Asia, Turkey (n = 39) and Japan (n = 36) were the countries with the most published articles.