Compensatory Breeding in Years Following Drought in a Desert-Dwelling Cooperative Breeder

Variation in weather patterns can influence reproductive effort and success not only within but also between breeding seasons. Where environmental conditions can be highly variable between years, the weather, and particularly extreme weather events such as heat waves and droughts, may exert a strong influence on reproductive effort (number of breeding attempts) and success (number of surviving young) from one breeding season to the next. We used a 15-year dataset for a cooperatively-breeding bird, the southern pied babbler Turdoides bicolor, to determine the impact of high temperatures and drought on reproductive effort and success. We tested the influence on reproductive effort and success of mean daily maximum air temperature and drought both within a breeding season, to determine the relative importance of current conditions, and during the previous breeding season, to determine the relative importance of compensatory effects in response to prior conditions. Reproductive effort and success were lower during breeding seasons characterised by drought, and higher in the breeding seasons that followed droughts, but were not predicted by mean daily maximum temperatures measured over the full length of the breeding season. We provide evidence of compensatory breeding following drought in a bird species endemic to a semi-arid ecosystem and suggest that compensatory mechanisms may be an important part of both long-term population persistence and post-drought population recovery.DST-NRF Centre of Excellence at the FitzPatrick Institute for African Ornithology Oppenheimer Memorial Trust (Grant No. 20747/01 to ARB) British Ornithologists’ Union Australian Research Council (Grant No. FT110100188 to ARR) National Research Foundation of South Africa (Grant No. 110506 to SJC

Hazard and risk assessments for induced seismicity in Groningen

Earthquakes associated with gas production have been recorded in the northern part of the Netherlands since 1986. The Huizinge earthquake of 16 August 2012, the strongest so far with a magnitude of M L = 3.6, prompted reassessment of the seismicity induced by production from the Groningen gas field. An international research programme was initiated, with the participation of many Dutch and international universities, knowledge institutes and recognised experts. The prime aim of the programme was to assess the hazard and risk resulting from the induced seismicity. Classic probabilistic seismic hazard and risk assessment (PSHA) was implemented using a Monte Carlo method. The scope of the research programme extended from the cause (production of gas from the underground reservoir) to the effects (risk to people and damage to buildings). Data acquisition through field measurements and laboratory experiments was a substantial element of the research programme. The existing geophone and accelerometer monitoring network was extended, a new network of accelerometers in building foundations was installed, geophones were placed at reservoir level in deep wells, GPS stations were installed and a gravity survey was conducted. Results of the probabilistic seismic hazard and risk assessment have been published in production plans submitted to the Minister of Economic Affairs, Winningsplan Groningen 2013 and 2016 and several intermediate updates. The studies and data acquisition further constrained the uncertainties and resulted in a reduction of the initially assessed hazard and risk

Liquefaction hazard of the Groningen region of the Netherlands due to induced seismicity

The operator of the Groningen gas field is leading an effort to quantify the seismic hazard and riskof the region due to induced earthquakes, includingoverseeing one of the most comprehensive liquefaction hazard studies performedgloballyto date. Due tothe unique characteristics of the seismic hazard and the geologic deposits in Groningen, efforts first focused on developing relationships for a Groningen-specific liquefaction triggering model. The liquefaction hazard was then assessedusing a Monte Carlo method, wherein a range of credibleevent scenarios were considered in computingliquefaction damage-potentialhazard curves. Thiseffort entailed the use of a regional stochastic seismic source model,ground motion prediction equation,site response model,and geologic model that were developed as part of the broader regional seismic hazardassessment.“No-to-Minor Surficial Liquefaction Manifestations”arepredicted for mostsites across the study areafor a 75-year return period. The only sites where “Moderate Surficial Liquefaction Manifestations” are predicted are in the town of Zandeweer, with only some of the sites in the townbeing predicted to experience this severityof liquefactionfor thisreturn period

Multidataset Incremental Training for Optic Disc Segmentation

When convolutional neural networks are applied to image segmentation results depend greatly on the data sets used to train the networks. Cloud providers support multi GPU and TPU virtual machines making the idea of cloud-based segmentation as service attractive. In this paper we study the problem of building a segmentation service, where images would come from different acquisition instruments, by training a generalized U-Net with images from a single or several datasets. We also study the possibility of training with a single instrument and perform quick retrains when more data is available. As our example we perform segmentation of Optic Disc in fundus images which is useful for glau coma diagnosis. We use two publicly available data sets (RIM-One V3, DRISHTI) for individual, mixed or incremental training. We show that multidataset or incremental training can produce results that are simi lar to those published by researchers who use the same dataset for both training and validation

SILAC-based proteomic quantification of chemoattractant-induced cytoskeleton dynamics on a second to minute timescale

Cytoskeletal dynamics during cell behaviours ranging from endocytosis and exocytosis to cell division and movement is controlled by a complex network of signalling pathways, the full details of which are as yet unresolved. Here we show that SILAC-based proteomic methods can be used to characterize the rapid chemoattractant-induced dynamic changes in the actin–myosin cytoskeleton and regulatory elements on a proteome-wide scale with a second to minute timescale resolution. This approach provides novel insights in the ensemble kinetics of key cytoskeletal constituents and association of known and novel identified binding proteins. We validate the proteomic data by detailed microscopy-based analysis of in vivo translocation dynamics for key signalling factors. This rapid large-scale proteomic approach may be applied to other situations where highly dynamic changes in complex cellular compartments are expected to play a key role

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the “ortholog conjecture” (or, more properly, the “ortholog functional conservation hypothesis”). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis

Molecular Modeling Study for Interaction between Bacillus subtilis Obg and Nucleotides

The bacterial Obg proteins (Spo0B-associated GTP-binding protein) belong to the subfamily of P-loop GTPase proteins that contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain which is referred as the “Obg fold” and now it is considered as one of the new targets for antibacterial drug. When the Obg protein is associated with GTP, it becomes activated, because conformation of Obg fold changes due to the structural changes of GTPase switch elements in GTP binding site. In order to investigate the effects and structural changes in GTP bound to Obg and GTPase switch elements for activation, four different molecular dynamics (MD) simulations were performed with/without the three different nucleotides (GTP, GDP, and GDP + Pi) using the Bacillus subtilis Obg (BsObg) structure. The protein structures generated from the four different systems were compared using their representative structures. The pattern of Cα-Cα distance plot and angle between the two Obg fold domains of simulated apo form and each system (GTP, GDP, and GDP+Pi) were significantly different in the GTP-bound system from the others. The switch 2 element was significantly changed in GTP-bound system. Also root-mean-square fluctuation (RMSF) analysis revealed that the flexibility of the switch 2 element region was much higher than the others. This was caused by the characteristic binding mode of the nucleotides. When GTP was bound to Obg, its γ-phosphate oxygen was found to interact with the key residue (D212) of the switch 2 element, on the contrary there was no such interaction found in other systems. Based on the results, we were able to predict the possible binding conformation of the activated form of Obg with L13, which is essential for the assembly with ribosome

Quantitative assessment of microbicide-induced injury in the ovine vaginal epithelium using confocal microendoscopy

<p>Abstract</p> <p>Background</p> <p>The development of safe topical microbicides that can preserve the integrity of cervicovaginal tract epithelial barrier is of great interest as this may minimize the potential for increased susceptibility to STI infections. High resolution imaging to assess epithelial integrity in a noninvasive manner could be a valuable tool for preclinical testing of candidate topical agents.</p> <p>Methods</p> <p>A quantitative approach using confocal fluorescence microendoscopy (CFM) for assessment of microbicide-induced injury to the vaginal epithelium was developed. Sheep were treated intravaginally with one of five agents in solution (PBS; 0.02% benzalkonium chloride (BZK); 0.2% BZK) or gel formulation (hydroxyethyl cellulose (HEC); Gynol II nonoxynol-9 gel (N-9)). After 24 hours the vaginal tract was removed, labeled with propidium iodide (PI), imaged, then fixed for histology. An automated image scoring algorithm was developed for quantitative assessment of injury and applied to the data set. Image-based findings were validated with histological visual gradings that describe degree of injury and measurement of epithelial thickness.</p> <p>Results</p> <p>Distinct differences in PI staining were detected following BZK and N-9 treatment. Images from controls had uniformly distributed nuclei with defined borders, while those after BZK or N-9 showed heavily stained and disrupted nuclei, which increased in proportion to injury detected on histology. The confocal scoring system revealed statistically significant scores for each agent versus PBS controls with the exception of HEC and were consistent with histology scores of injury.</p> <p>Conclusions</p> <p>Confocal microendoscopy provides a sensitive, objective, and quantitative approach for non-invasive assessment of vaginal epithelial integrity and could serve as a tool for real-time safety evaluation of emerging intravaginal topical agents.</p

Absence of polysialylated NCAM is an unfavorable prognostic phenotype for advanced stage neuroblastoma

<p>Abstract</p> <p>Background</p> <p>The expression of a neural crest stem cell marker, polysialic acid (polySia), and its main carrier, neural cell adhesion molecule (NCAM), have been detected in some malignant tumors with high metastatic activity and unfavorable prognosis, but the diagnostic and prognostic value of polySia-NCAM in neuroblastoma is unclear.</p> <p>Methods</p> <p>A tumor tissue microarray (TMA) of 36 paraffin-embedded neuroblastoma samples was utilized to detect polySia-NCAM expression with a polySia-binding fluorescent fusion protein, and polySia-NCAM expression was compared with clinical stage, age, <it>MYCN </it>amplification status, histology (INPC), and proliferation index (PI).</p> <p>Results</p> <p>PolySia-NCAM-positive neuroblastoma patients had more often metastases at diagnosis, and polySia-NCAM expression associated with advanced disease (<it>P </it>= 0.047). Most interestingly, absence of polySia-NCAM-expressing tumor cells in TMA samples, however, was a strong unfavorable prognostic factor for overall survival in advanced disease (<it>P </it>= 0.0004), especially when <it>MYCN </it>was not amplified. PolySia-NCAM-expressing bone marrow metastases were easily detected in smears, aspirates and biopsies.</p> <p>Conclusion</p> <p>PolySia-NCAM appears to be a new clinically significant molecular marker in neuroblastoma, hopefully with additional value in neuroblastoma risk stratification.</p