A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.

The genomic basis of the plant island syndrome in Darwin's giant daisies

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies.

Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.

What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

Little is known about the evolution of cold tolerance in polar plant species and how they differ from temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. We conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22°C, and after 3, 6, and 24 at 2°C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. Most differentially expressed genes were species‐specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, ~200 were shared among the three Arctic species and A. thaliana, while ~100 were exclusively shared among the three Arctic species. Our results show that cold response differs markedly between Arctic Brassicaceae species, but probably builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation.

A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY ® SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogotá, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones.

Importance

The continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.

RT-PCR and Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry Diagnostic Target Performance Reflects Circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variant Diversity in New York City

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The Agena MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2-positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3'-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3'-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of Agena MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.

Correlation between Identification of β-Lactamase Resistance Genes and Antimicrobial Susceptibility Profiles in Gram-Negative Bacteria: a Laboratory Data Analysis

We reported the frequency of resistance gene detection in Gram-negative blood culture isolates and correlated these findings with corresponding antibiograms. Data were obtained from 1045 isolates tested on the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panels at the Mount Sinai Hospital Clinical Microbiology Laboratory in New York from March 2019 to February 2021. Susceptibilities were performed using Vitek 2 (bioMérieux Clinical Diagnostics) or Microscan (Beckman Coulter Inc.). blaCTX-M was detected in 26.4% Klebsiella pneumoniae, 23.5% Escherichia coli, and 16.4% Proteus mirabilis isolates. As would be expected, both blaCTX-M and blaCTX-M negative isolates were likely to be susceptible to newer agents while blaCTX-M positive isolates were more likely to be resistant to earlier generations of beta-lactam antibiotics. 3/204 blaCTX-M-positive isolates were found to be ceftriaxone-susceptible. Conversely, 2.8% ceftriaxone nonsusceptible strains were negative for all β-lactamase genes on the ePlex BCID-GN panel, including blaCTX-M. The prevalence of CTX-M-producing Enterobacterales remains high in the United States. A small number of blaCTX-M-positive isolates were susceptible to ceftriaxone, and a small number of ceftriaxone nonsusceptible isolates were negative for blaCTX-M. Further studies are needed to determine the optimal management when an isolate is phenotypically susceptible to ceftriaxone, but blaCTX-M is detected. IMPORTANCE There is limited literature on corresponding results obtained from rapid molecular diagnostics with the antibiotic susceptibility profile. We reported a correlation between the results obtained from ePlex and the antibiograms against a large collection of Gram-negative bacteria. We reported that there can be a discrepancy in a small number of cases, but the clinical significance of that is unknown.

Utility of liquid biopsy in diagnosing isolated cerebral phaeohyphomycosis: illustrative case

BACKGROUND

Cladophialophora bantiana is a dematiaceous, saprophytic fungus and a rare but reported cause of intracranial abscesses due to its strong neurotropism. Although it predominantly affects immunocompetent individuals with environmental exposure, more recently, its significance as a highly lethal opportunistic infection in transplant recipients has been recognized. Successful treatment requires timely but often challenging diagnosis, followed by complete surgical excision. Next-generation sequencing of microbial cell-free DNA (cfDNA) from plasma is a novel diagnostic method with the potential to identify invasive fungal infections more rapidly and less invasively than conventional microbiological testing, including brain biopsy.

OBSERVATIONS

The authors described the case of a recipient of a liver transplant who presented with seizures and was found to have innumerable ring-enhancing intracranial lesions. The Karius Test, a commercially available method of next-generation sequencing of cfDNA, was used to determine the causative organism. Samples from the patient’s plasma identified C. bantiana 6 days before culture results of the surgical specimen, allowing optimization of the empirical antifungal regimen, which led to a reduction in the size of the abscesses.

LESSONS

The authors’ findings suggest that microbial cfDNA sequencing may be particularly impactful in improving the management of brain abscesses in which the differential diagnosis is wide because of immunosuppression.

Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach

The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

Catheter-related bloodstream infection due to biofilm-producing Capnocytophaga sputigena

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Capnocytophaga sputigena is a rare pathogen with diverse clinical presentations.

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We report a case of catheter-related C. sputigena bloodstream infection.

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C. sputigena clinical isolates can form biofilms in vitro.

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Biofilm development by Capnocytophaga species may potentiate disease pathogenesis.

Capnocytophaga sputigena is a facultatively-anaerobic bacterium that is part of the human oropharyngeal microflora. Although C. sputigena bacteremia is uncommon, systemic infections have been reported in both immunocompetent and immunocompromised patients. We report a case of catheter-related bloodstream infection by C. sputigena and highlight its enhanced biofilm-forming capacity in vitro.

Lemierre's syndrome associated with hypervirulent Klebsiella pneumoniae: A case report and genomic characterization of the isolate

We describe a case of Lemierre’s syndrome (LS) caused by a hypervirulent strain of Klebsiella pneumoniae in a 63-year-old female with hypertension, hyperlipidemia, and diabetes mellitus, who presented with right neck pain and fevers. Computerized tomography of the neck and chest revealed an occluded right internal jugular vein secondary to thrombosis and septic emboli in lungs. Blood cultures grew K. pneumoniae. The patient was treated with ampicillin-sulbactam and then transitioned to amoxicillin-clavulanate to complete a 6-week course of antibiotics, and a 3-month course of rivaroxaban. String test of the K. pneumoniae isolate was positive at 2 cm. Whole genome sequencing identified several genes associated with the hypervirulent strain, notably the genes encoding for aerobactin (iucA and iucB) and salmochelin (iroB) iron acquisition systems. LS can rarely be caused by K. pneumoniae. Clinicians should monitor for known complications, such as septic emboli in patients with LS.

RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

Asymmetries of reproductive isolation are reflected in directionalities of hybridization: integrative evidence on the complexity of species boundaries

The complex nature of species boundaries has been a central topic in evolutionary biology ever since Darwin. Despite numerous separate studies on reproductive isolation and hybridization, their relationship remains underinvestigated. Are the strengths and asymmetries of reproductive barriers reflected in the extent and directionalities of interspecific genetic exchange? We combined field, experimental, and molecular data to quantify strengths and asymmetries of sympatric reproductive barriers and hybridization between florally heteromorphic primroses. We also assessed whether generalist pollinators discriminate between different floral cues and contribute to reproductive isolation, a long-debated topic. Sympatric reproductive isolation is high but incomplete, and most phenotypic intermediates are genetic F₁ hybrids, whereas backcrosses are rare, revealing low interspecific gene flow. Species integrity rests on multiple barriers, but ethological isolation is among the strongest, demonstrating that even generalist pollinators crucially contribute to the maintenance of species boundaries. Furthermore, reproductive barriers are weaker for Primula veris and short-styled plants, results corroborated by molecular data. Thus, in florally heteromorphic systems, both species- and morph-dependent asymmetries affect permeability of species boundaries. Our study illustrates how the interactions between complex floral syndromes and pollinators shape species boundaries in unique, previously undescribed ways.

421. If at first you do not succeed…. Repeat SARS-COV2 PCR testing

Background

Nucleic Acid Amplification Tests (NAATs) of nasopharyngeal specimens (NPS) have become standard for diagnosis of SARS-COV2. IDSA guidelines suggest repeat testing after 24–48 h when initially negative and clinical suspicion persists. We characterized patients from whom initial NPS were NAAT-negative, but repeats were NAAT-positive, in order to identify which patients might benefit from repeat NAAT for SARS-CoV-2, and the appropriate interval.

Methods

We conducted an IRB-approved retrospective review of laboratory and electronic medical record data for all patients evaluated for SARS-CoV-2 infection at the Mount Sinai Health System, whose initial NAATs were done between March 16 – March 30, 2020, and who were retested within one month. NAATs were performed on NPS in viral transport medium using the Roche Diagnostics cobas® 6800 SARS-CoV-2 Test. Baseline patient characteristics, clinical and radiographic findings were identified.

Results

Of 235 patients eligible for inclusion, 172 (70.5%) were initially NAAT-negative, and 118 (68.6%) remained NAAT-negative over 1 month follow up. 54 (31.4%) converted to NAAT-positive over the next 1-month. Of patients who became NAAT-positive, 31 (57.4%) were inpatients who converted results within a single admission; the average interval was 6d 7h between the NAAT-negative and NAAT-positive results, and the minimum interval was 10.5 h. Symptoms examined for correlation for conversion to NAAT-positive were: fever, cough, shortness of breath, and combined nausea/vomiting/diarrhea. Duration of symptoms reported at triage did not appear to affect time to conversion to NAAT-positive. No individual symptom was more likely to be associated with conversion to NAAT- positive. However, time to conversion to NAAT-positive was shorter for patients with multiple symptoms. In general, chest radiography (CXR) findings correlated with NAAT results; interval to NAAT-positive was shorter for patients with worsening CXR findings.

Conclusion

Our data supports repeat testing in patients with multiple clinical symptoms suggestive of SARS CoV-2 infection and negative initial NP test results. Further studies are needed to determine the true clinical sensitivity and specificity of SARS-CoV-2 NAAT assays.

Disclosures

All Authors: No reported disclosures

Comparison of SARS-CoV-2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS-CoV-2 test and a laboratory-developed real-time RT-PCR test

The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed test (LDT) real‐time reverse transcription‐polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS‐CoV‐2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS‐CoV‐2 as part of routine clinical care using the cobas SARS‐CoV‐2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive (“detected” or “presumptive positive”), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS‐CoV‐2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875‐0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms.

In this study, we compared the detection of SARS‐CoV‐2 in clinical samples from patients being evaluated for CoVID‐19 infection by two different RT‐PCR assays, the cobas® 6800 SARS‐CoV‐2 test from Roche Molecular Systems and a laboratory‐developed test (LDT) using the Centers for Disease Control and Prevention 2019‐nCoV primers and probes. Overall there was excellent agreement between the two tests methods, although our results suggest that the cobas® SARSCoV‐2 test may have a lower limit of detection than the LDT.

Influence of Glenosphere and baseplate parameters on Glenoid bone strains in reverse shoulder Arthroplasty

Background

Little is known about the strains at the glenoid near the bone-implant interface in reverse shoulder arthroplasty. The purpose of the current study was to evaluate the strains on the glenoid bone under a compressive load after implantation of three different sizes of metal-backed baseplates in either inferior or superior position in combination with three different sizes of glenospheres and three different glenosphere designs.

Methods

Three sizes of baseplates (small, medium, large) were implanted in thirty-six paired human cadaveric scapulae either inferior, flush with the glenoid neck, or with a 5 mm superior offset. Glenospheres were available in three sizes (36 mm, 39 mm, 42 mm) and designs (standard, 4 mm lateralized, 2.5 mm inferiorized). Specimens were mounted in a servo-hydraulic testing apparatus at a 60° angle between the glenoid and actuator holding the humeral component. Four strain-gauge rosettes were placed around the glenoid rim to measure strains transferred to the scapular bone under a compressive load (750 N) relative to the various baseplate-glenosphere combinations. Following repeated compression, a load-to-failure test was performed.

Results

Mean overall registered strains were 161με (range: − 1165 to 2347) at the inferior sensor, −2με (range: − 213 to 90) at the superior sensor, −95με (range: − 381 to 254) at the anterior sensor, and 13με (range: − 298 to 128) at the posterior sensor. Measured bone strains did not show any significant differences across tested baseplate and glenosphere design, size, or positioning combinations (p > 0.05 for all sensors). Furthermore, linear regression analysis did not identify any of the evaluated parameters as an independent influential factor for strains (p > 0.05 for all sensors). Mean load-at-failure was significantly higher in the group of inferior (3347.0 N ± 704.4 N) compared to superior (2763.8 N ± 927.8 N) positioned baseplates (p = 0.046).

Conclusion

Different baseplate positions, baseplate sizes, glenosphere sizes, and glenosphere design or various combinations of these parameters did not significantly influence the measured bone strains at the glenoid near the bone-implant interface in a contemporary reverse shoulder arthroplasty system.

Level of evidence

Basic Science Study, Biomechanical Study.

2169. An Algorithm-Based Approach Reduces Overuse of Meningitis/Encephalitis Multiplex PCR Panel

Background

Syndromic molecular panels enable rapid diagnosis and optimized management of infections with significant morbidity and mortality, but may be overused without clear guidelines. A recent report indicated there was little clinical suspicion of infection in up to 1/3 of cases for which a FILMARRAY^® Meningitis/Encephalitis Panel (ME Panel, bioMérieux) was ordered. We recently implemented the ME Panel in our multicenter health system. We assessed ME Panel use for the 6-month period following test implementation.

Methods

A testing algorithm was developed, vetted with our system-wide Infectious Diseases (ID) and Neuro-ID Services, and used as the basis for the education of the Emergency Medicine, Internal Medicine, Hospitalist, Pediatric, and Critical Care Medicine Services. Algorithm elements were embedded in the electronic medical record (EMR). Lab records and EMRs were reviewed for all patients tested by ME Panel or cerebrospinal (CSF) culture. Lab results, baseline demographic and underlying medical history, and results of singleplex viral PCR CSF tests and the multiplex NY State Encephalitis PCR Panel (NYS Panel, Wadsworth Laboratory, Albany, NY) were recorded. ME Panel results were compared with other findings.

Results

115 ME Panels were performed, with 5 (4%) positives [1 N.meningitidis, 1 H.influenzae, 1 cytomegalovirus (CMV), 1 Herpes simplex virus type 1 (HSV1), and 1 varicella zoster virus (VZV)]. Other findings were consistent with true infection for the N. meningitis, HSV and VZV; the CMV was likely reactivation. Significance of the H. influenzae was unclear. There were 830 CSF cultures, with 38 (4%) positive; 5 of the 38 were ME Panel targets. 29 NYS Panels were sent [1 positive each for Human Herpesvirus 6 (HHV6) and Epstein Barr Virus (EBV)]. Finally, 7 singleplex PCRs were positive [5 HSV, 1 CMV and 1 HHV6], including one negative by ME Panel.

Conclusion

We did not find ME Panel overuse; rather, we found several cases for which the ME Panel could have given a more rapid diagnosis. We did identify areas for improvement in test ordering, such as minimizing duplicate testing (e.g., singleplex PCR) A multi-disciplinary approach engaging stakeholders in the lab, ID and Neuro-ID can assist appropriate test utilization and diagnostic stewardship.

Disclosures

All authors: No reported disclosures.

Contemporaneous radiations of fungi and plants linked to symbiosis

Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.

Plants and fungi interact widely and in diverse ways, from mutualism to parasitism and decomposition. Here, Lutzoni et al. analyse the timing of plant and fungal evolutionary radiations and identify four major periods in which plant-fungal interactions likely drove lineage diversification.

Logistical and safety implications of temperature-based acceptance of returned red blood cell units

BACKGROUND

AABB requires that red blood cells (RBCs) are maintained at 1 to 10°C during transport. Historically, blood banks used the 30-minute rule for returned RBCs transported outside of validated containers. The implications of this policy have not been previously reported in a real-life hospital setting.

STUDY DESIGN AND METHODS

A 2-year, retrospective review of RBC units returned outside of qualified containers was conducted. During the first year, the 30-minute rule was used to accept RBCs back into inventory. Sequentially, the following year, a temperature-based approach was implemented using a thermometer with an accuracy of ±1°C. Time out of the blood bank, temperature upon return, wastage, and transfusion reactions associated with the reissued RBCs were analyzed.

RESULTS

In our practice, the 30-minute rule would have accepted 15.2% of RBC units outside of the allowed temperature. Compared to the 30-minute rule, temperature-based acceptance was associated with a 13% increase in wastage (p < 0.001). During the 30-minute rule period, transfusion of returned and subsequently reissued RBCs was associated with a nonsignificant trend toward a higher transfusion reaction rate compared to the overall RBC transfusion reaction rate (1.4% vs. 0.6%, p = 0.084). During the temperature period, transfusion of returned and subsequently reissued RBCs had the same transfusion reaction rate compared to the overall RBC transfusion reaction rate (0.5% vs. 0.5%, p = 1.0).

CONCLUSION

Temperature-based acceptance of returned RBCs is associated with significantly higher wastage compared to the 30-minute rule. A temperature-based acceptance practice mitigates the risk of accepting RBCs with unacceptable temperatures returned within 30 minutes of issue.

Correction: Hybrid Origins of Carex rostrata var. borealis and C. stenolepis, Two Problematic Taxa in Carex Section Vesicariae (Cyperaceae)

[This corrects the article DOI: 10.1371/journal.pone.0165430.].

Hybrid Origins of Carex rostrata var. borealis and C. stenolepis, Two Problematic Taxa in Carex Section Vesicariae (Cyperaceae)

Hybridization is frequent in the large and ecologically significant genus Carex (Cyperaceae). In four important sections of the northern regions (Ceratocystis, Glareosae, Phacocystis and Vesicariae), the frequent occurrence of hybrids often renders the identification of "pure" species and hybrids difficult. In this study we address the origins and taxonomic rank of two taxa of section Vesicariae: Carex rostrata var. borealis and C. stenolepis. The origin and taxonomic status of C. stenolepis has been the subject of substantial debate over the years, whereas C. rostrata var. borealis has received very little attention in the years since its first description in the 19th century. By performing an extensive sampling of relevant taxa from a broad distribution range, and analyzing data from fifteen microsatellite loci developed specifically for our study together with pollen stainability measures, we resolve the hybrid origins of C. rostrata var. borealis and C. stenolepis and provide new insights into this taxonomically challenging group of sedges. Our results are in accordance with previous findings suggesting that C. stenolepis is a hybrid between C. vesicaria and C. saxatilis. They are also in accordance with a previous proposition that C. rostrata var. borealis is a hybrid between C. rostrata and C. rotundata, and furthermore suggest that both hybrids are the result of multiple, recent (i.e., postglacial) hybridization events. We found little evidence for successful sexual reproduction within C. rostrata var. borealis and C. stenolepis, but conclude that the common and recurrent, largely predictable occurrence of these taxa justifies accepting both hybrids as hybrid species with binomial names. There are, however, complications as to types and priority names, and we therefore choose to address these problems in a separate paper.

Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses

Heterostyly is a wide-spread floral adaptation to promote outbreeding, yet its genetic basis and evolutionary origin remain poorly understood. In Primula (primroses), heterostyly is controlled by the S-locus supergene that determines the reciprocal arrangement of reproductive organs and incompatibility between the two morphs. However, the identities of the component genes remain unknown. Here, we identify the Primula CYP734A50 gene, encoding a putative brassinosteroid-degrading enzyme, as the G locus that determines the style-length dimorphism. CYP734A50 is only present on the short-styled S-morph haplotype, it is specifically expressed in S-morph styles, and its loss or inactivation leads to long styles. The gene arose by a duplication specific to the Primulaceae lineage and shows an accelerated rate of molecular evolution. Thus, our results provide a mechanistic explanation for the Primula style-length dimorphism and begin to shed light on the evolution of the S-locus as a prime model for a complex plant supergene.

DOI:http://dx.doi.org/10.7554/eLife.17956.001

Flowers are highly specialized structures that many plants use to reproduce. Male organs called stamens on the flowers make pollen that can be transferred – usually by insect carriers or the wind – to a female structure called the stigma on another plant. However, since many flowers contain both male and female organs, it is also possible for the pollen to land on the stigma of the same flower, leading to a process called “self-fertilization”.

Many plants have developed mechanisms that prevent self-fertilization. For example, primroses produce two different types of flowers that arrange their stamens and stigmas differently. The stigma sits on the top of a stalk known as the style. Some primroses produce flowers with short stamens and a long style, resulting in the stigma being located high up in the flower (“pin” flowers), while others produce flowers with a short style and long stamens (“thrum” flowers). Primrose pollen is carried by insects and the different lengths of the styles and stamens make it more likely that pollen from a pin flower will land on the stigma of a thrum flower instead of a pin flower (and vice versa).

Although primrose flowers have fascinated botanists for centuries, the genes responsible for making the two types of flower had not been identified. Genetic studies indicated that different genes control the length of the stamens and style. However, these genes appear to be very close to each other on primrose DNA, which made it difficult to study them individually.

Huu et al. identified a gene called CYP734A50 that is responsible for the difference in style length in the flowers of a primrose called Primula veris. The gene is only present in the plants that have thrum flowers across a wide range of primrose species and genetic mutations that inactivate the gene in these plants result in flowers with longer styles. CYP734A50 encodes an enzyme that breaks down plant hormones called brassinosteroids, which normally promote growth. Treating thrum flowers with brassinosteroids increased the length of the styles. Future challenges are to identify the other genes that are responsible for producing pin and thrum flowers and to understand how this group of genes evolved.

DOI:http://dx.doi.org/10.7554/eLife.17956.002

RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae)

Many arctic-alpine plants display a highly disjunct distribution between the Arctic/Boreal regions and the southern Asian mountains. Two main hypotheses have been proposed to explain the origin of this biogeographic pattern: (1) south-to-north migration in the late Pliocene/early Pleistocene, and (2) north-to-south migration during the Miocene. The genus Cassiope is disjunctly distributed between the Arctic/Boreal regions and the Himalayan-Hengduan Mountains (HHM) and was selected to test these hypotheses. We constructed a fossil-calibrated phylogeny of Ericaceae using two plastid regions to estimate the crown group age of Cassiope, and used sequence data from thousands of loci produced by restriction site associated DNA sequencing (RAD-seq) to reconstruct the phylogeny of Cassiope. We also performed Bayesian divergence time analysis and biogeographic analysis. The Cassiope crown group was estimated to have originated in the Miocene, which predates the onset of Northern hemisphere glaciation. All HHM species formed a clade together with one eastern Siberian species, and this clade was sister to all other Arctic/Boreal species. This topology implies a northern origin of Cassiope, which is confirmed by our biogeographic analysis. Our results thus suggest that the ancient north-to-south migration hypothesis is most consistent with the origin of Cassiope.

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic reconstruction. The alpine-arctic genus Diapensia was selected to study the origin of the disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM). However, a previous phylogenetic analysis based on one nuclear and four plastid DNA regions failed to resolve the oldest divergences in Diapensia as well as the relationship between the two HHM species. Here we reconstruct a fully resolved phylogeny of Diapensia and address the conflict between the currently accepted taxonomy and the gene trees in the HHM species using RAD-seq. Based on a data set containing 2,650 loci selected to maximize the number of parsimony informative sites and allowing for a high level of missing data (51%), the phylogeny of Diapensia was fully resolved and each of the four species was reciprocally monophyletic. Whereas the arctic D. lapponica was inferred as sister to the HHM clade in the previous study, the RAD-seq data resolved the two arctic species as sisters to the HHM clade. Similar relationships were inferred from a differently filtered data set with far fewer loci (114) and less missing data (21%), but with lower support and with one of the two HHM species as non-monophyletic. Bayesian concordance analysis and Patterson’s D-statistic tests suggested that admixture has occurred between the two HHM species.

Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species

The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

The draft genome of Primula veris yields insights into the molecular basis of heterostyly

Background

The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.

Results

We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.

Conclusions

The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0567-z) contains supplementary material, which is available to authorized users.

The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event

The stochastic process of long-distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self-incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long-distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self-incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed of approximately 124 species with a paleotropical distribution. Phylogenetic evidence strongly supports a single colonization of the oceanic island of Mauritius from either Madagascar or Africa. We employ Bayesian divergence time analyses to show that the colonization of Mauritius was not a recent event. We genotype S-RNase alleles from Mauritian endemic Coffea, and using S-allele gene genealogies, we show that the Mauritian allelic diversity is confined to just seven deeply divergent Coffea S-RNase allelic lineages. Based on these data, we developed an individual-based model and performed a simulation study to estimate the most likely number of founding individuals involved in the colonization of Mauritius. Our simulations show that to explain the observed S-RNase allelic diversity, the founding population was likely composed of fewer than 31 seeds that were likely synchronously dispersed from an ancestral mainland species.

Development of 12 polymorphic microsatellite loci in the high alpine perennial Primula halleri (Primulaceae)

PREMISE OF THE STUDY

Primula halleri is a high alpine endemic species with a patchy distribution in Central and Eastern European mountains. Little is known about the structure of genetic variation and mating system in populations of this species. •

METHODS AND RESULTS

We report on the development of 12 novel, polymorphic microsatellite loci for P. halleri. Tests for amplification and polymorphism were performed on 45 individuals sampled from three populations in the Swiss Alps. Interspecific amplification of the loci was evaluated using samples of the closely related species P. farinosa, P. frondosa, and P. scotica. •

CONCLUSIONS

The results show that the new microsatellite loci will be useful to study the structure of genetic diversity and mating system of P. halleri, and possibly its closely related species.

A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates.

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae)

PREMISE OF THE STUDY

We developed microsatellite markers for the endangered plant Primula boveana, the Sinai primrose, and assessed the cross-transferability of these markers to six related taxa. •

METHODS AND RESULTS

DNA sequences containing microsatellites were isolated from a microsatellite-enriched library. We obtained successful amplification of 13 microsatellite primer pairs, seven of which were polymorphic in P. boveana. Eleven of these primers successfully cross-amplified to related taxa. •

CONCLUSIONS

The markers reported herein will be useful to characterize the genetic diversity of the endangered P. boveana and to evaluate its mating system, and have the potential to be useful for similar studies in close relatives.

Biomechanical evaluation of effect of coracoid tunnel placement on load to failure of fixation during repair of acromioclavicular joint dislocations

PURPOSE

To evaluate the effect of entry and exit points of the coracoid tunnel on load to failure and mode of failure, to reduce the incidence of coracoid fractures and acromioclavicular joint repair failures.

METHODS

This study investigates 5 tunnel placements based on different entry and exit points in the coracoid process: center-center orientation represents perfect placement of the bone tunnel and served as perfect tunnel placement in our study. Four common errors in drilling were then tested and acted as the experimental groups in our study (medial-center, center-medial, lateral-center, and center-lateral). Using 35 cadaveric shoulders (mean age, 68.0 ± 13.0 years), we tested these 5 tunnel orientations using a single repair technique (cortical button) loaded to failure on an MTS 858 Servohydraulic test system (MTS Systems, Eden Prairie, MN). A control group of 7 cadaveric shoulders without the presence of a coracoid tunnel was also tested to determine the type of fracture pattern that occurred.

RESULTS

The coracoids without tunnel drilling fractured in patterns similar to traumatic coracoid injuries. With regard to the 5 tunnel groups, it was found that the loads to failure with center-center and medial-center tunnel placement were significantly higher than those with center-medial, center-lateral, and lateral-center tunnel placement. The failure modes of the former were primarily within the repair constructs, whereas those of the latter were primarily due to bony failure.

CONCLUSIONS

Our biomechanical results showed a higher peak load to failure with a center-center or medial-center tunnel orientation, which may lessen the risk of coracoid fracture during drilling with a 6-mm cannulated drill bit.

CLINICAL RELEVANCE

Proper trajectory of the drill during formation of a coracoid bone tunnel can help reduce the risk of coracoid process fracture and repair failure.

Biomechanical comparison of arthroscopic repairs for acromioclavicular joint instability: suture button systems without biological augmentation

BACKGROUND

Arthroscopic procedures for reconstruction of acromioclavicular (AC) joint separations are increasingly used in clinical practice. Multiple surgical techniques exist, but there are still few data on biomechanical performances of commonly used arthroscopic techniques and fixation methods.

HYPOTHESIS

Single and double clavicular tunnel reconstructions show comparable primary stability with a modified Weaver-Dunn procedure, and double tunnel constructs show superior horizontal stability.

STUDY DESIGN

Controlled laboratory study.

METHODS

The AC joints of 40 cadaveric shoulders were tested for anterior, posterior, and superior translation (70-N load) and maximal load to failure (superior) with the MTS 858 Bionix II Servohydraulic testing system. Shoulders were assigned to 4 groups: (1) native (n = 18), (2) coracoclavicular (CC) reconstruction with 1 clavicular and 1 coracoid tunnel (SCT) fixed with a suture pulley and 2 buttons (n = 8), (3) CC reconstruction with 2 clavicular and 1 coracoid tunnel (DCT) fixed with a suture pulley and 3 buttons (n = 8), and (4) modified Weaver-Dunn reconstruction (n = 6).

RESULTS

Native specimens showed a mean anterior translation of 7.92 mm (±1.69 mm), a mean posterior translation of 7.84 mm (±2.09 mm), and a superior translation of 4.28 mm (±1.81 mm). Maximal load to failure was 579.44 N (±148.01 N). The SCT technique showed a mean anterior translation of 5.81 mm (±1.16 mm), posterior translation of 8.30 mm (±1.94 mm), and a superior translation of 2.28 mm (±0.52 mm). The maximal load to failure was 591.35 N (±231.17 N). Anterior and superior translations were significantly less compared with the native specimen (P = .005 and P = .003). The DCT technique had an anterior translation of 4.68 mm (±0.6 mm), posterior translation of 6.85 mm (±0.83 mm), and superior translation of 2.09 mm (±0.86 mm). The mean maximal load to failure was 651.16 N (±226.93 N). Anterior and superior translations were significantly less compared with the native specimens (P = .000 and P = .001). No statistically significant differences were shown between SCT and DCT reconstruction for all measurements (P > .05). One reconstruction of the modified Weaver-Dunn procedure failed directly after mounting it into the testing device. The remaining 5 showed a mean anterior translation of 11.36 mm (±3.17 mm), a mean posterior translation of 13.51 mm (±2.21 mm), and a mean superior translation of 3.31 mm (±0.47 mm). Anterior and posterior translations were significantly increased compared with the native specimen (P = .019 and P = .000). The mean maximal load to failure measured 311.13 N (±52.2 N) and was significantly less compared with the native specimen (P = .000). The Weaver-Dunn technique showed significantly less maximal load to failure and more anterior and posterior translation compared with SCT and DCT (P ≤ .05).

CONCLUSION

Isolated reconstruction of the CC ligaments using single and double clavicular tunnel techniques results in a high load to failure for superior translation, which is equal to the native stability, and less translation in all 3 directions as well as higher superior stability when compared with the modified Weaver-Dunn procedure. A potential drawback is the risk of coracoid fracture, as the high load to failure of the device may exceed load to failure of cortical bone prior to device breakage.

CLINICAL RELEVANCE

Single clavicular tunnel arthroscopic reconstructions of the coracoacromial ligaments show good biomechanical results.

Expression and trans-specific polymorphism of self-incompatibility RNases in coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.

Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands

Fruit bats of the genus Pteropus occur throughout the Austral-Asian region west to islands off the eastern coast of Africa. Recent phylogenetic analyses of Pteropus from the western Indian Ocean found low sequence divergence and poor phylogenetic resolution among several morphologically defined species. We reexamine the phylogenetic relationships of these taxa by using multiple individuals per species. In addition, we estimate population genetic structure in two well-sampled taxa occurring on Madagascar and the Comoro Islands (P. rufus and P. seychellensis comorensis). Despite finding a similar pattern of low sequence divergence among species, increased sampling provides insight into the phylogeographic history of western Indian Ocean Pteropus, uncovering high levels of gene flow within species.

Biomechanical evaluation of margin convergence

PURPOSE

The aim of this study was to examine rotator cuff strain and gap size after margin convergence was performed for a large retracted rotator cuff tear.

METHODS

We tested 20 cadaveric shoulders using a custom shoulder testing system. A large retracted rotator cuff tear was created by removing the supraspinatus muscle-tendon unit to provide a reproducible model. Margin convergence was performed and strain was measured by use of differential variable reluctance transducers in the intact state, after a massive rotator cuff tear was created, and after each of 5 margin convergence sutures were placed. Data were obtained at 0° and 60° of abduction and with internal and external rotational torques applied to the humerus. Gap size was measured before and after margin convergence sutures were placed.

RESULTS

Strain was significantly reduced at all degrees of rotation in 0° of abduction after margin convergence sutures were placed (P < .05). There was a significantly significant decrease in gap size with each suture: 50% with the first suture, 60% with the second suture, 67% with the third suture, and 75% with the fourth suture (P < .05). There was only minimal intrinsic rotator cuff tension during knot tying, with each subsequent suture having less of an effect than the previous. Four margin convergence sutures resulted in a mean of 5 mm of anterior humeral head translation.

CONCLUSIONS

There was a significant decrease in rotator cuff strain and gap size after margin convergence was performed for a large retracted tear. The first margin convergence suture caused the greatest increase in intrinsic rotator cuff tension, with each subsequent suture having a similar but less dramatic effect.

CLINICAL RELEVANCE

Biomechanical rationale exists for the use of margin convergence in large retracted rotator cuff tears.

Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae)

We examined patterns of genetic variation in Rousettus madagascariensis from Madagascar and R. obliviosus from the Comoros (Grande Comore, Anjouan, and Mohéli). Genetic distances among individuals on the basis of 1,130 base pairs of the mitochondrial cytochrome b (Cytb) locus were estimated from specimens collected from 17 sites on Madagascar, 3 sites on Grande Comore, 3 sites on Anjouan, and 2 sites on Mohéli. We observed little variation in Madagascar and nearshore island samples (maximum 1.1%) and interisland Comoros samples (maximum 1.8%). In contrast, pairwise distances between different sampled sites on Madagascar and the Comoros varied from 8.5% to 13.2%. For 131 Malagasy animals, 69 unique haplotypes were recovered with 86 variable sites, and for 44 Comorian individuals, 17 unique haplotypes were found with 30 variable sites. No haplotype was shared between Madagascar and the Comoros, adding to previous morphological evidence that these 2 populations should be considered separate species. Cytb data showed that Rousettus populations of Madagascar (including nearshore islands) and the Comoros are respectively monophyletic and display no geographic structure in haplotype diversity, and that R. madagascariensis and R. obliviosus are strongly supported as sister to each other relative to other Rousettus species. Genotypic data from 6 microsatellite loci confirm lack of geographic structure in either of the 2 species. In pairwise tests of population differentiation, the only significant values were between samples from the Comoro Islands and Madagascar (including nearshore islands). Estimates of current and historical demographic parameters support population expansion in both the Comoros and Madagascar. These data suggest a more recent and rapid demographic expansion in Madagascar in comparison with greater population stability on the Comoros. On the basis of available evidence, open-water crossings approaching 300 km seem rarely traversed by Rousettus, and, if successful, can result in genetic isolation and subsequent differentiation.

An in vitro study comparing the use of suture anchors and drill hole fixation for flexor digitorum longus transfer to the navicular

BACKGROUND

The surgical management of posterior tibial tendon dysfunction often includes transfer of the flexor digitorum longus (FDL) tendon through a tunnel in the navicular. Fixation often is obtained by sewing the tendon back onto itself. The purpose of this study was to compare this standard method of fixation with suture anchor fixation, a technique that may be associated with less surgical morbidity, because it requires the harvesting of less tendon length.

METHODS

FDL tendon transfer to the navicular was done in 13 fresh-frozen cadaver specimens. In six feet comprising the standard group, the FDL tendon was transected distal to the master knot of Henry, placed through a drill hole into the navicular, and sutured back onto itself. In seven feet the FDL tendon was transected proximal to the master knot of Henry, placed into a drill hole into the navicular, and fixed with a suture anchor. Load was applied to the proximal FDL muscle and tendon using a materials testing system (MTS) machine and peak load to failure was measured.

RESULTS

The mean load to failure was 142.48 N +/- 38.06 N for the standard group and 142.12 N +/- 59.26 N for the suture anchor group (p = 0.305 for the Student-t test and p = 0.945 for the Mann-Whitney test).

CONCLUSION

Transfer of the FDL tendon to the navicular using suture anchor fixation requires less tendon length yet provides similar fixation strength as compared to sewing the tendon back onto itself. However, suture anchors are considerably more expensive than sutures.

CLINICAL IMPLICATIONS

Suture anchors allow comparable fixation of FDL tendon transfer into a navicular without the need to disrupt the master knot of Henry. This technique may be associated with less morbidity including a shorter incision, decreased risk of medial plantar nerve injury, and decreased loss of lesser toe plantarflexion strength secondary to maintenance of the normal interconnections between the flexor hallucis longus (FHL) and FDL tendons.

Biomechanical evaluation of calcaneocuboid distraction arthrodesis: a cadaver study of two different fixation methods

Calcaneocuboid distraction arthrodesis can be used to treat stage 2 posterior tibial tendon dysfunction. Nonunion, graft resorption, and implant failure have been reported after this procedure. This study compared two of the most commonly used methods for fixation of calcaneocuboid distraction arthrodesis. Twelve pairs of cadaver feet underwent simulated calcaneocuboid distraction arthrodesis. One specimen in each pair was fixed with two crossed 3.5 mm cortical lag screws. The contralateral specimen was fixed with a cervical H-plate. The calcaneus was fixed and a load was applied to the plantar aspect of the cuboid at a rate of 5 mm/minute until joint separation of 3 mm or fracture occurred. The average applied load to failure at 1.0 mm of joint separation was 30.5 +/- 11.6 N for the crossed screws and 77.7 +/- 36.4 N for the cervical H-plate (p = 0.001). The average stiffness at 1.0 mm of joint separation was 27.5 +/- 10.9 N/mm for the crossed screws and 43 +/- 21.2 N/mm for the cervical H-plate (p = 0.036). The higher stiffness and load to failure may account for the decreased nonunion rate noted anecdotally by some surgeons with H-plate fixation over crossed screw fixation for calcaneocuboid distraction arthrodesis.

Design enhancement of a solid ankle-foot orthosis: real-time contact pressures evaluation

The purpose of our study was to evaluate all contact pressures between the molded ankle-foot orthosis (MAFO) and the subject during activities of daily living. The MAFOs studied are used clinically to reduce plantar contact pressures associated with foot ulcers in adult neuropathic diabetic subjects, alleviating abnormal pressures by redistributing them to low-pressure plantar regions. While effective, MAFOs are often not used by the subject due to weight and comfort issues. An understanding of the contact pressures between the subject and the orthosis is a first step in improving basic MAFO design. Four nonimpaired, young adult males were tested in this study. A right-side MAFO was custom-molded and fitted for each subject by the same orthotist. Real-time pressures were obtained for the entire contact area using the F-Scan pressure measurement system. The data obtained demonstrated high contact pressures along the metatarsals of the foot, around the heel and ankle, and adjacent to the strap attachment sites. No contact pressures were noted along the posterior calf region during any of the activities performed. These data suggest the calf region would be a suitable site for material removal for weight reduction and increased comfort, especially in warm weather. In addition, these data may be useful to orthotists in improving the basic design and to researchers as a starting point for performing complex finite element analysis on the MAFO.

Calcaneocuboid joint pressures with lateral column lengthening (Evans) procedure

Calcaneocuboid joint pressures were evaluated with eight cadaver specimens. Real-time pressures were recorded using a TekScan 4200 sensor pad at lengths of 0, 5, and 10 mm in both unloaded and 350-newton loaded models. Recorded pressures exceeded 2.3 MPa in the loaded model at 10 mm lateral column lengthening. Although an acceptable procedure in the pediatric population, application of the Evans lateral column lengthening procedure for management of adult acquired flatfoot may generate excessive pressures leading to joint arthrosis. Lengthening by calcaneocuboid distraction arthrodesis may avoid this problem.

Bend testing of wrought wire removable partial denture alloys

The flexibility of the wrought wire clasp is related to a number of factors, including the type and gauge of the alloy. The purpose of this study was to compare the bend behavior of five wrought wire alloys used in removable partial dentures. The alloys and their gauge diameters (in millimeters) were Ticonium (18, 19, 20), platinum-gold-palladium (18, 19), Wironium (18, 20), Jelenko Standard (18, 19, 20), and Denture Clasp (18, 19, 20). A total of 12 to 15 samples of each dental alloy were tested. Three-point bending was performed on a servohydraulic testing system controlled by a computer at 1.00 mm/sec until fracture or actuator contact occurred. Maximum stress and elastic modulus in bending were determined for each gauge diameter. Analysis of variance and post hoc Scheffe statistical analyses revealed significant maximum stress and elastic modulus in bending differences for different alloys of the same gauge and for different gauges of the same alloy. The choice of material and the gauge diameter significantly influenced the mechanical property of bending for wrought wire removable partial denture alloys. The Ticonium alloy had the greatest elastic modulus (stiffest) at all levels and the Denture Clasp and the Jelenko Standard alloys had the lowest elastic modulus (most flexible). These data indicate that knowledge of the bending properties of an alloy is equally as important as the gauge size when selecting a wire clasp.

Initial failure strength of open and arthroscopic Bankart repairs

Surgical repair of recurrent anterior shoulder instability requires secure fixation of the separated inferior glenohumeral complex to bone. Many techniques of fixation are in use for both arthroscopic and open repair. The specific aim of this study was to compare the initial failure strength of eight repair techniques using a previously described canine model of Bankart repair. Intact capsule-to-bone complexes failed at the bony interface at 236 N. Traditional Bankart repair failed at 122.1 N (2 sutures) and 74.7 N (1 suture), Acufex TAG rod (Acufex Microsurgical, Mansfield, MA) at 143.5 N (2 sutures) and 79.8 N (1 suture), transglenoid suture technique (2 sutures) at 166.6 N, Mitek GII (Mitek, Norwood, MA) (1 suture) at 96.4 N, Zimmer Statak (Zimmer Inc, Warsaw, IN)(1 suture) at 95.2 N, and Acufex bioasbsorpable Suretac at 82.2 N. The two-suture repairs were statistically equivalent in strength to each other, as were the one-suture repairs and the Suretac device. Two-suture repairs were significantly stronger than the one-suture repairs (P < .01) failure. In the single-suture specimens, failure occurred by suture breakage in 46% (18 of 39) of specimens and soft-tissue failure around the suture in 54% (21 of 39). Failure in the two-suture techniques primarily occurred by soft-tissue failure (23 of 25) and this proved a statistically significant difference (P < .003). No device broke or pulled out of bone.