Potential of high‐density pheromone‐releasing microtraps for control of codling moth Cydia pomonella and obliquebanded leafroller Choristoneura rosaceana

Recent large‐cage studies with codling moth Cydia pomonella (L.) reveal that the removal of moths from an apple orchard using pheromone‐releasing traps is more effective at reducing capture in a central monitoring trap than is a mating disruption protocol without kill/capture. The present study uses open orchard 0.2‐ha plots comparing a high‐density trapping scenario with mating disruption to confirm those results. Two tortricid moth pests of tree fruit are studied: codling moth and obliquebanded leafroller Choristoneura rosaceana (Harris). Codling moth treatments include Isomate CM FLEX (ShinEtsu Ltd, Japan), nonsticky traps baited with Trécé CM lures (Trécé, Inc., Adair, Oklahoma), and sticky traps baited with Trécé CM lures, all at equal application rates of 500 dispensers ha^?1, as well as a no pheromone control. These microtraps are of a novel design, small and easy to apply, and potentially inexpensive to produce. Mating disruption using Isomate CM FLEX and nonsticky traps reduces codling moth capture in standard monitoring traps by 58% and 71%, respectively. The attract‐and‐remove treatment with sticky traps reduces capture by 92%. Obliquebanded leafroller treatments include Isomate OBLR/PLR Plus and Pherocon IIB microtraps baited with Trécé OBLR lures, both applied at 500 dispensers ha^?1, as well as a no pheromone control. Mating disruption reduces capture in monitoring traps by 69%. The attract‐and‐remove treatment reduces capture by 85%. Both studies suggest that an attract‐and‐remove approach has the potential to provide superior control of moth populations compared with that achieved by mating disruption operating by competitive attraction.     

Improving our understanding of demographic monitoring: avian breeding productivity in a tropical dry forest

The ratio of juvenile to adult birds in mist‐net samples is used to monitor avian productivity, but whether it is a “true” estimate of per capita productivity or an index proportional to productivity depends on whether capture probability is not age‐dependent (true estimate) or age difference in capture probability is consistent among years (index). Better understanding of the processes affecting age‐ and year‐specific capture probabilities is needed to advance the application of constant‐effort mist‐netting for monitoring and conservation, particularly in many tropical settings where capture rates are often low. We ranked members of the avian community by capture frequencies, determined if temporary emigration influenced the availability of birds to be captured, and assessed the distribution of birds relative to mist‐nets and the parity between capture‐based productivity estimates and number of fledglings in nest plots in a tropical dry forest in Puerto Rico in 2009 and 2010. Few captures characterized the community of 25 resident species and, when estimable, capture probabilities were low, particularly for juveniles (typically < 0.1). Negative trends in capture probability, temporary emigration, and the distribution of birds suggest that avoidance of mist‐nets influenced capture rates in our study. Increasing mist‐net coverage or moving mist‐nets between sampling periods could increase capture rates. The number of fledglings observed in nest plots (25 ha/plot) did not correlate well with capture‐derived estimates (20 ha/net stations), suggesting the presence of immigrants or failure to find all nests. Our results suggest that indices of breeding productivity from mist‐netting data may track temporal changes in productivity, but such data likely do not reflect “true” productivity in most cases unless age‐specific differences in capture probability are incorporated into estimates. Pilot studies should be conducted to evaluate capture rates and the spatial extent sampled by mist‐nets to improve sampling design and inferences before informing decisions.     

Crossbow‐netting: a new method for capturing shorebirds

Capturing shorebirds during the non‐breeding season can be challenging because they are usually scattered over wide‐open intertidal areas while foraging and are sensitive to human disturbance at roosts where they gather during high tide in large vigilant flocks. Several techniques are available for capturing shorebirds, but, for a study of stopover ecology, we needed a method that would allow us to capture Dunlins (Calidris alpina) on a regular basis at high‐tide roosts during the day (ruling out mist‐nets), did not require the use of gun‐powder (ruling out cannon‐nets), and that would deploy a net faster than clap nets, whoosh nets, and wilsternets. Therefore, we developed a new method to capture shorebirds where a crossbow is used to pull a mist‐net over flocks of roosting birds. We tested this technique in four habitats (saltpans, salt marshes, beaches, and mudflats) in the Tagus estuary, Portugal, and captured over 380 birds representing eight different species. Advantages of this technique compared to other methods (e.g., mist‐nets, clap‐ and whoosh nets, and cannon‐nets) include (1) portability, (2) ease of set up, (3) minimal disturbance of birds near the capture area, and (4) no explosive materials are needed. Our results suggest that crossbow‐netting is a safe and useful capture technique, especially for studies requiring the capture of small numbers of birds on a regular basis.     

Synchrony in capture dates suggests cryptic social organization in sea snakes (Emydocephalus annulatus,Hydrophiidae)

Abstract Complex sociality is widespread in lizards, but the difficulties of directly observing social interactions in free‐ranging snakes have precluded such studies for most snake species. However, a type of data already available from mark‐recapture studies (dates of capture and recapture of individually marked animals) can reveal social substructure within snake populations. If individuals associate with each other in social groups, we expect synchrony in the dates of capture and recapture of those animals. A field study of turtle‐headed sea snakes (Emydocephalus annulatus) in New Caledonia reveals exactly this phenomenon. For example, animals that were captured on the same day in one year often were recaptured on the same day the following year. Analysis rejects non‐social interpretations of these data (such as spatial‐temporal confounding in sampling, intrapopulation heterogeneity in cues for activity), suggesting instead that many individual sea snakes belong to ‘social’ groups that consistently move about together. The phenomenon of capture synchrony during mark‐recapture studies can provide new insights into the occurrence and correlates of cryptic social aggregations.     

Differential interaction of PRMT1 with RGG‐boxes of the FET family proteins EWS and TAF15

The FET sub‐family (F US/T LS, E WS, T AF15) of RNA‐binding proteins have remarkably similar overall structure but diverse biological and pathological roles. The molecular basis for FET protein specialization is largely unknown. Gly‐Arg‐Rich regions (RGG‐boxes) within FET proteins are targets for methylation by Protein‐Arginine‐Methyl‐Transferase‐1 (PRMT1) and substrate capture is thought to involve electrostatic attraction between positively charged polyRGG substrates and negatively charged surface channels of PRMT1. Unlike FUS and EWS, a high proportion of TAF15 RGG‐boxes are embedded within neutrally charged YGGDR(S/G)G repeats, suggesting that they might not bind well to PRMT1. This notion runs contrary however to a report that YGGDR(S/G)G repeats are methylated by PRMT1. Using peptide‐based polyRGG substrates and a novel 2‐hybrid binding assay, we find that the Asp residue in YGGDR(S/G)G repeats confers poor binding to PRMT1. Our results therefore indicate that YGGDR(S/G)G repeats may contribute to TAF15 specialization by enabling differential interactions with PRMT1 and reduced overall levels of TAF15 methylation compared with other FET proteins. By analogy with molecular recognition of other disordered polyvalent ligands by globular protein partners, we also propose a dynamic polyelectrostatic model for substrate capture by PRMT1.     

A Novel IgM‐capture enzyme‐linked immunosorbent assay using recombinant Vag8 fusion protein for the accurate and early diagnosis of Bordetella pertussis infection

An ELISA that measures anti‐PT IgG antibody has been used widely for the serodiagnosis of pertussis; however, the IgG‐based ELISA is inadequate for patients during the acute phase of the disease because of the slow response of anti‐PT IgG antibodies. To solve this problem, we developed a novel IgM‐capture ELISA that measures serum anti‐Bordetella pertussis Vag8 IgM levels for the accurate and early diagnosis of pertussis. First, we confirmed that Vag8 was highly expressed in all B. pertussis isolates tested (n = 30), but little or none in other Bordetella species, and that DTaP vaccines did not induce anti‐Vag8 IgG antibodies in mice (i.e. the antibody level could be unaffected by the vaccination). To determine the immune response to Vag8 in B. pertussis infection, anti‐Vag8 IgM levels were compared between 38 patients (acute phase of pertussis) and 29 healthy individuals using the anti‐Vag8 IgM‐capture ELISA. The results revealed that the anti‐Vag8 IgM levels were significantly higher in the patients compared with the healthy individuals (P < 0.001). ROC analysis also showed that the anti‐Vag8 IgM‐capture ELISA has higher diagnostic accuracy (AUC, 0.92) than a commercial anti‐PT IgG ELISA kit. Moreover, it was shown that anti‐Vag8 IgM antibodies were induced earlier than anti‐PT IgG antibodies on sequential patients’ sera. These data indicate that our novel anti‐Vag8 IgM‐capture ELISA is a potentially useful tool for making the accurate and early diagnosis of B. pertussis infection.     

Cormack–Jolly–Seber model with environmental covariates: A P‐spline approach

In capture–recapture models, survival and capture probabilities can be modelled as functions of time‐varying covariates, such as temperature or rainfall. The Cormack–Jolly–Seber (CJS) model allows for flexible modelling of these covariates; however, the functional relationship may not be linear. We extend the CJS model by semi‐parametrically modelling capture and survival probabilities using a frequentist approach via P‐splines techniques. We investigate the performance of the estimators by conducting simulation studies. We also apply and compare these models with known semi‐parametric Bayesian approaches on simulated and real data sets.     

Particle capture in ciliary filter‐feeding gymnolaemate and phylactolaemate bryozoans – a comparative study

Riisgård, H.U., Okamura, B. and Funch, P. 2009. Particle capture in ciliary filter‐feeding gymnolaemate and phylactolaemate bryozoans – a comparative study. —Acta Zoologica (Stockholm) 91 : 416–425. We studied particle capture using video‐microscopy in two gymnolaemates, the marine cheilostome Electra pilosa and the freshwater ctenostome Paludicella articulata, and three phylactolaemates, Fredericella sultana with a circular funnel‐shaped lophophore, and Cristatella mucedo and Lophophus crystallinus, both with a horseshoe‐shaped lophophore. The video‐microscope observations along with studies of lophophore morphology and ultrastructure indicated that phylactolaemate and gymnolaemate bryozoans with a diversity of lophophore shapes rely on the same basic structures and mechanisms for particle capture. Our study also demonstrates that essential features of the particle capture process resemble one another in bryozoans, brachiopods and phoronids.     

Human heat-shock protein 60 receptor-coated paramagnetic beads show improved capture of Listeria monocytogenes in the presence of other Listeria in food

Aims: To investigate the suitability of human Hsp60, a receptor for Listeria adhesion protein (LAP), on paramagnetic beads (PMB) to capture Listeria monocytogenes from food in the presence of other Listeria to facilitate rapid and specific detection of this pathogen. Methods and Results: Commercially available streptavidin‐coated PMBs were linked with biotinylated Hsp60 (PMB‐Hsp60), and the bacterial capture efficiency from pure culture and meat samples was determined. Capture rate was also compared with the monoclonal antibody (MAb)‐C11E9‐coated beads (PMB‐C11E9) and the commercial Dynabeads anti‐Listeria. Captured cells were detected and quantified by plating on selective medium, quantitative real‐time PCR (qPCR) and a light‐scattering sensor. Overall, all ligand‐coated beads had similar capture efficiency (varied from 1·8 to 9·2%) for L. monocytogenes under the conditions employed, and the minimum cell number required to achieve such capture was 10³ CFU ml^?1. PMB‐Hsp60 had significantly greater capture efficiency for pathogenic Listeria (P < 0·0001) than the nonpathogenic Listeria. In contrast, PMB‐C11E9 and Dynabeads anti‐Listeria had similar capture efficiency for both. The efficacy of all PMBs to capture L. monocytogenes in the presence of Listeria innocua from food matrices was compared. Although Dynabeads anti‐Listeria had the overall best capture efficiency, PMB‐Hsp60 was able to selectively capture L. monocytogenes even in the presence of 10–100‐fold more L. innocua cells from enriched meat samples. Conclusions: Data show that the human cell receptor, Hsp60, is suitable for the capture of pathogenic Listeria on PMB in the presence of other Listeria in food. Significance and Impact of the Study: As pathogen interaction with host cells is highly specific, host cell receptors could be used as alternate capture molecules on PMB to aid in specific detection of pathogens.     

Comparison of whole‐genome (13X) and capture (87X) resequencing methods for SNP and genotype callings

The number of polymorphisms identified with next‐generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole‐genome resequencing (WGS). For this reason, capture resequencing is used for studies focusing on only some specific regions of the genome. However, several biases in capture resequencing are known to have a negative impact on the sensitivity of SNP detection. Within this framework, the aim of this study was to compare the accuracy of WGS and capture resequencing on SNP detection and genotype calling, which differ in terms of both sequencing depth and biases. Indeed, we have evaluated the SNP calling and genotyping accuracy in a WGS dataset (13X) and in a capture resequencing dataset (87X) performed on 11 individuals. The percentage of SNPs not identified due to a sevenfold sequencing depth decrease was estimated at 7.8% using a down‐sampling procedure on the capture sequencing dataset. A comparison of the 87X capture sequencing dataset with the WGS dataset revealed that capture‐related biases were leading with the loss of 5.2% of SNPs detected with WGS. Nevertheless, when considering the SNPs detected by both approaches, capture sequencing appears to achieve far better SNP genotyping, with about 4.4% of the WGS genotypes that can be considered as erroneous and even 10% focusing on heterozygous genotypes. In conclusion, WGS and capture deep sequencing can be considered equivalent strategies for SNP detection, as the rate of SNPs not identified because of a low sequencing depth in the former is quite similar to SNPs missed because of method biases of the latter. On the other hand, capture deep sequencing clearly appears more adapted for studies requiring great accuracy in genotyping.     

Experimental conditions improving in‐solution target enrichment for ancient DNA

High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.     

Cell‐free production of a therapeutic protein: Expression,purification, and characterization of recombinant streptokinase using a CHO lysate

The use of cell‐free systems to produce recombinant proteins has grown rapidly over the past decade. In particular, cell‐free protein synthesis (CFPS) systems based on mammalian cells provide alternative methods for the production of many proteins, including those that contain disulfide bonds, glycosylation, and complex structures such as monoclonal antibodies. In the present study, we show robust production of turbo green fluorescent protein (tGFP) and streptokinase in a cell‐free system using instrumented mini‐bioreactors for highly reproducible protein production. We achieved recombinant protein production (～600 μg/ml of tGFP and 500 μg/ml streptokinase) in 2.5 hr of expression time, comparable to previously reported yields for cell‐free protein expression. Also, we demonstrate the use of two different affinity tags for product capture and compare those to a tag‐free self‐cleaving intein capture technology. The intein purification method provided a product recovery of 86%, compared with 52% for conventionally tagged proteins, while resulting in a 30% increase in total units of activity of purified recombinant streptokinase compared with conventionally tagged proteins. These promising beneficial features combined with the intein technology makes feasible the development of dose‐level production of therapeutic proteins at the point‐of‐care.     

Estimating Alpine ibex Capra ibex abundance from photographic sampling

Monitoring procedures for Alpine ibex Capra ibex are limited in habitats with reduced visibility and when physical capture and marking of the animals is not intended. Photographic sampling, involving using camera‐trap data and identifying ibex from natural markings, was adopted with capture‐recapture models to estimate the abundance of ibex in Austria. The software CAPTURE's model produced an average capture probability of 0.44 with an estimate of 34–51 ibex and a mean population size of 38 ibex. This first study showed the applicability of photographic capture‐recapture techniques to estimate the abundance of ibex based on their natural markings.     

Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel

The performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.     

Electron‐deficient p‐benzoyl‐l‐phenylalanine derivatives increase covalent chemical capture yields for protein–protein interactions

The photoactivatable amino acid p‐benzoyl‐l ‐phenylalanine (pBpa) has been used for the covalent capture of protein–protein interactions (PPIs) in vitro and in living cells. However, this technique often suffers from poor photocrosslinking yields due to the low reactivity of the active species. Here we demonstrate that the incorporation of halogenated pBpa analogs into proteins leads to increased crosslinking yields for protein–protein interactions. The analogs can be incorporated into live yeast and upon irradiation capture endogenous PPIs. Halogenated pBpas will extend the scope of PPIs that can be captured and expand the toolbox for mapping PPIs in their native environment.     

Sequence capture using PCR‐generated probes: a cost‐effective method of targeted high‐throughput sequencing for nonmodel organisms

Recent advances in high‐throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in‐solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR‐generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25–100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.     

Capturing Common Loons during prenesting and nesting periods

ABSTRACT Several techniques have been used to capture Common Loons (Gavia immer), but effectiveness is limited during periods of the breeding season when loons do not have chicks. From 2005 to 2008, we studied loons in northern Wisconsin and used night lighting to capture loons on nests and also designed a lift net for capturing loons prior to nesting. At night, incubating loons were approached by boat and, when within about 30–60 m, we focused a spotlight on the loon and, once at the nest, captured loons using a landing net. Using this technique, we captured 23 loons in 29 attempts (79%). In addition, taped calls and loon decoys were used to entice prenesting, territorial loons into a shoreline‐based, lift‐net trap at a capture efficiency of 67% (10 captures in 15 attempts) during the second year of use. Our diurnal lift‐net trap and night‐light nest‐capture techniques allowed us to capture adult Common Loons during periods of the breeding season when previous investigators have found loons difficult to catch. These techniques may also be useful for capturing other species of territorial waterbirds, especially other species of loons.     

The Petersen–Lincoln Estimator and its Extension to Estimate the Size of a Shared Population

The Petersen–Lincoln estimator has been used to estimate the size of a population in a single mark release experiment. However, the estimator is not valid when the capture sample and recapture sample are not independent. We provide an intuitive interpretation for “independence” between samples based on 2 × 2 categorical data formed by capture/non‐capture in each of the two samples. From the interpretation, we review a general measure of “dependence” and quantify the correlation bias of the Petersen–Lincoln estimator when two types of dependences (local list dependence and heterogeneity of capture probability) exist. An important implication in the census undercount problem is that instead of using a post enumeration sample to assess the undercount of a census, one should conduct a prior enumeration sample to avoid correlation bias. We extend the Petersen–Lincoln method to the case of two populations. This new estimator of the size of the shared population is proposed and its variance is derived. We discuss a special case where the correlation bias of the proposed estimator due to dependence between samples vanishes. The proposed method is applied to a study of the relapse rate of illicit drug use in Taiwan. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Continuous Covariates in Mark‐Recapture‐Recovery Analysis: A Comparison of Methods

Summary Time varying, individual covariates are problematic in experiments with marked animals because the covariate can typically only be observed when each animal is captured. We examine three methods to incorporate time varying, individual covariates of the survival probabilities into the analysis of data from mark‐recapture‐recovery experiments: deterministic imputation, a Bayesian imputation approach based on modeling the joint distribution of the covariate and the capture history, and a conditional approach considering only the events for which the associated covariate data are completely observed (the trinomial model). After describing the three methods, we compare results from their application to the analysis of the effect of body mass on the survival of Soay sheep (Ovis aries) on the Isle of Hirta, Scotland. Simulations based on these results are then used to make further comparisons. We conclude that both the trinomial model and Bayesian imputation method perform best in different situations. If the capture and recovery probabilities are all high, then the trinomial model produces precise, unbiased estimators that do not depend on any assumptions regarding the distribution of the covariate. In contrast, the Bayesian imputation method performs substantially better when capture and recovery probabilities are low, provided that the specified model of the covariate is a good approximation to the true data‐generating mechanism.