Probing the Bottleneck of Awareness Formed by Foveal Crowding: A Neurophysiological Study

Crowding occurs when an easily identified isolated stimulus is surrounded by stimuli with similar properties, making it very difficult to identify. Crowding is suggested as a mechanism that creates a bottleneck in object recognition and awareness. Recently, we showed that brief presentation times at the fovea resulted in a significant crowding effect on target identification, impaired the target's color awareness, and resulted in a slower reaction time. However, when tagging the target with a red letter, the crowding effect is abolished. Crowding is widely considered a grouping; hence, it is pre-attentive. An event-related potential (ERP) study that investigated the spatial-temporal properties of crowding suggested the involvement of higher-level visual processing. Here, we investigated whether ERP's components may be affected by crowding and tagging, and whether the temporal advantage of ERP can be utilized to gain further information about the crowding mechanism. The participants reported target identification using our standard foveal crowing paradigm. It is assumed that crowding occurs due to a suppressive effect; thus, it can be probed by changes in perceptual (N1, ~160 ms) and attentive (P3 ~300-400 ms) components. We found a suppression effect (less negative ERP magnitude) in N1 under foveal crowding, which was recovered under tagging conditions. ERP's amplitude components (N1 and P3) and the behavioral proportion correct are highly correlated. These findings suggest that crowding is an early grouping mechanism that may be combined with later processing involving the segmentation mechanism.

Exploring the Perspectives of Patients Living With Lupus: Retrospective Social Listening Study

BACKGROUND

Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease affecting various organs with a wide range of clinical manifestations. Cutaneous lupus erythematosus (CLE) can manifest as a feature of SLE or an independent skin ailment. Health-related quality of life (HRQoL) is frequently compromised in individuals living with lupus. Understanding patients' perspectives when living with a disease is crucial for effectively meeting their unmet needs. Social listening is a promising new method that can provide insights into the experiences of patients living with their disease (lupus) and leverage these insights to inform drug development strategies for addressing their unmet needs.

OBJECTIVE

The objective of this study is to explore the experience of patients living with SLE and CLE, including their disease and treatment experiences, HRQoL, and unmet needs, as discussed in web-based social media platforms such as blogs and forums.

METHODS

A retrospective exploratory social listening study was conducted across 13 publicly available English-language social media platforms from October 2019 to January 2022. Data were processed using natural language processing and knowledge graph tagging technology to clean, format, anonymize, and annotate them algorithmically before feeding them to Pharos, a Semalytix proprietary data visualization and analysis platform, for further analysis. Pharos was used to generate descriptive data statistics, providing insights into the magnitude of individual patient experience variables, their differences in the magnitude of variables, and the associations between algorithmically tagged variables.

RESULTS

A total of 45,554 posts from 3834 individuals who were algorithmically identified as patients with lupus were included in this study. Among them, 1925 (authoring 5636 posts) and 106 (authoring 243 posts) patients were identified as having SLE and CLE, respectively. Patients frequently mentioned various symptoms in relation to SLE and CLE including pain, fatigue, and rashes; pain and fatigue were identified as the main drivers of HRQoL impairment. The most affected aspects of HRQoL included "mobility," "cognitive capabilities," "recreation and leisure," and "sleep and rest." Existing pharmacological interventions poorly managed the most burdensome symptoms of lupus. Conversely, nonpharmacological treatments, such as exercise and meditation, were frequently associated with HRQoL improvement.

CONCLUSIONS

Patients with lupus reported a complex interplay of symptoms and HRQoL aspects that negatively influenced one another. This study demonstrates that social listening is an effective method to gather insights into patients' experiences, preferences, and unmet needs, which can be considered during the drug development process to develop effective therapies and improve disease management.

Insights into vertebral band pair deposition rate in the juvenile common thresher shark (Alopias vulpinus) in the northeastern Pacific Ocean

Validation of band pair deposition rates in elasmobranch vertebrae is essential for accurate age estimation using band pair counting techniques. We present a validation study of the vertebral band pair deposition rate for juvenile common thresher sharks Alopias vulpinus in the northeastern Pacific Ocean (NEPO) using tag and recapture with oxytetracycline (OTC) injection. A total of 14 juvenile A. vulpinus marked with OTC from 1998 through 2013 were recaptured with times at liberty ranging from 1.08 to 3.81 years with an average of 2.14 years (±0.97 years standard deviation, SD). Shark size ranged from 80 to 128 cm fork length (LF) at the time of OTC injection and from 112 to 168 cm LF for those measured at recapture. The slopes of the relationships between band pairs post OTC and years at liberty for each reader ranged from 0.84 to 0.95, slightly lower than the 1.0 slope expected from annual band pair formation. These findings preliminarily support previous age and growth assumptions based on a one band pair per year deposition rate. However, high variation in band pair deposition rates between samples, coupled with regression slopes falling just under one band pair per year, indicates that further investigation is needed to refine band pair deposition rate estimates.

Tagged IDS causes efficient and engraftment-independent prevention of brain pathology during lentiviral gene therapy for Mucopolysaccharidosis type II

Mucopolysaccharidosis type II (OMIM 309900) is a lysosomal storage disorder caused by iduronate 2-sulfatase (IDS) deficiency and accumulation of glycosaminoglycans, leading to progressive neurodegeneration. As intravenously infused enzyme replacement therapy cannot cross the blood-brain barrier (BBB), it fails to treat brain pathology, highlighting the unmet medical need to develop alternative therapies. Here, we test modified versions of hematopoietic stem and progenitor cell (HSPC)-mediated lentiviral gene therapy (LVGT) using IDS tagging in combination with the ubiquitous MND promoter to optimize efficacy in brain and to investigate its mechanism of action. We find that IDS tagging with IGF2 or ApoE2, but not RAP12x2, improves correction of brain heparan sulfate and neuroinflammation at clinically relevant vector copy numbers. HSPC-derived cells engrafted in brain show efficiencies highest in perivascular areas, lower in choroid plexus and meninges, and lowest in parenchyma. Importantly, the efficacy of correction was independent of the number of brain-engrafted cells. These results indicate that tagged versions of IDS can outperform untagged IDS in HSPC-LVGT for the correction of brain pathology in MPS II, and they imply both cell-mediated and tag-mediated correction mechanisms, including passage across the BBB and increased uptake, highlighting their potential for clinical translation.

Tensile strength and knot security of five suture materials exposed to natural summer conditions of a temperate lake

OBJECTIVE

Wild fish and other aquatic ectotherms are often subjected to procedures during field research that require wound closure using sutures. A variety of absorbable sutures are available for such purposes, yet degradation processes are highly dependent on temperature, and the environments in which wild ectotherms are released are almost always colder than the conditions for which absorbable sutures are typically designed (i.e., ~37°C). We therefore studied the degradation of various suture materials under a set of biologically relevant conditions for temperate freshwater fish.

METHODS

Using a force gauge, we tested the tensile strengths and knot securities of loops tied with five different absorbable suture materials (PDS-II, dyed coated Vicryl, undyed coated Vicryl, plain gut, and chromic gut) prior to and during submersion in a temperate lake over an 8-week period.

RESULT

The naturally derived collagen-based suture materials (i.e., plain gut and chromic gut) exhibited major decreases in tensile strength within 2 weeks of submersion but maintained relatively high knot security throughout the study period. The synthetic suture loops had poorer initial knot securities that increased following submersion and showed little to no evidence of degradation after 8 weeks.

CONCLUSION

Variable rates of absorbable suture degradation, or lack thereof, were observed. We discuss the implications of these trends for fish welfare considerations such as suture retention, wound healing, inflammation, and infection under natural conditions.

Subcellular protein localisation of Trypanosoma brucei bloodstream form-upregulated proteins maps stage-specific adaptations

Background: Genome-wide subcellular protein localisation in Trypanosoma brucei, through our TrypTag project, has comprehensively dissected the molecular organisation of this important pathogen. Powerful as this resource is , T. brucei has multiple developmental forms and we previously only analysed the procyclic form. This is an insect life cycle stage, leaving the mammalian bloodstream form unanalysed. The expectation is that between life stages protein localisation would not change dramatically (completely unchanged or shifting to analogous stage-specific structures). However, this has not been specifically tested. Similarly, which organelles tend to contain proteins with stage-specific expression can be predicted from known stage specific adaptations but has not been comprehensively tested. Methods: We used endogenous tagging with mNG to determine the sub-cellular localisation of the majority of proteins encoded by transcripts significantly upregulated in the bloodstream form, and performed comparison to the existing localisation data in procyclic forms. Results: We have confirmed the localisation of known stage-specific proteins and identified the localisation of novel stage-specific proteins. This gave a map of which organelles tend to contain stage specific proteins: the mitochondrion for the procyclic form, and the endoplasmic reticulum, endocytic system and cell surface in the bloodstream form. Conclusions: This represents the first genome-wide map of life cycle stage-specific adaptation of organelle molecular machinery in T. brucei.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

Deployment of biologging tags on free swimming large whales using uncrewed aerial systems

Suction-cup-attached biologging tags have led to major advances in our understanding of large whale behaviour. Getting close enough to a whale at sea to safely attach a tag is a major limiting factor when deploying these systems. Here we present an uncrewed aerial system (UAS)-based tagging technique for free-swimming large whales and provide data on efficacy from field testing on blue (Balaenoptera musculus) and fin (B. physalus) whales. Rapid transit speed and the bird's-eye view of the animal during UAS tagging contributed to the technique's success. During 8 days of field testing, we had 29 occasions when a focal animal was identified for attempted tagging and tags were successfully attached 21 times. The technique was efficient, with mean flight time of 2 min 45 s from launch to deployment and a mean distance of 490 m from the launch vessel to tagged animal, reducing potential adverse effects resulting from close approaches for tagging. These data indicate that UAS are capable of attaching biologging tags to free-swimming large whales quickly and from large distances, potentially increasing success rates, decreasing attempt times, and reducing animal disruption during tagging.

Identification of Inhibitors of Tubulin Polymerization Using a CRISPR-Edited Cell Line with Endogenous Fluorescent Tagging of β-Tubulin and Histone H1

Tubulin is a protein that plays a critical role in maintaining cellular structure and facilitating cell division. Inhibiting tubulin polymerization has been shown to be an effective strategy for inhibiting the proliferation of cancer cells. In the past, identifying compounds that could inhibit tubulin polymerization has required the use of in vitro assays utilizing purified tubulin or immunofluorescence of fixed cells. This study presents a novel approach for identifying tubulin polymerization inhibitors using a CRISPR-edited cell line that expresses fluorescently tagged β-tubulin and a nuclear protein, enabling the visualization of tubulin polymerization dynamics via high-content imaging analysis (HCI). The cells were treated with known tubulin polymerization inhibitors, colchicine, and vincristine, and the resulting phenotypic changes indicative of tubulin polymerization inhibition were confirmed using HCI. Furthermore, a library of 429 kinase inhibitors was screened, resulting in the identification of three compounds (ON-01910, HMN-214, and KX2-391) that inhibit tubulin polymerization. Live cell tracking analysis confirmed that compound treatment leads to rapid tubulin depolymerization. These findings suggest that CRISPR-edited cells with fluorescently tagged endogenous β-tubulin can be utilized to screen large compound libraries containing diverse chemical families for the identification of novel tubulin polymerization inhibitors.

Observations on the use of passive integrated transponder (PIT) tags in teleosts and elasmobranchs at a public aquarium, 728 cases, 2007-2020

Between 2007 and 2020 at New England Aquarium, Boston, MA, USA, we implanted passive integrated transponder (PIT) tags into 728 fish representing 105 teleost and elasmobranch species to identify animals as individuals. At the time of retrospective data analysis, mean longevity interval (median, range) after tag placement for animals that remained alive (n = 236) was 4.7 years (4.5, 0.3-13.8). Mean interval (median, range) between tag placement and death (n = 317) was 2.1 years (1.6, 0-11.2); and mean interval (median, range) between tag placement and transfer to other facilities (n = 175) was 2.5 years (3.1, 0.1-9.3). Possible adverse effects of tagging were extremely rare. Using the described methods, the equipment cost for every 10 PIT tag implantations was $2.83. PIT tag implantation in fishes is a safe and cost effective method to identify individuals, providing an opportunity to accumulate valuable data regarding individual longevity, welfare, basic demographics, and outcome of medical management. PIT tag implantation is recommended as a routine aspect of acquisition, quarantine, and medical management of fish under human care.

Experimental techniques and terminology in gas-phase ion spectroscopy

This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.

V5 and GFP Tagging of Viral Gene pp38 of Marek's Disease Vaccine Strain CVI988 Using CRISPR/Cas9 Editing

Marek's disease virus (MDV) is a member of alphaherpesviruses associated with Marek's disease, a highly contagious neoplastic disease in chickens. The availability of the complete sequence of the viral genome allowed for the identification of major genes associated with pathogenicity using different techniques, such as bacterial artificial chromosome (BAC) mutagenesis and the recent powerful clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-based editing system. Thus far, most studies on MDV genome editing using the CRISPR/Cas9 system have focused on gene deletion. However, analysis of the expression and interactions of the viral proteins during virus replication in infected cells and tumor cells is also important for studying its role in MDV pathogenesis. The unavailability of antibodies against most of the MDV proteins has hindered the progress in such studies. This prompted us to develop pipelines to tag MDV genes as an alternative method for this purpose. Here we describe the application of CRISPR/Cas9 gene-editing approaches to tag the phosphoprotein 38 (pp38) gene of the MDV vaccine strain CVI988 with both V5 and green fluorescent protein (GFP). This rapid and efficient viral-gene-tagging technique can overcome the shortage of specific antibodies and speed up the MDV gene function studies significantly, leading to a better understanding of the molecular mechanisms of MDV pathogenesis.

First evidence of regional migration of the copper shark Carcharhinus brachyurus (Günther, 1870) in the Southwest Atlantic

Regional migration of the copper shark Carcharhinus brachyurus was recorded for the first time in the Southwest Atlantic (SWA) from Argentina (latitude: -38.1037, longitude: -57.5371) to Brazil (latitude: -20.6833, longitude: -40.2846) as a result of a citizen science tagging project. The recaptured specimen was a female (103 kg weight), with 18 developing embryos within the uterus. The total distance was at least 2566 km, and it is the longest ever recorded for the species. Furthermore, it extends its northern distribution in the SWA.

Animal tag technology keeps coming of age: an engineering perspective

Animal-borne tags (biologgers) have now become extremely sophisticated, recording data from multiple sensors at high frequencies for long periods and, as such, have become a powerful tool for behavioural ecologists and physiologists studying wild animals. But the design and implementation of these tags is not trivial because engineers have to maximize performance and ability to function under onerous conditions while minimizing tag mass and volume (footprint) to maximize the wellbeing of the animal carriers. We present some of the major issues faced by tag engineers and show how tag designers must accept compromises while maintaining systems that can answer the questions being posed. We also argue that basic understanding of engineering issues in tag design by biologists will help feedback to engineers to better tag construction but also reduce the likelihood that tag-deploying biologists will misunderstand their own results. Finally, we suggest that proper consideration of conventional technology together with new approaches will lead to further step changes in our understanding of wild-animal biology using smart tags. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Left Ventricular Diastolic Function Studied with Magnetic Resonance Imaging: A Systematic Review of Techniques and Relation to Established Measures of Diastolic Function

Purpose: In recent years, cardiac magnetic resonance (CMR) has been used to assess LV diastolic function. In this systematic review, studies were identified where CMR parameters had been evaluated in healthy and/or patient groups with proven diastolic dysfunction or known to develop heart failure with preserved ejection fraction. We aimed at describing the parameters most often used, thresholds where possible, and correlation to echocardiographic and invasive measurements. Methods and results: A systematic literature review was performed using the databases of PubMed, Embase, and Cochrane. In total, 3808 articles were screened, and 102 studies were included. Four main CMR techniques were identified: tagging; time/volume curves; mitral inflow quantification with velocity-encoded phase-contrast sequences; and feature tracking. Techniques were described and estimates were presented in tables. From published studies, peak change of torsion shear angle versus volume changes in early diastole (−dφ′/dV′) (from tagging analysis), early peak filling rate indexed to LV end-diastolic volume <2.1 s⁻¹ (from LV time-volume curve analysis), enlarged LA maximal volume >52 mL/m², lowered LA total (<40%), and lowered LA passive emptying fractions (<16%) seem to be reliable measures of LV diastolic dysfunction. Feature tracking, especially of the atrium, shows promise but is still a novel technique. Conclusion: CMR techniques of LV untwisting and early filling and LA measures of poor emptying are promising for the diagnosis of LV filling impairment, but further research in long-term follow-up studies is needed to assess the ability for the parameters to predict patient related outcomes.

An off-resonance insensitive orthogonal CSPAMM sequence (ORI-O-CSPAMM) for the acquisition of CSPAMM and MICSR grids in half scan time

PURPOSE

To develop an Off-Resonance Insensitive Orthogonal CSPAMM sequence (ORI-O-CSPAMM) for the acquisition of CSPAMM and MICSR grids in half of the acquisition time.

METHODS

Phantom and mid-level left ventricle short-axis tagged images were acquired using CSPAMM, ORI-CSPAMM, O-CSPAMM, and the proposed ORI-O-CPAMM sequences to interrogate and compare its behavior under off-resonance effects produced by vegetable oil and subcutaneous and epicardial fat. The images were compared in terms of signal and the capacity to obtain complex difference and MICSR images.

RESULTS

Like ORI-CSPAMM, the proposed ORI-O-CSPAMM sequence removed almost completely the off-resonance artifacts produced during the tagging preparation. Tagging grids without DC components were obtained with ORI-O-CSPAMM using complex difference and MICSR from only two complementary images, which reduced the scan time to a half compared to CSPAMM and ORI-CSPAMM. The removal of off-resonance effects and the capacity to obtain MICSR images are advantages of ORI-O-CSPAMM over the O-CSPAMM sequence.

CONCLUSION

We developed a novel and fast tagging sequence designed to remove off-resonance effects during the tagging preparation, and to obtain complex difference and MICSR grids in half of the scan time compared to CSPAMM and ORI-CSPAMM sequences, which could allow its application to clinical protocols.

Endovascular reversal of renovascular hypertension blunts cardiac dysfunction and deformation in swine

OBJECTIVE

Renovascular hypertension (RVH) induces hemodynamic and humoral aberrations that may impair cardiac function, structure and mechanics, including cardiac twist and deformation. Revascularization of a stenotic renal artery can decrease blood pressure (BP), but its ability to restore cardiac mechanics in RVH remains unclear. We hypothesized that percutaneous transluminal renal angioplasty (PTRA) would improve cardiac function and left ventricular (LV) deformation in swine RVH.

METHODS

Seventeen domestic pigs were studied for 16 weeks: RVH, RVH + PTRA and normal controls (n = 5-6 each). Global LV function was estimated by multidetector computed-tomography, and LV deformation by electrocardiographically triggered MRI tagging at the apical, mid, and basal LV levels. Cardiomyocyte hypertrophy, myocardial capillary density, and fibrosis were evaluated ex vivo.

RESULTS

BP and wall thickness were elevated in RVH and decreased by PTRA, yet remained higher than in controls. LV myocardial muscle mass increased in RVH pigs, which also developed diastolic dysfunction, whereas cardiac output increased. Furthermore, both apical rotation and peak torsion angle increased in RVH compared with controls. Ex vivo, RVH induced myocardial fibrosis and vascular rarefaction. PTRA restored cardiac function and alleviated hypertrophy, vascular rarefaction, and fibrosis. PTRA also normalized apical rotation and peak torsion angle, and elevated basal peak radial strain and apical peak radial strain compared with RVH.

CONCLUSION

In addition to cardiac LV adaptive hypertrophy and diastolic dysfunction, short-term RVH causes cardiac deformation. Despite only partial improvement in BP, PTRA effectively restored cardiac function and reversed abnormal mechanics. Hence, renal revascularization may be a useful strategy to preserve cardiac function in RVH.

Identification of Individual Zebrafish (Danio rerio): A Refined Protocol for VIE Tagging Whilst Considering Animal Welfare and the Principles of the 3Rs

In aquatic ecology, studies have commonly employed a tagging technique known as visible implant elastomer (VIE). This method has not been widely adopted by the zebrafish research community and also lacks refinement with regard to animal welfare. The current paper introduces a new VIE tagging protocol, with the aim of improving existing tagging techniques by placing particular emphasis on the Three Rs. To improve animal welfare and fish survival, we added the use of an analgesic compound (lidocaine) through the marking procedure, followed by after-treatment with antiseptics (melaleuca, aloe vera, and PVP-I as active ingredients) to improve tissue regeneration and healing. The newly improved protocol has been quantitatively evaluated on different populations and age groups of zebrafish. This study will be useful to the scientific zebrafish community and to the wider field including biologist and aquarists, especially in consideration of animal welfare, where tagging techniques are considered as a potential noxious stimulus for fish.

Further Insights on the Migration Biology of Monarch Butterflies, Danaus plexippus (Lepidoptera: Nymphalidae) from the Pacific Northwest

The fall migration of monarch butterflies, Danaus plexippus (L.), in the Pacific Northwest was studied during 2017-2019 by tagging 14,040 captive-reared and 450 wild monarchs. One hundred and twenty-two captive-reared monarchs (0.87%) were recovered at distances averaging 899.9 ± 98.6 km for Washington-released and 630.5 ± 19.9 km for Oregon-released monarchs. The greatest straight-line release to recovery distance was 1392.1 km. A mean travel rate of 20.7 ± 2.2 km/day and maximum travel of 46.1 km/day were recorded. Recovery rates were greater for Oregon-released monarchs (0.92%) than Washington-released (0.34%) or Idaho-released monarchs (0.30%). Most monarchs (106/122) were recovered SSW-S-SSE in California, with 82 at 18 coastal overwintering sites. Two migrants from Oregon were recovered just weeks after release ovipositing in Santa Barbara and Palo Alto, CA. Two migrants released in central Washington recovered up to 360.0 km to the SE, and recoveries from Idaho releases to the S and SE suggests that some Pacific Northwest migrants fly to an alternative overwintering destination. Monarchs released in southern Oregon into smoky, poor quality air appeared to be as successful at reaching overwintering sites and apparently lived just as long as monarchs released into non-smoky, good quality air. Migration and lifespan for monarchs infected with the protozoan parasite, Ophryocystis elektroscirrha (McLaughlin and Myers), appeared to be similar to the migration and survival of uninfected monarchs, although data are limited. Our data improve our understanding of western monarch migration, serving as a basis for further studies and providing information for conservation planning.

DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce “molecular signposts” that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells.

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Asymmetric DNA signpost origami tags (SPOTs) precisely localize proteins

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SPOTs identify specific proteins in electron cryomicroscopy

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SPOTs have a high contrast “sign” and functionalized “post” base for targeting

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SPOTs recognize fluorescent fusion proteins on vesicles, viruses, and cell surfaces

Serial Cardiovascular Magnetic Resonance Strain Measurements to Identify Cardiotoxicity in Breast Cancer: Comparison With Echocardiography

OBJECTIVES

This study sought to compare the prognostic value of cardiovascular magnetic resonance (CMR) and 2-dimensional echocardiography (2DE) derived left ventricular (LV) strain, volumes, and ejection fraction for cancer therapy-related cardiac dysfunction (CTRCD) in women with early stage breast cancer.

BACKGROUND

There are limited comparative data on the association of CMR and 2DE derived strain, volumes, and LVEF with CTRCD.

METHODS

A total of 125 prospectively recruited women with HER2+ early stage breast cancer receiving sequential anthracycline/trastuzumab underwent 5 serial CMR and 6 of 2DE studies before and during treatment. CMR LV volumes, left ventricular ejection fraction tagged-CMR, and feature-tracking (FT) derived global systolic longitudinal (GLS) and global circumferential strain (GCS) and 2DE-based LV volumes, function, GLS, and GCS were measured. CTRCD was defined by the cardiac review and evaluation committee criteria.

RESULTS

Twenty-eight percent of patients developed CTRCD by CMR and 22% by 2DE. A 15% relative reduction in 2DE-GLS increased the CTRCD odds by 133% at subsequent follow-up, compared with 47%/50% by tagged-CMR GLS/GCS and 87% by FT-GCS. CMR and 2DE-LVEF and indexed left ventricular end-systolic volume (LVESVi) were also associated with subsequent CTRCD. The prognostic threshold change in CMR-left ventricular ejection fraction and FT strain for subsequent CTRCD was similar to the known minimum-detectable difference for these measures, whereas for tagged-CMR strain it was lower than the minimum-detectable difference; for 2DE, only the prognostic threshold for GLS was greater than the minimum-detectable difference. Of all strain methods, 2DE-GLS provided the highest increase in discriminatory value over baseline clinical risk factors for subsequent CTRCD. The combination of 2DE-left ventricular ejection fraction or LVESVi and strain provided greater increase in the area under the curve for subsequent CTRCD over clinical risk factors than CMR left ventricular ejection fraction or LVESVi and strain (18% to 22% vs. 9% to 14%).

CONCLUSIONS

In women with HER2+ early stage breast cancer, changes in CMR and 2DE strain, left ventricular ejection fraction, and LVESVi were prognostic for subsequent CTRCD. When LVEF can be measured precisely by CMR, FT strain may function as an additional confirmatory prognostic measure, but with 2DE, GLS is the optimal prognostic measure. (Evaluation of Myocardial Changes During BReast Adenocarcinoma Therapy to Detect Cardiotoxicity Earlier With MRI [EMBRACE-MRI]; NCT02306538).

Nanobody-Based Probes for Subcellular Protein Identification and Visualization

Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.

Defining the Reference Range for Left Ventricular Strain in Healthy Patients by Cardiac MRI Measurement Techniques: Systematic Review and Meta-Analysis

BACKGROUND. Echocardiography is the primary noninvasive technique for left ventricular (LV) strain measurement. MRI has potential advantages, although reference ranges and thresholds to differentiate normal from abnormal left ventricular global longitudinal strain (LVGLS), left ventricular global circumferential strain (LVGCS), and left ventricular global radial strain (LVGRS) are not yet established. OBJECTIVE. The purpose of our study was to determine the mean and lower limit of normal (LLN) of MRI-derived LV strain measurements in healthy patients and explore factors potentially influencing these measurements. EVIDENCE ACQUISITION. PubMed, Embase, and Cochrane Library databases were searched for studies published through January 1, 2020, that reported MRI-derived LV strain measurements in at least 30 healthy individuals. Mean and LLN measurements of LV strain were pooled using random-effects models overall and for studies stratified by measurement method (feature tracking [FT] or tagging). Additional subgroup and meta-regression analyses were performed. EVIDENCE SYNTHESIS. Twenty-three studies with a total of 1782 healthy subjects were included. Pooled means and LLNs for all studies were -18.6% (95% CI, -19.5% to -17.6%) and -13.3% (-13.9% to 12.7%) for LVGLS, -21.0% (-22.4% to -19.6%) and -15.6% (-17.0% to -14.3%) for LVGCS, and 38.7% (30.5-46.9%) and 20.6% (15.1-26.1%) for LVGRS. Pooled means and LLNs for LVGLS by strain measurement method were -19.4% (95% CI, -20.6% to -18.1%) and -13.1% (-14.2% to -12.0%) for FT and -15.6% (-16.2% to -15.1%) and -13.1% (-14.1% to -12.2%) for tagging. A later year of study publication, increasing patient age, and increasing body mass index were associated with more negative mean LVGLS values. An increasing LV end-diastolic volume index was associated with less negative mean LVGLS values. No factor was associated with LLN of LVGLS. CONCLUSION. We determined the pooled means and LLNs, with associated 95% CIs, for LV strain by cardiac MRI to define thresholds for normal, abnormal, and borderline strain in healthy patients. The method of strain measurement by MRI affected the mean LVGLS. No factor affected the LLN of LVGLS. CLINICAL IMPACT. This meta-analysis lays a foundation for clinical adoption of MRI-derived LV strain measurements, with management implications in both healthy patients and patients with various disease states.

Myocardial strain imaging: review of general principles, validation, and sources of discrepancies

Myocardial tissue tracking imaging techniques have been developed for a more accurate evaluation of myocardial deformation (i.e. strain), with the potential to overcome the limitations of ejection fraction (EF) and to contribute, incremental to EF, to the diagnosis and prognosis in cardiac diseases. While most of the deformation imaging techniques are based on the similar principles of detecting and tracking specific patterns within an image, there are intra- and inter-imaging modality inconsistencies limiting the wide clinical applicability of strain. In this review, we aimed to describe the particularities of the echocardiographic and cardiac magnetic resonance deformation techniques, in order to understand the discrepancies in strain measurement, focusing on the potential sources of variation: related to the software used to analyse the data, to the different physics of image acquisition and the different principles of 2D vs. 3D approaches. As strain measurements are not interchangeable, it is highly desirable to work with validated strain assessment tools, in order to derive information from evidence-based data. There is, however, a lack of solid validation of the current tissue tracking techniques, as only a few of the commercial deformation imaging softwares have been properly investigated. We have, therefore, addressed in this review the neglected issue of suboptimal validation of tissue tracking techniques, in order to advocate for this matter.

Head-to-head comparison of cardiovascular MR feature tracking cine versus acquisition-based deformation strain imaging using myocardial tagging and strain encoding

PURPOSE

Myocardial feature-tracking (FT) deformation imaging is superior for risk stratification compared with volumetric approaches. Because there is no clear recommendation regarding FT postprocessing, we compared different FT-strain analyses with reference standard techniques, including tagging and strain-encoded (SENC) MRI.

METHODS

Feature-tracking software from four different vendors (TomTec, Medis, Circle [CVI], and Neosoft), tagging (Segment), and fastSENC (MyoStrain) were used to determine left ventricular global circumferential strains (GCS) and longitudinal strains (GLS) in 12 healthy volunteers and 12 patients with heart failure. Variability and agreements were assessed using intraclass correlation coefficients for absolute agreement (ICCa) and consistency (ICCc) as well as Pearson correlation coefficients.

RESULTS

For FT-GCS, consistency was excellent comparing different FT vendors (ICCc = 0.84-0.97, r = 0.86-0.95) and in comparison to fast SENC (ICCc = 0.78-0.89, r = 0.73-0.81). FT-GCS consistency was excellent compared with tagging (ICCc = 0.79-0.85, r = 0.74-0.77) except for TomTec (ICCc = 0.68, r = 0.72). Absolute FT-GCS agreements among FT vendors were highest for CVI and Medis (ICCa = 0.96) and lowest for TomTec and Neosoft (ICCa = 0.32). Similarly, absolute FT-GCS agreements were excellent for CVI and Medis compared with both tagging and fast SENC (ICCa = 0.84-0.88), good to excellent for Neosoft (ICCa = 0.77 and 0.64), and lowest for TomTec (ICCa = 0.41 and 0.47). For FT-GLS, consistency was excellent (ICCc ≥ 0.86, r ≥ 0.76). Absolute agreements among FT vendors were excellent (ICCa = 0.91-0.93) or good to excellent for TomTec (ICCa = 0.69-0.85). Absolute agreements (ICCa) were good (CVI 0.70, Medis 0.60) and fair (TomTec 0.41, Neosoft 0.59) compared with tagging, but excellent compared with fast SENC (ICCa = 0.77-0.90).

CONCLUSION

Although absolute agreements differ depending on deformation assessment approaches, consistency and correlation are consistently high regardless of the method chosen, thus indicating reliable strain assessment. Further standardisation and introduction of uniform references is warranted for routine clinical implementation.

Expression of a Malassezia Codon Optimized mCherry Fluorescent Protein in a Bicistronic Vector

The use of fluorescent proteins allows a multitude of approaches from live imaging and fixed cells to labeling of whole organisms, making it a foundation of diverse experiments. Tagging a protein of interest or specific cell type allows visualization and studies of cell localization, cellular dynamics, physiology, and structural characteristics. In specific instances fluorescent fusion proteins may not be properly functional as a result of structural changes that hinder protein function, or when overexpressed may be cytotoxic and disrupt normal biological processes. In our study, we describe application of a bicistronic vector incorporating a Picornavirus 2A peptide sequence between a NAT antibiotic selection marker and mCherry. This allows expression of multiple genes from a single open reading frame and production of discrete protein products through a cleavage event within the 2A peptide. We demonstrate integration of this bicistronic vector into a model Malassezia species, the haploid strain M. furfur CBS 14141, with both active selection, high fluorescence, and proven proteolytic cleavage. Potential applications of this technology can include protein functional studies, Malassezia cellular localization, and co-expression of genes required for targeted mutagenesis.

Preparation of Complex Glycans From Natural Sources for Functional Study

One major barrier in glycoscience is the lack of diverse and biomedically relevant complex glycans in sufficient quantities for functional study. Complex glycans from natural sources serve as an important source of these glycans and an alternative to challenging chemoenzymatic synthesis. This review discusses preparation of complex glycans from several classes of glycoconjugates using both enzymatic and chemical release approaches. Novel technologies have been developed to advance the large-scale preparation of complex glycans from natural sources. We also highlight recent approaches and methods developed in functional and fluorescent tagging and high-performance liquid chromatography (HPLC) isolation of released glycans.

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.

Progress and pitfalls of using isobaric mass tags for proteome profiling

Introduction: Quantitative proteomics using mass spectrometry is performed via label-free or label-based approaches. Labeling strategies rely on the incorporation of stable heavy isotopes by metabolic, enzymatic, or chemical routes. Isobaric labeling uses chemical labels of identical masses but of different fragmentation behaviors to allow the relative quantitative comparison of peptide/protein abundances between biological samples.Areas covered: We have carried out a systematic review on the use of isobaric mass tags in proteomic research since their inception in 2003. We focused on their quantitative performances, their multiplexing evolution, as well as their broad use for relative quantification of proteins in pre-clinical models and clinical studies. Current limitations, primarily linked to the quantitative ratio distortion, as well as state-of-the-art and emerging solutions to improve their quantitative readouts are discussed.Expert opinion: The isobaric mass tag technology offers a unique opportunity to compare multiple protein samples simultaneously, allowing higher sample throughput and internal relative quantification for improved trueness and precision. Large studies can be performed when shared reference samples are introduced in multiple experiments. The technology is well suited for proteome profiling in the context of proteomic discovery studies.

Tagged Core-Satellite Nanoassemblies: Role of Assembling Sequence on Surface-Enhanced Raman Scattering (SERS) Performance

Plasmonic nanoassemblies with amplified optical responses are attractive as chemo/bio sensors and diagnostic tracking agents. For real-life implementation, such nanostructures require a well-designed and controlled formation for maximizing the optical amplification. Forming these nanoassemblies typically requires numerous steps; however, the importance of the sequence of the steps is typically not discussed. Thus, here we have investigated the role of the sequence of tagging (or labeling, barcoding) of such plasmonic nanoassemblies with Raman active molecules in a quest to maximize the surface-enhanced Raman scattering (SERS) enhancement that could be achieved from the nanoassemblies. We have chosen the core-satellite nanoassembly arrangement to study the role of tagging sequence because it allows us to keep structural parameters constant that would otherwise influence the SERS amplification. We demonstrate that incorporating the tag molecule at an assembly point before formation of the nanojunctions leads to more tag molecules being positioned at the core-satellite nanojunctions, thereby resulting in higher SERS signal enhancement. This will thus prove to be a useful tool in fully utilizing the nanoassembly morphology generated hot-spot and maximizing its SERS performance.

Design patterns for wildlife-related camera trap image analysis

This paper describes and explains design patterns for software that supports how analysts can efficiently inspect and classify camera trap images for wildlife-related ecological attributes. Broadly speaking, a design pattern identifies a commonly occurring problem and a general reusable design approach to solve that problem. A developer can then use that design approach to create a specific software solution appropriate to the particular situation under consideration. In particular, design patterns for camera trap image analysis by wildlife biologists address solutions to commonly occurring problems they face while inspecting a large number of images and entering ecological data describing image attributes. We developed design patterns for image classification based on our understanding of biologists' needs that we acquired over 8 years during development and application of the freely available Timelapse image analysis system. For each design pattern presented, we describe the problem, a design approach that solves that problem, and a concrete example of how Timelapse addresses the design pattern. Our design patterns offer both general and specific solutions related to: maintaining data consistency, efficiencies in image inspection, methods for navigating between images, efficiencies in data entry including highly repetitious data entry, and sorting and filtering image into sequences, episodes, and subsets. These design patterns can inform the design of other camera trap systems and can help biologists assess how competing software products address their project-specific needs along with determining an efficient workflow.

Atlantic salmon Salmo salar passing a natural barrier before and after construction of a hydroelectric station

A hydro power plant constructed around a waterfall on a coastal spate river, used the fall as a natural fish pass and applied a previous telemetry study on local Atlantic salmon Salmo salar to determine the abstraction conditions for the site. The current study used the same telemetry approach to monitor the efficacy of S. salar passage and to compare migratory behaviour at the waterfall pre and post the hydro development. The probability of S. salar successfully crossing the waterfall was higher post-hydro when 80% of tagged fish successfully crossed in comparison to the pristine pre-hydro period when 44% of tagged fish ascended. The flow range used by tagged S. salar to cross the waterfall ranged from 2.49-7.87 m³ s^-1 in the pre-hydro period but broadened to 1.32-12.91 m³ s^-1 during the post-hydro period. This was principally due to the hydro diverting water away from the waterfall during spate conditions, damping the flow across the barrier and facilitating upstream migration within a more suitable discharge range. During 2017-2018 implementation of the hydro-operation protocol elongated the duration of the migratory window for successful upstream migration by 36-128%. A strong diurnal pattern was observed for movements across the Salmon Leap waterfall during both the pre-hydro and post-hydro monitoring periods with most tagged S. salar crossing the complex obstacle in daylight.

Assessment of Global Longitudinal and Circumferential Strain Using Computed Tomography Feature Tracking: Intra-Individual Comparison with CMR Feature Tracking and Myocardial Tagging in Patients with Severe Aortic Stenosis

In this study, we used a single commercially available software solution to assess global longitudinal (GLS) and global circumferential strain (GCS) using cardiac computed tomography (CT) and cardiac magnetic resonance (CMR) feature tracking (FT). We compared agreement and reproducibility between these two methods and the reference standard, CMR tagging (TAG). Twenty-seven patients with severe aortic stenosis underwent CMR and cardiac CT examinations. FT analysis was performed using Medis suite version 3.0 (Leiden, The Netherlands) software. Segment (Medviso) software was used for GCS assessment from tagged images. There was a trend towards the underestimation of GLS by CT-FT when compared to CMR-FT (19.4 ± 5.04 vs. 22.40 ± 5.69, respectively; p = 0.065). GCS values between TAG, CT-FT, and CMR-FT were similar (p = 0.233). CMR-FT and CT-FT correlated closely for GLS (r = 0.686, p < 0.001) and GCS (r = 0.707, p < 0.001), while both of these methods correlated moderately with TAG for GCS (r = 0.479, p < 0.001 for CMR-FT vs. TAG; r = 0.548 for CT-FT vs. TAG). Intraobserver and interobserver agreement was excellent in all techniques. Our findings show that, in elderly patients with severe aortic stenosis (AS), the FT algorithm performs equally well in CMR and cardiac CT datasets for the assessment of GLS and GCS, both in terms of reproducibility and agreement with the gold standard, TAG.

Intermittently tagged real-time MRI reveals internal tongue motion during speech production

PURPOSE

To demonstrate a tagging method compatible with RT-MRI for the study of speech production.

METHODS

Tagging is applied as a brief interruption to a continuous real-time spiral acquisition. Tagging can be initiated manually by the operator, cued to the speech stimulus, or be automatically applied with a fixed frequency. We use a standard 2D 1-3-3-1 binomial SPAtial Modulation of Magnetization (SPAMM) sequence with 1 cm spacing in both in-plane directions. Tag persistence in tongue muscle is simulated and validated in vivo. The ability to capture internal tongue deformations is tested during speech production of American English diphthongs in native speakers.

RESULTS

We achieved an imaging window of 650-800 ms at 1.5T, with imaging signal to noise ratio ≥ 17 and tag contrast to noise ratio ≥ 5 in human tongue, providing 36 frames/s temporal resolution and 2 mm in-plane spatial resolution with real-time interactive acquisition and view-sharing reconstruction. The proposed method was able to capture tongue motion patterns and their relative timing with adequate spatiotemporal resolution during the production of American English diphthongs and consonants.

CONCLUSION

Intermittent tagging during real-time MRI of speech production is able to reveal the internal deformations of the tongue. This capability will allow new investigations of valuable spatiotemporal information on the biomechanics of the lingual subsystems during speech without reliance on binning speech utterance repetition.

Luminescent peptide tagging enables efficient screening for CRISPR-mediated knock-in in human induced pluripotent stem cells

Human pluripotent stem cells are increasingly used for CRISPR-mediated gene targeting in efforts to generate models of human diseases. This is a challenging task because of the high sensitivity of these cells to suboptimal conditions, including CRISPR-associated DNA damage and subsequent rounds of single-cell cloning. We sought to develop a sensitive method that enables rapid screening of CRISPR targeted cells, while preserving cell viability and eliminating the need for expensive sequencing of a large number of clones. A protocol was designed in which the luminescent peptide tag, HiBiT, is appended to the extracellular portion of an inert surface membrane protein (CD46), using synthetic CRISPR reagents and a widely distributed human induced pluripotent stem cell (iPSC) line. We find that this approach substantially reduces labour-intensive screening of CRISPR-targeted iPSCs and minimises the number of subcloning steps. Successfully edited iPSCs could be identified within a week of targeting, based only on extracellular luminescence detection in live cells. The total screening time in each round was less than 30 minutes and no sequencing was required. This method can be developed further to serve as a highly sensitive co-selection strategy in CRISPR knock-in experiments, particularly in the context of challenging cell lines.

Luminescent peptide tagging enables efficient screening for CRISPR-mediated knock-in in human induced pluripotent stem cells

Human pluripotent stem cells are increasingly used for CRISPR-mediated gene targeting in efforts to generate models of human diseases. This is a challenging task because of the high sensitivity of these cells to suboptimal conditions, including CRISPR-associated DNA damage and subsequent rounds of single-cell cloning. We sought to develop a sensitive method that enables rapid screening of CRISPR targeted cells, while preserving cell viability and eliminating the need for expensive sequencing of a large number of clones. A protocol was designed in which the luminescent peptide tag, HiBiT, is appended to the extracellular portion of an inert surface membrane protein (CD46), using synthetic CRISPR reagents and a widely distributed human induced pluripotent stem cell (iPSC) line. We find that this approach substantially reduces labour-intensive screening of CRISPR-targeted iPSCs and minimises the number of subcloning steps. Successfully edited iPSCs could be identified within a week of targeting, based only on extracellular luminescence detection in live cells. The total screening time in each round was less than 30 minutes and no sequencing was required. This method can be developed further to serve as a highly sensitive co-selection strategy in CRISPR knock-in experiments, particularly in the context of challenging cell lines.

Luminescent peptide tagging enables efficient screening for CRISPR-mediated knock-in in human induced pluripotent stem cells

Human pluripotent stem cells are increasingly used for CRISPR-mediated gene targeting in efforts to generate models of human diseases. This is a challenging task because of the high sensitivity of these cells to suboptimal conditions, including CRISPR-associated DNA damage and subsequent rounds of single-cell cloning. We sought to develop a sensitive method that enables rapid screening of CRISPR targeted cells, while preserving cell viability and eliminating the need for expensive sequencing of a large number of clones. A protocol was designed in which the luminescent peptide tag, HiBiT, is appended to the extracellular portion of an inert surface membrane protein (CD46), using synthetic CRISPR reagents and a widely distributed human induced pluripotent stem cell (iPSC) line. We find that this approach substantially reduces labour-intensive screening of CRISPR-targeted iPSCs and minimises the number of subcloning steps. Successfully edited iPSCs could be identified within a week of targeting, based only on extracellular luminescence detection in live cells. The total screening time in each round was less than 30 minutes and no sequencing was required. This method can be developed further to serve as a highly sensitive co-selection strategy in CRISPR knock-in experiments, particularly in the context of challenging cell lines.

Primed to Sleep: The Dynamics of Synaptic Plasticity Across Brain States

It is commonly accepted that brain plasticity occurs in wakefulness and sleep. However, how these different brain states work in concert to create long-lasting changes in brain circuitry is unclear. Considering that wakefulness and sleep are profoundly different brain states on multiple levels (e.g., cellular, molecular and network activation), it is unlikely that they operate exactly the same way. Rather it is probable that they engage different, but coordinated, mechanisms. In this article we discuss how plasticity may be divided across the sleep-wake cycle, and how synaptic changes in each brain state are linked. Our working model proposes that waking experience triggers short-lived synaptic events that are necessary for transient plastic changes and mark (i.e., 'prime') circuits and synapses for further processing in sleep. During sleep, synaptic protein synthesis at primed synapses leads to structural changes necessary for long-term information storage.

Chromatic Bacteria - A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria

Differential fluorescent labeling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behavior in complex environments. We designed a variety of plasmids, each bearing one of eight unique, constitutively expressed fluorescent protein genes in conjunction with one of four different antibiotic resistance combinations. The fluorophores mTagBFP2, mTurquoise2, sGFP2, mClover3, sYFP2, mOrange2, mScarlet-I, and mCardinal, encoding for blue, cyan, green, green-yellow, yellow, orange, red, and far-red fluorescent proteins, respectively, were combined with selectable markers conferring tetracycline, gentamicin, kanamycin, and/or chloramphenicol resistance. These constructs were cloned into three different plasmid backbones: a broad host-range plasmid, a Tn5 transposon delivery plasmid, and a Tn7 transposon delivery plasmid. The utility of the plasmids and transposons was tested in bacteria from the phyla Actinobacteria, Proteobacteria, and Bacteroidetes. We were able to tag representatives from the phylum Proteobacteria at least via our Tn5 transposon delivery system. The present study enables labeling bacteria with a set of plasmids available to the community. One potential application of fluorescently-tagged bacterial species is the study of bacteria-bacteria, bacteria-host, and bacteria-environment interactions.

CTLA4 tagging polymorphisms and risk of colorectal cancer: a case-control study involving 2,306 subjects

Background

CTLA4 is a candidate gene which has been implicated in the development of colorectal cancer (CRC).

Patients and Methods

To determine the important role of CTLA-4 polymorphisms on risk of CRC, we genotyped four CTLA-4 tagging polymorphisms and calculated crude/adjusted ORs with their 95% CIs. We recruited 1,003 sporadic CRC cases and 1,303 controls.

Results

The findings suggested that CTLA-4 rs231775 G>A polymorphism increased the risk of CRC (homozygote model: adjusted OR=1.40, 95% CI=1.05-1.87, P=0.022; dominant model: adjusted OR=1.19, 95% CI=1.00-1.41, P=0.047; and recessive model: adjusted OR=1.38, 95% CI=1.05-1.82, P=0.021). In a stratified analysis by site of tumor, this association was also found in colon cancer. We also found that CTLA-4 rs231775 GA/AA genotypes might be associated with an increased risk of CRC in Zhenjiang cohort. In addition, we found the CTLA-4 rs16840252 C>T polymorphism was associated with the risk of colon cancer. Haplotype comparison analysis showed that CTLA-4 G_rs3087243C_rs16840252C_rs733618 A_rs231775, G_rs3087243C_rs16840252T_rs733618A_rs231775, and other haplotypes increased the risk of CRC (P<0.001, <0.001, and 0.002, respectively).

Conclusion

This study evidences an association of CTLA-4 tagging polymorphisms and haplotypes with CRC risk. Additional well-designed studies with large sample sizes are required to confirm our findings.

The Tagging Procedure of Visible Implant Elastomers Influences Zebrafish Individual and Social Behavior

One commonly used method to preserve individual identity in the study of social behavior of zebrafish is through silicone-based visible implant elastomers (VIEs), which represent a safe and durable tagging procedure. While the effects of VIE tagging on welfare and general health have been addressed in detail, whether this procedure influences social behavior remains unclear. In this study, we compared individual and group behaviors exhibited by shoals composed of three individuals: two nontagged and one (focal subject) that was either nontagged (control condition) or sham-, purple-, blue-, or yellow tagged. Traditional behavioral parameters of activity, shoaling, and schooling (speed, polarization, and interindividual distances), along with an information-theoretic measure of social interaction (transfer entropy), were used to study the effect of tagging. Our findings indicate that tagging procedure per se significantly increased individual speed of the tagged subjects and of the group. The tagging procedure also altered the level of interaction between individuals, measured by transfer entropy. Conversely, tagging procedure did not influence shoaling and schooling tendencies. These findings suggest that VIE tagging may elicit some level of stress, which may affect some behavioral responses more than others. We recommend use of alternative methods such as multitracking systems when possible.

At-vessel mortality of skates (Rajidae) taken in coastal fisheries and evidence of longer-term survival

Data on the vigour and at-vessel mortality (AVM) of 6798 skates (comprising Raja clavata n = 6295; R. brachyura n = 208; R. undulata n = 185, R. montagui n = 98 and R. microocellata n = 12) captured by commercial fishing vessels in the inshore waters of the southern North Sea and English Channel were recorded. AVM in longline fisheries averaged 0·44% across five vessels (0-1·47%), although skates were usually unhooked manually and did not usually pass through a bait-stripper. AVM in otter trawls averaged 0·76% (0-2·35%), from four vessels fishing with tow durations of <1·5 h (southern North Sea) or 1-4 h (English Channel). No AVM was noted for skates taken as a by-catch in drift trammel nets (soak times <4 h). Anchored tangle nets resulted in an overall AVM of 2·0-2·7%, but increased from 1·47% (13-28 h soak time) to 6·16% (42-53 h soak time). There were significant differences in the vigour of skates between gears, with R. clavata caught by longline and tangle nets in better condition than those captured by otter trawl or drift trammel net. Similarly, R. undulata caught by tangle net were in better condition than those caught by otter trawl. The vigour of R. undulata was also found to be higher than other skate species for both trawl and tangle net. In total, 5283 skates were tagged with Petersen discs and released, with recapture rates for the various combinations of vessel and gear ranging up to 24·8% for R. clavata. Whilst confirming a degree of post-release survival, quantitative estimates of post-release mortality for skates remain unknown.

Combining abundance and performance data reveals how temperature regulates coastal occurrences and activity of a roaming apex predator

The redistribution of species has emerged as one of the most pervasive impacts of anthropogenic climate warming, and presents many societal challenges. Understanding how temperature regulates species distributions is particularly important for mobile marine fauna such as sharks given their seemingly rapid responses to warming, and the socio-political implications of human encounters with some dangerous species. The predictability of species distributions can potentially be improved by accounting for temperature's influence on performance, an elusive relationship for most large animals. We combined multi-decadal catch data and bio-logging to show that coastal abundance and swimming performance of tiger sharks Galeocerdo cuvier are both highest at ~22°C, suggesting thermal constraints on performance may regulate this species' distribution. Tiger sharks are responsible for a large proportion of shark bites on humans, and a focus of controversial control measures in several countries. The combination of distribution and performance data moves towards a mechanistic understanding of tiger shark's thermal niche, and delivers a simple yet powerful indicator for predicting the location and timing of their occurrences throughout coastlines. For example, tiger sharks are mostly caught at Australia's popular New South Wales beaches (i.e. near Sydney) in the warmest months, but our data suggest similar abundances will occur in winter and summer if annual sea surface temperatures increase by a further 1-2°C.

One-Year Follow-up Study Detects Myocardial Changes with Cardiovascular Magnetic Resonance Tagging in Active Rheumatoid Arthritis

RATIONALE AND OBJECTIVES

To evaluate the effects of 1 year of medical treatment on myocardial function in active rheumatoid arthritis (RA).

MATERIALS AND METHODS

Thirty-nine female patients with RA without any known cardiovascular disease underwent a cardiovascular magnetic resonance (CMR) examination before and after 1 year of antirheumatic treatment. The population comprised untreated active early RA (ERA) and chronic RA patients, who were grouped accordingly. The CMR protocol included volumetric determinations, late gadolinium enhancement imaging, myocardial tagging, and native T1 mapping. DAS28-CRP disease activity scores were calculated before and after the treatment.

RESULTS

Results are reported as median (quartile 1-quartile 3). Time to peak diastolic filling rate improved in ERA (495 [443-561] ms vs 441 [340-518] ms, P = .018). Peak diastolic mean mid short-axis circumferential strain rate of all six segments was improved (82 [74-91] %/s vs 91 [77-100] %/s, P = .05), particularly in the anterior segment (82 [63-98] %/s vs 86 [77-109] %/s, P = .013). DAS28-CRP decreased in ERA (3.8 [3.2-4.1] vs 1.6 [1.4-2.2], P < .001). In chronic RA, no statistically significant improvement was detected.

CONCLUSIONS

Early treatment of active RA is important, as myocardial function detected with CMR tagging improved in ERA in parallel with decreasing inflammatory activity.

GRAPHITE: A Graphical Environment for Scalable in situ Video Tracking of Moving Insects

1. Methods for measuring animal movement are critical for understanding numerous ecological and evolutionary processes. However, few methods are available for small organisms, and even fewer methods offer consistent individual-level resolution while remaining affordable, scalable and operable in the field. 2. We describe a low-cost animal movement tracking method with a user-friendly graphical interface, called GRAPHITE. Our automated software can quantify motions of insects by offline video analysis of inexpensive and lightweight human-readable tags attached to individual insects. The integrated graphical editor provides a full-featured environment for users to review the generated tracking data and make individual- or group-level edits. 3. GRAPHITE is a novel video analysis and graphical editing software (MATLAB v.9.0.0+) that identifies tags in image frames with a minimal false negative rate, links sequences of corresponding tags into "tracks" for each individual insect, infers the tag identifier, and provides a user-friendly graphical environment for editing tracking data. Users can either batch process raw video data using the full analysis pipeline or execute GRAPHITE modules independently for a tailored analysis. 4. We demonstrate the efficacy of the developed software with a specific application to the movement of honey bees at the entrance of hives. However, this system can be easily modified to track individually marked insects of 3 mm and larger. A notable advantage of this method is its ability to provide easy access to individual-level tracking data using human-readable tags.

Using visible implant elastomer to study ammocoete populations with Cormack-Jolly-Seber models

This study examined the efficacy of marking wild populations of lampreys with visible implant elastomer (VIE) for 6-18 months to examine ammocoete movements using Cormack-Jolly-Seber (CJS) open-population models. These methods were tested on two lamprey populations in different river systems. American brook lamprey Lethenteron appendix at Dyke Creek apparent survival (φ) was high in the summer and winter (c. 0·7), but declined after flow events in the spring and autumn. Sea lamprey Petromyzon marinus at Oquaga Creek φ in the top-ranked models varied with stream location and time. Estimates of φ were similar to Dyke Creek during the summer (c. 0·7), but declined after flow events and remained low (c. 0·1) in winter. Open-population models support current understanding of ammocoete movement, i.e. dispersal is driven by high-flow events at certain times of the year. The present study provides a framework to study ammocoetes with VIE.

Infrared ion spectroscopy inside a mass-selective cryogenic 2D linear ion trap

We demonstrate operation of the first cryogenic 2D linear ion trap (LIT) with mass-selective capabilities. This trap presents a number of advantages for infrared ion "action" spectroscopy studies, particularly those employing the "tagging/messenger" spectroscopy approach. The high trapping efficiencies, trapping capacities, and low detection limits make 2D LITs a highly suitable choice for low-concentration analytes from scarce biological samples. In our trap, ions can be cooled down to cryogenic temperatures to achieve higher-resolution infrared spectra, and individual ions can be mass selected prior to irradiation for a background-free photodissociation scheme. Conveniently, multiple tagged analyte ions can be mass isolated and efficiently irradiated in the same experiment, allowing their infrared spectra to be recorded in parallel. This multiplexed approach is critical in terms of increasing the duty cycle of infrared ion spectroscopy, which is currently a key weakness of the technique. The compact design of this instrument, coupled with powerful mass selection capabilities, set the stage for making cryogenic infrared ion spectroscopy viable as a bioanalytical tool in small molecule identification.

Diving behaviour of Cuvier's beaked whales exposed to two types of military sonar

Cuvier's beaked whales (Ziphius cavirostris) have stranded in association with mid-frequency active sonar (MFAS) use, and though the causative mechanism linking these events remains unclear, it is believed to be behaviourally mediated. To determine whether MFAS use was associated with behavioural changes in this species, satellite tags were used to record the diving and movements of 16 Cuvier's beaked whales for up to 88 days in a region of frequent MFAS training off the coast of Southern California. Tag data were combined with summarized records of concurrent bouts of high-power, surface-ship and mid-power, helicopter-deployed MFAS use, along with other potential covariates, in generalized additive mixed-effects models. Deep dives, shallow dives and surface intervals tended to become longer during MFAS use, with some variation associated with the total amount of overlapping MFAS during the behaviour. These changes in dives and surface intervals contributed to a longer interval between deep dives, a proxy for foraging disruption in this species. Most responses intensified with proximity and were more pronounced during mid-power than high-power MFAS use at comparable distances within approximately 50 km, despite the significantly lower source level of mid-power MFAS. However, distance-mediated responses to high-power MFAS, and increased deep dive intervals during mid-power MFAS, were evident up to approximately 100 km away.

Diving behaviour of Cuvier's beaked whales exposed to two types of military sonar

Cuvier's beaked whales (Ziphius cavirostris) have stranded in association with mid-frequency active sonar (MFAS) use, and though the causative mechanism linking these events remains unclear, it is believed to be behaviourally mediated. To determine whether MFAS use was associated with behavioural changes in this species, satellite tags were used to record the diving and movements of 16 Cuvier's beaked whales for up to 88 days in a region of frequent MFAS training off the coast of Southern California. Tag data were combined with summarized records of concurrent bouts of high-power, surface-ship and mid-power, helicopter-deployed MFAS use, along with other potential covariates, in generalized additive mixed-effects models. Deep dives, shallow dives and surface intervals tended to become longer during MFAS use, with some variation associated with the total amount of overlapping MFAS during the behaviour. These changes in dives and surface intervals contributed to a longer interval between deep dives, a proxy for foraging disruption in this species. Most responses intensified with proximity and were more pronounced during mid-power than high-power MFAS use at comparable distances within approximately 50 km, despite the significantly lower source level of mid-power MFAS. However, distance-mediated responses to high-power MFAS, and increased deep dive intervals during mid-power MFAS, were evident up to approximately 100 km away.

Left ventricular function and regional strain with subtly-tagged steady-state free precession feature tracking

PURPOSE

To provide regional strain and ventricular volume from a single acquisition, using subtly tagged steady-state free precession (SubTag SSFP) feature tracking.

MATERIALS AND METHODS

The effects on regional strain of tag strength in gradient recalled echo (GRE) tagging, flip angle in untagged balanced SSFP, and both in SubTag SSFP were examined in the mid left ventricle of 15 healthy volunteers at 3T. Optimal parameters were determined from varying both tag strength and SSFP flip angle using full tag saturation GRE as the reference standard. SubTag SSFP was acquired in 15 additional healthy volunteers for whole-heart volume and strain assessment using the optimized parameters. Values measured by two image analysts were compared to clinical reference standards from untagged SSFP (volumes) and GRE tagging (strains).

RESULTS

Regional strain accuracy was maintained with decreasing total tagging flip angle (β); less than 3% differences for β ≥ 26°. For untagged SSFP flip angle (α), whole-wall strain differences became statistically significant when α < 40°. A SubTag SSFP acquisition with α = 40° and β = 46° showed the best combination of tagging strength, blood-myocardial contrast, and tag persistence at end-systole for regional strain estimation. SubTag SSFP also showed excellent agreement with untagged SSFP for volumetrics (percent difference: end-diastolic volume = 0.6%, end-systolic volume = 0.4%, stroke volume = 1.2%, ejection fraction = 0.6%, mass = 1.1%).

CONCLUSION

Feature tracking for regional myocardial strain assessment is dependent on image features, mainly the tag strength, persistence, and image contrast. SubTag SSFP balances these criteria to provide accurate regional strain and volumetric assessment in a single acquisition.

LEVEL OF EVIDENCE

1 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2018;47:787-797.