Genome and secretome analyses provide insights into keratin decomposition by novel proteases from the non-pathogenic fungus <i>Onygena corvina</i>

Poultry processing plants and slaughterhouses produce huge quantities of feathers and hair/bristle waste annually. These keratinaceous wastes are highly resistant to degradation. Onygena corvina, a non-pathogenic fungus, grows specifically on feathers, hooves, horn, and hair in nature. Hence, the proteases secreted by O. corvina are interesting in view of their potential relevance for industrial decomposition of keratinaceous wastes. We sequenced and assembled the genome of O. corvina and used a method called peptide pattern recognition to identify 73 different proteases. Comparative genome analysis of proteases in keratin-degrading and non-keratin-degrading fungi indicated that 18 putative secreted proteases from four protease families (M36, M35, M43, and S8) may be responsible for keratin decomposition. Twelve of the 18 predicted protease genes could be amplified from O. corvina grown on keratinaceous materials and were transformed into Pichia pastoris. One of the recombinant proteases belonging to the S8 family showed high keratin-degrading activity. Furthermore, 29 different proteases were identified by mass spectrometry in the culture broth of O. corvina grown on feathers and bristle. The culture broth was fractionated by ion exchange chromatography to isolate active fractions with five novel proteases belonging to three protease families (S8, M28, and M3). Enzyme blends composed of three of these five proteases, one from each family, showed high degree of degradation of keratin in vitro. A blend of novel proteases, such as those we discovered, could possibly find a use for degrading keratinaceous wastes and provide proteins, peptides, and amino acids as valuable ingredients for animal feed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-015-6805-9) contains supplementary material, which is available to authorized users

Identifying predictive features of autism spectrum disorders in a clinical sample of adolescents and adults using machine learning

Diagnosing autism spectrum disorders (ASD) is a complicated, time-consuming process which is particularly challenging in older individuals. One of the most widely used behavioral diagnostic tools is the Autism Diagnostic Observation Schedule (ADOS). Previous work using machine learning techniques suggested that ASD detection in children can be achieved with substantially fewer items than the original ADOS. Here, we expand on this work with a specific focus on adolescents and adults as assessed with the ADOS Module 4. We used a machine learning algorithm (support vector machine) to examine whether ASD detection can be improved by identifying a subset of behavioral features from the ADOS Module 4 in a routine clinical sample of N = 673 high-functioning adolescents and adults with ASD (n = 385) and individuals with suspected ASD but other best-estimate or no psychiatric diagnoses (n = 288). We identified reduced subsets of 5 behavioral features for the whole sample as well as age subgroups (adolescents vs. adults) that showed good specificity and sensitivity and reached performance close to that of the existing ADOS algorithm and the full ADOS, with no significant differences in overall performance. These results may help to improve the complicated diagnostic process of ASD by encouraging future efforts to develop novel diagnostic instruments for ASD detection based on the identified constructs as well as aiding clinicians in the difficult question of differential diagnosis

Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader

Huge quantities of keratinaceous waste are a substantial and almost totally unexploited protein resource which could be upgraded for use as high value-added products by efficient keratinolytic enzymes. In this study, we found that Bacillus sp. 8A6 can efficiently degrade chicken feather after 24h growth. According to phylogenetic analysis, the strain (formerly identified as Bacillus pumilus 8A6) belongs to the B. pumilus species clade but it is more closely related to B. safensis. Hotpep predicted 233 putative proteases from Bacillus sp. 8A6 genome. Proteomic analysis of culture broths from Bacillus sp. 8A6 cultured on chicken feathers or on a mixture of bristles and hooves showed high abundance of proteins with functions related to peptidase activity. Five proteases (one from family M12, one from family S01A, two from family S08A and one from family T3) and four oligopeptide and dipeptide binding proteins were highly expressed when Bacillus sp. 8A6 was grown in keratin media compared to LB medium. This study is the first to report that bacterial proteases in families M12, S01A and T3 are involved in keratin degradation together with proteases from family S08

X-ray CT adaptation based on a 2D–3D deformable image registration framework using simulated in-room proton radiographies

The aim of this work is to investigate in-room proton radiographies to compensate realistic rigid and non-rigid transformations in clinical-like scenarios based on 2D–3D deformable image registration (DIR) framework towards future clinical implementation of adaptive radiation therapy (ART). Monte Carlo simulations of proton radiographies (pRads) based on clinical x-ray CT of a head and neck, and a brain tumor patients are simulated for two different detector configurations (i.e. integration-mode and list-mode detectors) including high and low proton statistics. A realistic deformation, derived from cone beam CT of the patient, is applied to the treatment planning CT. Rigid inaccuracies in patient positioning are also applied and the effect of small, medium and large fields of view (FOVs) is investigated. A stopping criterion, as desirable in realistic scenarios devoid of ground truth proton CT (pCT), is proposed and investigated. Results show that rigid and non-rigid transformations can be compensated based on a limited number of low dose pRads. The root mean square error with respect to the pCT shows that the 2D–3D DIR of the treatment planning CT based on 10 pRads from integration-mode data and 2 pRads from list-mode data is capable of achieving comparable accuracy (∼90% and >90%, respectively) to conventional 3D–3D DIR. The dice similarity coefficient over the segmented regions of interest also verifies the improvement in accuracy prior to and after 2D–3D DIR. No relevant changes in accuracy are found between high and low proton statistics except for 2 pRads from integration-mode data. The impact of FOV size is negligible. The convergence of the metric adopted for the stopping criterion indicates the optimal convergence of the 2D–3D DIR. This work represents a further step towards the potential implementation of ART in proton therapy. Further computational optimization is however required to enable extensive clinical validation

An integrated sequence stratigraphic, palaeoenvironmental, and chronostratigraphic analysis of the Tangahoe Formation, southern Taranaki coast, with implications for mid-Pliocene (c. 3.4–3.0 Ma) glacio-eustatic sea-level changes

Sediments of the mid-Pliocene (c. 3.4–3.0 Ma) Tangahoe Formation exposed in cliffs along the South Taranaki coastline of New Zealand comprise a 270 m thick, cyclothemic shallow-marine succession that has been gently warped into a north to south trending, low angle anticline. This study examines the sedimentologic, faunal, and petrographic characteristics of 10 Milankovitch-scale (6th order), shallow-marine depositional sequences exposed on the western limb of the anticline. The sequences are recognised on the basis of the cyclic vertical stacking of their constituent lithofacies, which are bound by sharp wave cut surfaces produced during transgressive shoreface erosion. Each sequence comprises three parts: (1) a 0.2–2 m thick, deepening upwards, basal suite of reworked bioclastic lag deposits (onlap shellbed) and/or an overlying matrix supported, molluscan shellbed of offshore shelf affinity (backlap shellbed); (2) a 5–20 m thick, gradually shoaling, aggradational siltstone succession; and (3) a 5–10 m thick, strongly progradational, well sorted “forced regressive” shoreline sandstone. The three-fold subdivision corresponds to transgressive, highstand, and regressive systems tracts (TSTs, HSTs, and RSTs) respectively, and represents deposition during a glacio-eustatic sea-level cycle. Lowstand systems tract sediments are not recorded because the outcrop is situated c. 100 km east of the contemporary shelf edge and was subaerially exposed at that time. Well developed, sharp- and gradational-based forced regressive sandstones contain a variety of storm-emplaced sedimentary structures, and represent the rapid and abrupt basinward translation of the shoreline on to a storm dominated, shallow shelf during eustatic sea-level fall. Increased supply of sediment from north-west South Island during “forced regression” is indicated from petrographic analyses of the heavy mineralogy of the sandstones. A chronology based on biostratigraphy and the correlation of a new magnetostratigraphy to the magnetic polarity timescale allows: (1) identification of the Mammoth (C2An.2r) and Kaena (C2An.1r) subchrons; (2) correlation of the coastal section to the Waipipian Stage; and (3) estimation of the age of the coastal section as 3.36–3.06 Ma. Qualitative assessment of foraminiferal census data and molluscan palaeoecology reveals cyclic changes in water depth from shelf to shoreline environments during the deposition of each sequence. Seven major cycles in water depth of between 20 and 50m have been correlated to individual 40 ka glacio-eustatic sea-level cycles on the marine oxygen isotope timescale. The coastal Tangahoe Formation provides a shallow-marine record of global glacio-eustasy prior to the development of significant ice sheets on Northern Hemisphere continents, and supports evidence from marine δ18O archives that changes in Antarctic ice volume were occurring during the Pliocene

Declining human pressure and opportunities for rewilding in the steppes of Eurasia

Large and ecologically functioning steppe complexes have been lost historically across the globe, but recent land‐use changes may allow the reversal of this trend in some regions. We aimed to develop and map indicators of changing human influence using satellite imagery and historical maps, and to use these indicators to identify areas for broad‐scale steppe rewilding.Peer Reviewe