A historical biogeographical protocol for studying biotic diversification by taxon pulses

Aim To present a historical biogeographical protocol for distinguishing biotic diversification by taxon pulse radiations from biotic diversification by vicariance. Location Mexico and northern Central America. Methods Brooks Parsimony Analysis (BPA), phylogenetic inference, linear correlation analysis. Results The taxon pulse radiation of 33 clades in nine areas of endemism in Mesoamerica is based on nine episodes of biotic expansion from three areas, and six episodes of vicariance, involving four geographical splits. Nineteen per cent of speciation events are due to vicariance, 25% to peripheral isolates speciation and 56% are within‐area events. The species–area curve has a correlation coefficient (r²) of 0.47. Extinction events and species richness are highly correlated (r² = 0.75), but colonization events and species richness are poorly correlated (r² = 0.36), suggesting that colonization is not the main determinant of the species–area relationship. Colonization events are more poorly correlated with size of area (r² = 0.05) than are in situ speciation events (r² = 0.60). Colonization events and in situ events are poorly correlated (r² = 0.02). All areas of endemism have reticulated histories, and have acted as both sources and islands at various times. Main conclusions Taxon pulses can be distinguished from maximum vicariance using this protocol; refining it requires a method for generating area cladograms from complex data and incorporation of direct dating of evolutionary events.     

A novel,versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum

Objectives

To investigate the properties of a novel metagenome-derived member of the hormone-sensitive lipase family of lipolytic enzymes.

Results

A forest soil metagenome-derived gene encoding an esterase (Est06) belonging to the hormone-sensitive lipase family of lipolytic enzymes was subcloned, heterologously expressed and characterized. Est06 is a polypeptide of 295 amino acids with a molecular mass of 31 kDa. The deduced protein sequence shares 61% similarity with a hypothetical protein from the marine symbiont Candidatus Entotheonella sp. TSY1. Purified Est06 exhibited high affinity for acyl esters with short-chain fatty acids, and showed optimum activity with p-nitrophenyl valerate (C5). Maximum enzymatic activity was at 50 °C and pH 7. Est06 exhibited high stability at moderate temperatures by retaining all of its catalytic activity below 30 °C over 13 days. Additionally, Est06 displayed high stability between pH 5 and 9. Esterase activity was not inhibited by metal ions or detergents, although organic solvents decreased activity.

Conclusions

The combination of Est06 properties place it among novel biocatalysts that have potential for industrial use including low temperature applications.

     

Osteochondritis dissecans-like lesions of the occipital condyle and cervical articular process joints in a Saddlebred colt horse

Background

Osteochondritis dissecans (OCD) is a sequela to osteochondrosis, whereby the cartilage superficial to the site of osteochondrosis fractures and gives rise to osteochondral fragments in the affected joint. In this case, both the radiological and computed tomography findings were supportive of classical severe OCD but the histologic findings were not supportive of the diagnosis of OCD.

Case presentation

A 1 year and 6 months old, Saddlebred, colt was presented for evaluation of chronic cervical pain. Standing laterolateral radiographs revealed an osteochondral fragment with corresponding irregular subchondral bone defect at one of the occipital condyle. Computed tomography confirmed the presence of osteochondral fragments at the left occipital condyle and several articular process joints of the cervical spine, with associated subchondral bone defects and sclerosis, suggestive of OCD. However, the lack of ischemic chondronecrosis microscopically was not supportive of a histologic diagnosis of OCD. Therefore, the term ‘OCD-like lesions’ was deemed most appropriate for these cervical lesions.

Conclusion

In the event where imaging features were characteristics of OCD but lack of histologic evidence of ischemic chondronecrosis, the term ‘OCD-like lesion’ is deemed most appropriate.

     

Robust factor selection in early cell culture process development for the production of a biosimilar monoclonal antibody

This work presents a multivariate methodology combining principal component analysis, the Mahalanobis distance and decision trees for the selection of process factors and their levels in early process development of generic molecules. It is applied to a high throughput study testing more than 200 conditions for the production of a biosimilar monoclonal antibody at microliter scale. The methodology provides the most important selection criteria for the process design in order to improve product quality towards the quality attributes of the originator molecule. Robustness of the selections is ensured by cross‐validation of each analysis step. The concluded selections are then successfully validated with an external data set. Finally, the results are compared to those obtained with a widely used software revealing similarities and clear advantages of the presented methodology. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:181–191, 2017     

The BEACH protein LRBA is required for hair bundle maintenance in cochlear hair cells and for hearing

Lipopolysaccharide‐responsive beige‐like anchor protein (LRBA) belongs to the enigmatic class of BEACH domain‐containing proteins, which have been attributed various cellular functions, typically involving intracellular protein and membrane transport processes. Here, we show that LRBA deficiency in mice leads to progressive sensorineural hearing loss. In LRBA knockout mice, inner and outer hair cell stereociliary bundles initially develop normally, but then partially degenerate during the second postnatal week. LRBA deficiency is associated with a reduced abundance of radixin and Nherf2, two adaptor proteins, which are important for the mechanical stability of the basal taper region of stereocilia. Our data suggest that due to the loss of structural integrity of the central parts of the hair bundle, the hair cell receptor potential is reduced, resulting in a loss of cochlear sensitivity and functional loss of the fraction of spiral ganglion neurons with low spontaneous firing rates. Clinical data obtained from two human patients with protein‐truncating nonsense or frameshift mutations suggest that LRBA deficiency may likewise cause syndromic sensorineural hearing impairment in humans, albeit less severe than in our mouse model.     

Outdoor recreation causes effective habitat reduction in capercaillie Tetrao urogallus: a major threat for geographically restricted populations

Outdoor recreation inflicts a wide array of impacts on individual animals, many of them reflected in the avoidance of disturbed areas. The scale and spatial extent, however, at which wildlife populations are affected, are mostly unclear. Particularly in geographically isolated populations, where restricted habitat availability may preclude a relocation to undisturbed areas, effective habitat reduction may remain underestimated or even unnoticed, when animals stay in disturbed areas and only show small‐scale responses. Based on telemetry data, we investigated the spatial and seasonal effects of outdoor recreation – in relation to landscape and vegetation conditions – on western capercaillie Tetrao urogallus, considering two scales, home range and within‐home range habitat selection. We determined the distance‐thresholds up to which recreation infrastructures were avoided and estimated the extent of affected habitat for the isolated Black Forest (southwestern Germany) study population. While outdoor recreation did not affect home range selection, strong effects on habitat use within the home range were detected: distance to recreation infrastructure (hiking and cross‐country skiing trails, ski pistes) was the main determinant of habitat selection in winter; in summer, mountain bike trails and hiker's restaurants were avoided up to an average distance of 145 m (CI: 60–1092 m). Around winter‐infrastructure, relative avoidance was recorded up to 320 m (CI: 36–327 m), it was reduced, however, when dense understory provided visual cover. Of the entire population area, between 8–20% (summer) and 8–40% (winter) were affected by outdoor recreation, mainly in the high altitudes. Even without evident large‐scale shifts in species distribution, local‐scale avoidance of outdoor recreation can substantially contribute to effective habitat reduction. Based on our results we recommend a general reduction in recreation infrastructure density in key habitats, the establishment of undisturbed wildlife refuges with a diameter of at least 800 m, as well as enhancing visual protection by maintaining a strip of dense understory along trails.     

The Role of Ca<Superscript>2+</Superscript> Imbalance in the Induction of Acute Oxidative Stress and Cytotoxicity in Cultured Rat Cerebellar Granule Cells Challenged with Tetrabromobisphenol A

Using primary cultures of rat cerebellar granule cells (CGC) we examined the role of calcium transients induced by tetrabromobisphenol A (TBBPA) in triggering oxidative stress and cytotoxicity. CGC were exposed for 30 min to 10 or 25 µM TBBPA. Changes in intracellular calcium concentration ([Ca²⁺]_i), in the production of reactive oxygen species (ROS), and in the potential of mitochondria (?Ψm) were measured fluorometrically during the exposure. The intracellular glutathione (GSH) and catalase activity were determined after the incubation; cell viability was evaluated 24 h later. TBBPA concentration-dependently increased [Ca²⁺]_i and ROS production, and reduced GSH content, catalase activity, ?Ψm and neuronal viability. The combination of NMDA and ryanodine receptor antagonists, MK-801 and bastadin 12 with ryanodine, respectively, prevented Ca²⁺ transients and partially reduced cytotoxicity induced by TBBPA at both concentrations. The antagonists also completely inhibited oxidative stress and depolarization of mitochondria evoked by 10 µM TBBPA, whereas these effects were only partially reduced in the 25 µM TBBPA treatment. Free radical scavengers prevented TBBPA-induced development of oxidative stress and improved CGC viability without having any effect on the rises in Ca²⁺ and drop in ?Ψm. The co-administration of scavengers with NMDA and ryanodine receptor antagonists provided almost complete neuroprotection. These results indicate that Ca²⁺ imbalance and oxidative stress both mediate acute toxicity of TBBPA in CGC. At 10 µM TBBPA Ca²⁺ imbalance is a primary event, inducing oxidative stress, depolarization of mitochondria and cytotoxicity, whilst at a concentration of 25 µM TBBPA an additional Ca²⁺-independent portion of oxidative stress and cytotoxicity emerges.     

Serum uromodulin predicts graft failure in renal transplant recipients

Objective and methods: Test the ability of serum uromodulin concentrations 1–3 months after renal transplantation to predict all-cause mortality (ACM) and graft loss (GL) in 91 patients.

Results: uromodulin predicted GL equivalently to the other markers studied: the risk for GL was reduced by 0.21 per one standard deviation (SD) increase (cystatin C: hazard ratio [HR] 4.57, creatinine: HR 4.53, blood-urea-nitrogen [BUN]: HR 2.50, estimated glomerular filtration rate [eGFR]: HR 0.10). In receiver-operating-characteristic (ROC) analysis, uromodulin predicted GL with an area-under-the curve of 0.782 at an optimal cut-off (OCO) of 24.0?ng/ml with a sensitivity of 90.0% and a specificity of 70.2%.

Conclusion: Serum uromodulin predicted GL equivalently compared to conventional biomarkers of glomerular filtration.