The role of insulators and transcription in 3D chromatin organization of flies.

The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.

Teprotumumab-Related Adverse Events in Thyroid Eye Disease: A Multicenter Study.

PURPOSE: To assess the duration, incidence, reversibility, and severity of adverse events (AEs) in patients with thyroid eye disease (TED) treated with teprotumumab. DESIGN: Multicenter, retrospective, observational cohort study. PARTICIPANTS: Patients with TED of all stages and activity levels treated with at least 4 infusions of teprotumumab. METHODS: Patients were treated with teprotumumab between February 2020 and October 2022 at 6 tertiary centers. Adverse event metrics were recorded at each visit. MAIN OUTCOME MEASURES: The primary outcomes measure was AE incidence and onset. Secondary outcome measures included AE severity, AE reversibility, AE duration, proptosis response, clinical activity score (CAS) reduction, and Gorman diplopia score improvement. RESULTS: The study evaluated 131 patients. Proptosis improved by 2 mm or more in 77% of patients (101/131), with average proptosis improvement of 3.0 ± 2.1 mm and average CAS reduction of 3.2 points. Gorman diplopia score improved by at least 1 point for 50% of patients (36/72) with baseline diplopia. Adverse events occurred in 81.7% of patients (107/131). Patients experienced a median of 4 AEs. Most AEs were mild (74.0% [97/131]), 28.2% (37/131) were moderate, and 8.4% (11/131) were severe. Mean interval AE onset was 7.9 weeks after the first infusion. Mean resolved AE duration was 17.6 weeks. Forty-six percent of patients (60/131) demonstrated at least 1 persistent AE at last follow-up. Mean follow-up was 70.2 ± 38.5 weeks after the first infusion. The most common type of AEs was musculoskeletal (58.0% [76/131]), followed by gastrointestinal (38.2% [50/131]), skin (38.2% [50/131]), ear and labyrinth (30.5% [40/131]), nervous system (20.6% [27/131]), metabolic (15.3% [20/131]), and reproductive system (12.2% [16/131]). Sixteen patients (12.2%) discontinued therapy because of AEs, including hearing loss (n = 4), inflammatory bowel disease flare (n = 2), hyperglycemia (n = 1), muscle spasms (n = 1), and multiple AEs (n = 8). CONCLUSIONS: Adverse events are commonly reported while receiving teprotumumab treatment. Most are mild and reversible; however, serious AEs can occur and may warrant treatment cessation. Treating physicians should inform patients about AE risk, properly screen patients before treatment, monitor patients closely throughout therapy, and understand how to manage AEs should they develop. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

"Blue Scrub Lid Retraction": Changes in Eyelid Position on the Day of Surgery.

PURPOSE: The aim of this study is to test the hypothesis that margin-reflex distance 1 (MRD1) on the day of surgery will be higher than the MRD1 measured at the in-clinic consult visit among patients undergoing blepharoptosis repair due to an increased sympathetic drive. METHODS: Patients evaluated for involutional blepharoptosis repair were prospectively enrolled over a 12-month period in this single-center, self-controlled study. Three investigators independently determined MRD1 using cropped photos taken of patients at the in-clinic consult visit and on the day of surgery. A difference in height was tested for by using the 2-tailed Wilcoxon signed rank test. RESULTS: Evaluated in this study were 76 eyelids from 38 patients. Over 3-quarters of study participants had a higher MRD1 in the right and OSs on the day of surgery than at their in-clinic consultation visit (p < 0.001). The mean increase in MRD1 for the right eyelid and left eyelid was 1.0 mm (range: 0-3.15 mm) and 1.1 mm (range: 0-2.7 mm), respectively. CONCLUSIONS: In patients with involutional blepharoptosis, we conclude that MRD1 is higher on the day of surgery as compared with the in-clinic consult visit. This may be secondary to the stress of surgery and an associated increase in sympathetic drive. In some cases, this change in eyelid position led to resolution of apparent involutional ptosis altogether. Caution should be used when considering deferral of ptosis repair on the basis of exam findings present on the day of surgery.

The Relationship Between the Isometric Squat and Stretch Shortening Cycle Function and Sprint Acceleration Performance in Hurling Players.

ABSTRACT: Brady, CJ, Harrison, AJ, Flanagan, EP, Haff, GG, and Comyns, TM. The relationship between the isometric squat and stretch shortening cycle function and sprint acceleration performance in hurling players. J Strength Cond Res 38(6): e288-e298, 2024-The primary aim was to examine the relationship between sprint acceleration performance and the performance tests: isometric squat (ISqT), countermovement jump (CMJ), and reactive strength index (RSI). The secondary aim determined whether these tests could distinguish between sprint performance levels. Twenty-six male under-21 subjects completed the ISqT, with peak force (PF), relative PF, force at 100, 150, and 200 milliseconds (ms), and impulse (0-200 ms) measured. Jump height (JH) was calculated from the CMJ and RSI during the 10-5 repeated jump test. Subjects completed 3 × 30-m sprints with splits taken at 5, 10, 20, and 30 m. Pearson's product moment correlations were used to assess the relationships between measures, and independent samples t tests were used to determine whether differences existed in sprint ability of those in the top and bottom quartiles for force at 100 ms, CMJ, and RSI. Significant negative moderate correlations were reported between force at 100 ms and 0-5 m and 5-10 m, significant moderate and large negative correlations between CMJ and all splits and significant large correlations between RSI and splits over 5 m. Force at 100 ms distinguished between performance levels from 0 to 5 m, CMJ from 10 to 20 m, and RSI from 20 to 30 m; faster subjects produced significantly higher force, JHs, and RSI scores. Three principal components explaining 86.1% of the variation in the data set were identified: sprint times and stretch shortening cycle capabilities (33.3%), time-specific force (29.9%), and absolute and relative strength (22.8%).

ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.

MOTIVATION: Several computational and statistical methods have been developed to analyze data generated through the 3C-based methods, especially the Hi-C. Most of the existing methods do not account for dependency in Hi-C data. RESULTS: Here, we present ZipHiC, a novel statistical method to explore Hi-C data focusing on the detection of enriched contacts. ZipHiC implements a Bayesian method based on a hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC) to detect interactions in two-dimensional space based on a Hi-C contact frequency matrix. ZipHiC uses data on the sources of biases related to the contact frequency matrix, allows borrowing information from neighbours using the Potts model and improves computation speed using the ABC model. In addition to outperforming existing tools on both simulated and real data, our model also provides insights into different sources of biases that affects Hi-C data. We show that some datasets display higher biases from DNA accessibility or Transposable Elements content. Furthermore, our analysis in Drosophila melanogaster showed that approximately half of the detected significant interactions connect promoters with other parts of the genome indicating a functional biological role. Finally, we found that the micro-C datasets display higher biases from DNA accessibility compared to a similar Hi-C experiment, but this can be corrected by ZipHiC. AVAILABILITY AND IMPLEMENTATION: The R scripts are available at https://github.com/igosungithub/HMRFHiC.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks.

MOTIVATION: Protein-protein interaction (PPI), as a relative property, is determined by two binding proteins, which brings a great challenge to design an expert model with an unbiased learning architecture and a superior generalization performance. Additionally, few efforts have been made to allow PPI predictors to discriminate between relative properties and intrinsic properties. RESULTS: We present a sequence-based approach, DeepTrio, for PPI prediction using mask multiple parallel convolutional neural networks. Experimental evaluations show that DeepTrio achieves a better performance over several state-of-the-art methods in terms of various quality metrics. Besides, DeepTrio is extended to provide additional insights into the contribution of each input neuron to the prediction results. AVAILABILITY AND IMPLEMENTATION: We provide an online application at http://bis.zju.edu.cn/deeptrio. The DeepTrio models and training data are deposited at https://github.com/huxiaoti/deeptrio.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mechanisms of SARS-CoV-2 Transmission and Pathogenesis.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) marks the third highly pathogenic coronavirus to spill over into the human population. SARS-CoV-2 is highly transmissible with a broad tissue tropism that is likely perpetuating the pandemic. However, important questions remain regarding its transmissibility and pathogenesis. In this review, we summarize current SARS-CoV-2 research, with an emphasis on transmission, tissue tropism, viral pathogenesis, and immune antagonism. We further present advances in animal models that are important for understanding the pathogenesis of SARS-CoV-2, vaccine development, and therapeutic testing. When necessary, comparisons are made from studies with SARS to provide further perspectives on coronavirus infectious disease 2019 (COVID-19), as well as draw inferences for future investigations.

UBX Domain Protein 6 Positively Regulates JAK-STAT1/2 Signaling.

Type I/III IFNs induce expression of hundreds of IFN-stimulated genes through the JAK/STAT pathway to combat viral infections. Although JAK/STAT signaling is seemingly straightforward, it is nevertheless subjected to complex cellular regulation. In this study, we show that an ubiquitination regulatory X (UBX) domain-containing protein, UBXN6, positively regulates JAK-STAT1/2 signaling. Overexpression of UBXN6 enhanced type I/III IFNs-induced expression of IFN-stimulated genes, whereas deletion of UBXN6 inhibited their expression. RNA viral replication was increased in human UBXN6-deficient cells, accompanied by a reduction in both type I/III IFN expression, when compared with UBXN6-sufficient cells. Mechanistically, UBXN6 interacted with tyrosine kinase 2 (TYK2) and inhibited IFN-ß-induced degradation of both TYK2 and type I IFNR. These results suggest that UBXN6 maintains normal JAK-STAT1/2 signaling by stabilizing key signaling components during viral infection.

Optimizing 3D Rotational Angiography for Congenital Cardiac Catheterization.

The aim of the study was to determine the variables associated with high-quality (HQ) versus low-quality (LQ) three-dimensional rotational angiography (3DRA) and create guides for optimization of approach to 3DRA in congenital cardiac catheterization (CCC). CCC has adopted 3DRA as a mainstay, but there has not been systematic analysis of approach to and factors associated with HQ 3DRA. This was a single-center, retrospective study of 3DRAs using Canon Infinix-I platform. Reconstructions were graded by 3 interventionalists. Quality was dichotomized into HQ and LQ. Univariable analyses and multivariable logistic regression models were performed. From 8/2016 to 12/2018, 208 3DRAs were performed in 195 CCCs; median age 7 years (2, 16), weight 23 kg (12, 57). The majority of 3DRAs were performed in patients with biventricular physiology (N = 137, 66%) and in pulsatile sites (N = 144, 69%). HQ 3DRA (N = 182, 88%) was associated with greater total injection volume [2.20 mL/kg (1.44, 3.29) vs. 1.62 mL/kg (1.10, 1.98), p = 0.005] and more dilute contrast solution [60% (50, 100) vs. 100% (60, 100), p = 0.007], but not with contrast volume administered (p = 0.2) on univariable analysis. On multivariable logistic regression, HQ 3DRA was significantly associated with patient weight [OR 0.97 (95% CI (0.94, 0.99), p = 0.018], total injection volume [OR 1.04 (95% CI 1.01, 1.07) p = 0.011], and percent contrast solution [OR 0.97 (95% CI 0.95, 1.00), p = 0.022]. These data resulted in creation of scatter plots and a novel 3DRA Nomogram for estimating the probability of HQ 3DRA. This is the first study to create evidence-based contrast dose guides and nomogram for 3DRA in CCC. HQ 3DRA was associated with lower weight, higher total injection volumes, and more dilute contrast solution.

A Case of the Blues-Colored Pencil Orbitopathy in an 18-Month-Old Boy.

Orbital penetrating injuries from pencils are rare. This report describes a case of penetrating orbital injury in a young child with a retained blue-colored pencil core foreign body, which led to rapid onset of orbital abscess requiring surgical drainage. Intraoperatively, orbital tissues were stained a bright-blue color. Histopathological study of specimen also highlighted bright blue aggregates of foreign material infiltrating the orbital tissues. Cultures grew Streptococcus mitis and Exophiala jeanselmei , which are rare causes of orbital abscess. Unique properties of retained colored pencil core as compared to graphite pencil core are herein discussed. Due to differences in composition, colored pencil core foreign bodies may require more timely surgical intervention compared to noncolored graphite pencil core.

Outcomes of Patients With Thyroid Eye Disease Partially Treated With Teprotumumab.

PURPOSE: In response to the coronavirus (COVID-19) pandemic, teprotumumab production was temporarily halted with resources diverted toward vaccine production. Many patients who initiated treatment with teprotumumab for thyroid eye disease were forced to deviate from the standard protocol. This study investigates the response of teprotumumab when patients receive fewer than the standard 8-dose regimen. METHODS: This observational cross-sectional cohort study included patients from 15 institutions with active or minimal to no clinical activity thyroid eye disease treated with the standard teprotumumab infusion protocol. Patients were included if they had completed at least 1 teprotumumab infusion and had not yet completed all 8 planned infusions. Data were collected before teprotumumab initiation, within 3 weeks of last dose before interruption, and at the visit before teprotumumab reinitiation. The primary outcome measure was reduction in proptosis more than 2 mm. Secondary outcome measures included change in clinical activity score (CAS), extraocular motility restriction, margin reflex distance-1 (MRD1), and reported adverse events. RESULTS: The study included 74 patients. Mean age was 57.8 years, and 77% were female. There were 62 active and 12 minimal to no clinical activity patients. Patients completed an average of 4.2 teprotumumab infusions before interruption. A significant mean reduction in proptosis (-2.9 mm in active and -2.8 mm in minimal to no clinical activity patients, P < 0.01) was noted and maintained during interruption. For active patients, a 3.4-point reduction in CAS ( P < 0.01) and reduction in ocular motility restriction ( P < 0.01) were maintained during interruption. CONCLUSIONS: Patients partially treated with teprotumumab achieve significant reduction in proptosis, CAS, and extraocular muscle restriction and maintain these improvements through the period of interruption.

Size Exclusion and Ion Exchange Chromatographic Hardware Modified with a Hydrophilic Hybrid Surface.

Certain biomolecules have proven to be difficult to analyze by liquid chromatography (LC), especially under certain chromatographic conditions. The separation of proteins in aqueous mobile phases is one such example because there is the potential for both hydrophobic and ionic secondary interactions to occur with chromatographic hardware to the detriment of peak recovery, peak shape, and the overall sensitivity of the LC analysis. To decrease non-specific adsorption and undesired secondary interactions between column hardware and biomolecules, we have developed and applied a new hydrophilically modified hybrid surface (h-HST) for size exclusion chromatography (SEC) and anion exchange (AEX) separations of proteins and nucleic acids. This surface incorporates additional oxygen and carbon atoms onto an ethylene bridge hybrid siloxane polymer. As a result, it exhibits reduced electrostatic properties and hydrophilicity that facilitates challenging aqueous separations. Flow injection tests with a phosphate buffer showed superior protein recovery from an h-HST frit when compared to unmodified ethylene-bridged hybrid HST, titanium, stainless steel, and PEEK frits. When applied to SEC of rituximab, ramucirumab, and trastuzumab emtansine with a 50 mM ammonium acetate buffer, this new hydrophilic chromatographic hardware yielded improved monomer and aggregate recovery, higher plate numbers, and more symmetrical peaks. AEX columns also benefited from h-HST hardware. An acidic mAb (eculizumab) showed improved recovery, more stable retention, and a sharper peak when eluted from an h-HST versus SS column. Moreover, AEX separations of intact mRNA samples (Cas9 and EPO mRNA) were improved, where it was seen that h-HST column hardware provided higher sensitivity and more repeatable peak areas from injection to injection. As such, there is significant potential in the use of h-HST chromatographic hardware to facilitate more robust and more sensitive analyses for a multitude of challenging separations and analytes.

Expert Consensus on the Use of Teprotumumab for the Management of Thyroid Eye Disease Using a Modified-Delphi Approach.

BACKGROUND: Teprotumumab is the first treatment for thyroid eye disease (TED), a debilitating autoinflammatory condition, approved by the Food and Drug Administration in the United States, which reduces proptosis and improves quality of life. In the absence of guidelines, clinical recommendations were developed for using teprotumumab in patients with TED in the United States. METHODS: A 3-round modified-Delphi panel was conducted between October 2020 and February 2021 with experts in the management of patients with TED. Key areas regarding the use of teprotumumab were investigated, including eligible patient populations, concomitant treatments, and assessment of response and adverse events. This used 2 survey rounds via an online questionnaire, where statements were scored using 9-point Likert scales. Statements with conflict were included in the third round, involving a consensus meeting via videoconference. RESULTS: Consensus was obtained for all statements (n = 75); of which, 56% were revised to enable agreement of the group. The consensus meeting provided agreement regarding which populations should receive teprotumumab therapy, including all adult patients with TED with a clinical activity score of ≥4. Treatment with teprotumumab can also be considered for TED patients displaying the following characteristics: a CAS of <3, lid retraction of ≥2, and mild or early optic neuropathy with close clinical observation. Further recommendations included suitability of treatment for those beyond 16 months following the initial diagnosis of TED, low CAS concomitant treatment with steroids in some cases, retreatment for those who have relapses, and finally a recommendation to continue therapy for all 8 infusions despite the lack of response by the fourth infusion. CONCLUSIONS: This work constitutes the first consensus on guidelines for the use of teprotumumab. The modified Delphi approach involved physicians with significant experience with the clinical use of teprotumumab, and recommendations were based on current evidence.

Pre-clinical Evolution of a Novel Transcatheter Bioabsorbable ASD/PFO Occluder Device.

To date, there has been limited investigation of bioabsorbable atrial septal defect (ASD) or patent foramen ovale (PFO) closure devices using clinically relevant large animal models. The purpose of this study is to explore the function and safety of a bioabsorbable ASD occluder (BAO) system for PFO and/or secundum ASD transcatheter closure. Using a sheep model, the intra-atrial septum was evaluated by intracardiac echo (ICE). If a PFO was not present, atrial communication was created via transseptal puncture. Device implantation across the intra-atrial communication was performed with fluoroscopic and ICE guidance. Our 1st generation device consisted of a main structure of thin Poly(L-lactide-co-epsilon-caprolactone) (PLCL) fibers, and an internal Poly glycolic acid (PGA) fabric. Four procedures validated procedure feasibility. Subsequently, device design was modified for improved transcatheter delivery. The 2nd generation device has a two-layered structure and was implanted in six sheep. Results showed procedural success in 9/10 (90%) animals. With deployment, the 1st generation device did not reform into its original disk shape and did not conform nicely along the atrial septum. The 2nd generation device was implanted in six animals, 3 out of 6 survived out to 1 year. At 1 year post implantation, ICE confirmed no residual shunting. By necropsy, biomaterials had partially degraded, and histology of explanted samples revealed significant device endothelialization and biomaterial replacement with a collagen layer. Our results demonstrate that our modified 2nd generation BAO can be deployed via minimally invasive percutaneous transcatheter techniques. The BAO partially degrades over 1 year and is replaced by host native tissues. Future studies are needed prior to clinical trials.

Antineutrophil Cytoplasmic Antibody-Associated Vasculitis With Immunoglobulin G4 Involvement in Lacrimal Sac Squamous Cell Carcinoma.

Lacrimal sac squamous cell carcinoma is a rare but life-threatening disease that is often a delayed diagnosis secondary to difficulty in differentiating from other causes of dacrocystitis and acquired nasolacrimal duct obstruction. Chronic inflammation, including that of an underlying autoimmune disease, prior instrumentation, and poor wound healing, may be risk factors in the development to lacrimal sac squamous cell carcinoma. The authors present the first case of lacrimal sac squamous cell carcinoma associated with antineutrophil cytoplasmic antibody-associated vasculitis and immunoglobulin G4 positivity. Rather than an overlap syndrome between antineutrophil cytoplasmic antibody-associated vasculitis and immunoglobulin G4-related disease, high immunoglobulin G4 positivity may be considered an inflammatory marker of disease severity in the setting of antineutrophil cytoplasmic antibody-associated vasculitis and underlying malignancy. Inflammation-mediated tumorangiogenesis should be considered in the development of malignancy and red flags of chronic uncontrolled inflammation should warrant a lower threshold for further workup.

Delayed-Onset Inflammatory Optic Nerve Sheath Mass and Perineuritis Following Cessation of Ipilimumab and Nivolumab Therapy.

A 65-year-old male presented with headaches and painless episodes of unilateral vision loss. He had a history of renal cell carcinoma, in remission following surgery and immunotherapy with ipilimumab and nivolumab, discontinued 2 years and 3 months before presentation, respectively. MRI revealed an optic nerve sheath mass and perineuritis. After 1 month of corticosteroid therapy, there was a robust clinical and radiographic response, which relapsed dramatically following cessation. An optic nerve sheath biopsy showed chronic mild inflammation, and extensive work-up for alternative etiologies of orbital inflammation was negative. Following a prolonged taper of corticosteroids, he demonstrated complete response. In the setting of ocular immune privilege, ophthalmic immune-related adverse events (irAE) are rare, although multifarious. While on-treatment irAE are well-characterized, posttreatment irAE have become increasingly recognized across multiple organ systems. We report a case of a delayed-onset inflammatory optic nerve sheath mass and perineuritis after cessation of immunotherapy.

Predictive Modeling of New-Onset Postoperative Diplopia Following Orbital Decompression for Thyroid Eye Disease.

PURPOSE: To identify risk factors for the development of new-onset, postoperative diplopia following orbital decompression surgery based on patient demographics, clinical exam characteristics, radiographic parameters, and surgical techniques. METHODS: We conducted a multi-center retrospective chart review of patients who underwent orbital decompression for thyroid eye disease (TED). Patient demographics, including age, gender, smoking history, preoperative exophthalmometry, clinical activity score (CAS), use of peribulbar and/or systemic steroids, and type of orbital decompression were reviewed. Postoperative diplopia was determined at a minimum of 3 months postoperatively and before any further surgeries. Cross-sectional area ratios of each extraocular muscle to orbit and total fat to orbit were calculated from coronal imaging in a standard fashion. All measurements were carried out using PACS imaging software. Multivariable logistic regression modeling was performed using Stata 14.2 (StataCorp, College Station, TX). RESULTS: A total of 331 patients without preoperative diplopia were identified. At 3 months postoperatively, 249 patients had no diplopia whereas 82 patients developed diplopia. The average postoperative follow-up was 22 months (range 3-156) months. Significant preoperative clinical risk factors for postoperative diplopia included older age at surgery, proptosis, use of peribulbar or systemic steroids, elevated clinical activity score, and presence of preoperative compressive optic neuropathy. Imaging findings of enlarged cross-sectional areas of each rectus muscle to the overall orbital area also conferred a significant risk of postoperative diplopia. Regarding surgical factors, postoperative diplopia was more common among those undergoing medial wall decompression, bilateral orbital surgery, and balanced decompression, whereas endoscopic medial wall decompression was found to be relatively protective. CONCLUSIONS: This study identifies risk factors associated with the development of diplopia following orbital decompression using multivariable data. This study demonstrates that several characteristics including age, clinical activity score, the cross-sectional muscle to orbit ratios, in addition to the type of orbital decompression surgery, are predictive factors for the development of new-onset postoperative diplopia.

A noninvasive eDNA tool for detecting sea lamprey larvae in river sediments: Analytical validation and field testing in a low-abundance ecosystem.

Anthropogenic activities are increasingly threatening aquatic biodiversity, especially anadromous species. Monitoring and conservation measures are thus required to protect, maintain and restore imperilled populations. While many species can be surveyed using traditional capture and visual census techniques, species that use riverine habitats in a less conspicuous manner, such as sea lamprey Petromyzon marinus, can be more challenging to monitor. Sea lamprey larvae (ammocoetes) can spend several years in freshwater burrowed within soft sediments, inhibiting their detection and assessment. Here, we present a qPCR assay based on the detection of environmental DNA (eDNA) to identify the presence of ammocoetes burrowed in the sediment. We present an extensively validated method that ensured both species-specificity of the assay as well as the capacity to detect ammocoetes when abundances are low. Experiments on burrowing activity suggested that most of the DNA released into the sediment occurs during burrowing. Overall, we demonstrate this new molecular-based tool is an efficient and effective complement to traditional monitoring activities targeting larval stages of sea lampreys.

A Critical Role for STING Signaling in Limiting Pathogenesis of Chikungunya Virus.

The stimulator of interferon gene (STING) pathway controls both DNA and RNA virus infection. STING is essential for induction of innate immune responses during DNA virus infection, while its mechanism against RNA virus remains largely elusive. We show that STING signaling is crucial for restricting chikungunya virus infection and arthritis pathogenesis. Sting-deficient mice (Stinggt/gt) had elevated viremia throughout the viremic stage and viral burden in feet transiently, with a normal type I IFN response. Stinggt/gt mice presented much greater foot swelling, joint damage, and immune cell infiltration than wild-type mice. Intriguingly, expression of interferon-γ and Cxcl10 was continuously upregulated by approximately 7 to 10-fold and further elevated in Stinggt/gt mice synchronously with arthritis progression. However, expression of chemoattractants for and activators of neutrophils, Cxcl5, Cxcl7, and Cxcr2 was suppressed in Stinggt/gt joints. These results demonstrate that STING deficiency leads to an aberrant chemokine response that promotes pathogenesis of CHIKV arthritis.

Using Hybrid Organic-Inorganic Surface Technology to Mitigate Analyte Interactions with Metal Surfaces in UHPLC.

Interactions of analytes with metal surfaces in high-performance liquid chromatography (HPLC) instruments and columns have been reported to cause deleterious effects ranging from peak tailing to a complete loss of the analyte signal. These effects are due to the adsorption of certain analytes on the metal oxide layer on the surface of the metal components. We have developed a novel surface modification technology and applied it to the metal components in ultra-HPLC (UHPLC) instruments and columns to mitigate these interactions. A hybrid organic-inorganic surface, based on an ethylene-bridged siloxane chemistry, was developed for use with reversed-phase and hydrophilic interaction chromatography. We have characterized the performance of UHPLC instruments and columns that incorporate this surface technology and compared the results with those obtained using their conventional counterparts. We demonstrate improved performance when using the hybrid surface technology for separations of nucleotides, a phosphopeptide, and an oligonucleotide. The hybrid surface technology was found to result in higher and more consistent analyte peak areas and improved peak shape, particularly when using low analyte mass loads and acidic mobile phases. Reduced abundances of iron adducts in the mass spectrum of a peptide were also observed when using UHPLC systems and columns that incorporate hybrid surface technology. These results suggest that this technology will be particularly beneficial in UHPLC/mass spectrometry investigations of metal-sensitive analytes.