Properties of age compositions and mortality estimates derived from cohort slicing of length data

Cohort slicing can be used to obtain catch-at-age data from length frequency distributions when directly measured age data are unavailable. The procedure systematically underestimates the relative abundance of the youngest age groups and overestimates abundance at older ages. Cohort-sliced catch-at-age data can be used to estimate total mortality rate (Z) using a regression estimator or the Chapman-Robson estimator for right truncated data. However, the effect of cohort slicing on accuracy and precision of resulting Z estimates remains to be determined. We used Monte Carlo simulation to estimate the per cent bias and per cent root mean square error of the unweighted regression, weighted regression, and Chapman-Robson mortality estimators applied to cohort-sliced data. Incompletely recruited age groups were truncated from the cohort-sliced catch-at-age data using previously established recommendations and a variety of plus groups was used to combine older age groups. The sensitivity of the results to a range of plausible biological combinations of Z, growth parameters, recruitment variability, and length-at-age error was tested. Our simulation shows that cohort slicing can work well in some cases and poorly in others. Overall, plus group selection was more important in high K scenarios than it was in low K scenarios. Surprisingly, defining the plus group to start at a high age worked well in some cases, although length and age are poorly correlated for old ages. No one estimator was uniformly superior; we therefore provide recommendations concerning the appropriate estimator and plus group to use, depending on the parameters characterizing the stock. We further recommend that simulations be performed to determine exactly which plus group would be most appropriate given the scenario at hand

A general nonlinear least squares data reconciliation and estimation method for material flow analysis

© 2015 The Authors. Journal of Industrial Ecology, published by Wiley Periodicals, Inc., on behalf of Yale University. The extraction, transformation, use, and disposal of materials can be represented by directed, weighted networks, known in the material flow analysis (MFA) community as Sankey or flow diagrams. However, the construction of such networks is dependent on data that are often scarce, conflicting, or do not directly map onto a Sankey diagram. By formalizing the forms of data entry, a nonlinear constrained optimization program for data estimation and reconciliation can be formulated for reconciling data sets for MFA problems where data are scarce, in conflict, do not directly map onto a Sankey diagram, and are of variable quality. This method is demonstrated by reanalyzing an existing MFA of global steel flows, and the resulting analytical solution measurably improves upon their manual solution.The authors gratefully acknowledge the financial support of BP as part of its Energy Sustainability Challenge for this research

Measuring measurement

Measurement connects the world of quantum phenomena to the world of classical events. It plays both a passive role, observing quantum systems, and an active one, preparing quantum states and controlling them. Surprisingly - in the light of the central status of measurement in quantum mechanics - there is no general recipe for designing a detector that measures a given observable. Compounding this, the characterization of existing detectors is typically based on partial calibrations or elaborate models. Thus, experimental specification (i.e. tomography) of a detector is of fundamental and practical importance. Here, we present the realization of quantum detector tomography: we identify the optimal positive-operator-valued measure describing the detector, with no ancillary assumptions. This result completes the triad, state, process, and detector tomography, required to fully specify an experiment. We characterize an avalanche photodiode and a photon number resolving detector capable of detecting up to eight photons. This creates a new set of tools for accurately detecting and preparing non-classical light.Comment: 6 pages, 4 figures,see video abstract at http://www.quantiki.org/video_abstracts/0807244

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene

Post-translational modifications (PTMs) of histones exert fundamental roles in regulating gene expression. During development, groups of PTMs are constrained by unknown mechanisms into combinatorial patterns, which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell lineages. Repressive histone modifications such as H3K9me3 or H3K27me3 have been investigated in detail, but the role of H4K20me3 in development is currently unknown. Here we show that Xenopus laevis Suv4-20h1 and h2 histone methyltransferases (HMTases) are essential for induction and differentiation of the neuroectoderm. Morpholino-mediated knockdown of the two HMTases leads to a selective and specific downregulation of genes controlling neural induction, thereby effectively blocking differentiation of the neuroectoderm. Global transcriptome analysis supports the notion that these effects arise from the transcriptional deregulation of specific genes rather than widespread, pleiotropic effects. Interestingly, morphant embryos fail to repress the Oct4-related Xenopus gene Oct-25. We validate Oct-25 as a direct target of xSu4-20h enzyme mediated gene repression, showing by chromatin immunoprecipitaton that it is decorated with the H4K20me3 mark downstream of the promoter in normal, but not in double-morphant, embryos. Since knockdown of Oct-25 protein significantly rescues the neural differentiation defect in xSuv4-20h double-morphant embryos, we conclude that the epistatic relationship between Suv4-20h enzymes and Oct-25 controls the transit from pluripotent to differentiation-competent neural cells. Consistent with these results in Xenopus, murine Suv4-20h1/h2 double-knockout embryonic stem (DKO ES) cells exhibit increased Oct4 protein levels before and during EB formation, and reveal a compromised and biased capacity for in vitro differentiation, when compared to normal ES cells. Together, these results suggest a regulatory mechanism, conserved between amphibians and mammals, in which H4K20me3-dependent restriction of specific POU-V genes directs cell fate decisions, when embryonic cells exit the pluripotent state

A codon-optimized luciferase from Gaussia princeps facilitates the in vivo monitoring of gene expression in the model alga Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii has emerged as a superb model species in plant biology. Although the alga is easily transformable, the low efficiency of transgene expression from the Chlamydomonas nuclear genome has severely hampered functional genomics research. For example, poor transgene expression is held responsible for the lack of sensitive reporter genes to monitor gene expression in vivo, analyze subcellular protein localization or study protein–protein interactions. Here, we have tested the luciferase from the marine copepod Gaussia princeps (G-Luc) for its suitability as a sensitive bioluminescent reporter of gene expression in Chlamydomonas. We show that a Gaussia luciferase gene variant, engineered to match the codon usage in the Chlamydomonas nuclear genome, serves as a highly sensitive reporter of gene expression from both constitutive and inducible algal promoters. Its bioluminescence signal intensity greatly surpasses previously developed reporters for Chlamydomonas nuclear gene expression and reaches values high enough for utilizing the reporter as a tool to monitor responses to environmental stresses in vivo and to conduct high-throughput screenings for signaling mutants in Chlamydomonas

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

<p>Abstract</p> <p>Background</p> <p>To enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expressed Sequence Tags (ESTs) have been used for single nucleotide polymorphism (SNP) discovery in salmonids. In those strategies, the salmonid semi-tetraploid genomes often led to assemblies of paralogous sequences and therefore resulted in a high rate of false positive SNP identification. Sequencing genomic DNA using primers identified from ESTs proved to be an effective but time consuming methodology of SNP identification in rainbow trout, therefore not suitable for high throughput SNP discovery. In this study, we employed a high-throughput strategy that used pyrosequencing technology to generate data from a reduced representation library constructed with genomic DNA pooled from 96 unrelated rainbow trout that represent the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock population.</p> <p>Results</p> <p>The reduced representation library consisted of 440 bp fragments resulting from complete digestion with the restriction enzyme <it>Hae</it>III; sequencing produced 2,000,000 reads providing an average 6 fold coverage of the estimated 150,000 unique genomic restriction fragments (300,000 fragment ends). Three independent data analyses identified 22,022 to 47,128 putative SNPs on 13,140 to 24,627 independent contigs. A set of 384 putative SNPs, randomly selected from the sets produced by the three analyses were genotyped on individual fish to determine the validation rate of putative SNPs among analyses, distinguish apparent SNPs that actually represent paralogous loci in the tetraploid genome, examine Mendelian segregation, and place the validated SNPs on the rainbow trout linkage map. Approximately 48% (183) of the putative SNPs were validated; 167 markers were successfully incorporated into the rainbow trout linkage map. In addition, 2% of the sequences from the validated markers were associated with rainbow trout transcripts.</p> <p>Conclusion</p> <p>The use of reduced representation libraries and pyrosequencing technology proved to be an effective strategy for the discovery of a high number of putative SNPs in rainbow trout; however, modifications to the technique to decrease the false discovery rate resulting from the evolutionary recent genome duplication would be desirable.</p

A Systems Approach for Tumor Pharmacokinetics

Recent advances in genome inspired target discovery, small molecule screens, development of biological and nanotechnology have led to the introduction of a myriad of new differently sized agents into the clinic. The differences in small and large molecule delivery are becoming increasingly important in combination therapies as well as the use of drugs that modify the physiology of tumors such as anti-angiogenic treatment. The complexity of targeting has led to the development of mathematical models to facilitate understanding, but unfortunately, these studies are often only applicable to a particular molecule, making pharmacokinetic comparisons difficult. Here we develop and describe a framework for categorizing primary pharmacokinetics of drugs in tumors. For modeling purposes, we define drugs not by their mechanism of action but rather their rate-limiting step of delivery. Our simulations account for variations in perfusion, vascularization, interstitial transport, and non-linear local binding and metabolism. Based on a comparison of the fundamental rates determining uptake, drugs were classified into four categories depending on whether uptake is limited by blood flow, extravasation, interstitial diffusion, or local binding and metabolism. Simulations comparing small molecule versus macromolecular drugs show a sharp difference in distribution, which has implications for multi-drug therapies. The tissue-level distribution differs widely in tumors for small molecules versus macromolecular biologic drugs, and this should be considered in the design of agents and treatments. An example using antibodies in mouse xenografts illustrates the different in vivo behavior. This type of transport analysis can be used to aid in model development, experimental data analysis, and imaging and therapeutic agent design.National Institutes of Health (U.S.) (grant T32 CA079443

Comparison of Two Multilocus Sequence Based Genotyping Schemes for Leptospira Species

Two independent multilocus sequence based genotyping schemes (denoted here as 7L and 6L for schemes with 7 and 6 loci, respectively) are in use for Leptospira spp., which has led to uncertainty as to which should be adopted by the scientific community. The purpose of this study was to apply the two schemes to a single collection of pathogenic Leptospira, evaluate their performance, and describe the practical advantages and disadvantages of each scheme. We used a variety of phylogenetic approaches to compare the output data and found that the two schemes gave very similar results. 7L has the advantage that it is a conventional multi-locus sequencing typing (MLST) scheme based on housekeeping genes and is supported by a publically accessible database by which genotypes can be readily assigned as known or new sequence types by any investigator, but is currently only applicable to L. interrogans and L. kirschneri. Conversely, 6L can be applied to all pathogenic Leptospira spp., but is not a conventional MLST scheme by design and is not available online. 6L sequences from 271 strains have been released into the public domain, and phylogenetic analysis of new sequences using this scheme requires their download and offline analysis

The breast feeding mother and xenon anaesthesia: four case reports. Breast feeding and xenon anaesthesia

<p>Abstract</p> <p>Background</p> <p>Four nursing mothers consented to anaesthesia for urgent surgery only on condition that their ability to breast feed would not be impaired.</p> <p>Methods</p> <p>Following induction of general anaesthesia with propofol and remifentanil, 65-69% xenon supplemented with remifentanil was used as an inhalational anaesthetic for maintenance.</p> <p>Results</p> <p>After finishing surgery the women could be extubated between 2:52 and 7:22 minutes. The women were fully alert just minutes after extubation and spent about 45 minutes in the recovery room before discharge to a regular ward. They resumed regular breast feeding some time later. The propofol concentration in the blood was measured after 0, 30, 90, and 300 minutes and in the milk after 90 and 300 minutes. Just 90 minutes after extubation, the concentration of propofol in the milk was limited (> 3 mg/l) so that pharmacological effects on the babies were excluded after oral intake. Also, no traces of xenon gas were found in the maternal milk at any time. After propofol induction and maintenance of anaesthesia with xenon in combination with a water-soluble short-acting drug like remifentanil, the concentration of propofol in maternal milk is low (> 3 mg/l 90 min after anesthesia) and harmless after oral intake.</p> <p>Conclusions</p> <p>These results, as well as the rapid elimination and absence of metabolism of xenon, are of great interest to nursing mothers. General anaesthesia with propofol for induction only, combined with remifentanil and xenon for maintenance, has not yet been described in breast feeding mothers.</p