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1.
Article En | MEDLINE | ID: mdl-38331034

OBJECTIVE: The aim of this study was to compare stiffness and strain of an in vitro fracture-gap model secured with a primary 3.5-mm locking compression plate (LCP) at three primary plate working lengths without and with an orthogonal 2.7-mm LCP. STUDY DESIGN: Primary plate screw configurations modeled short working length (SWL), medium working length (MWL), and long working length (LWL) constructs. Construct stiffness with and without an orthogonal plate during nondestructive four-point bending and torsion, and plate surface strain measured during bending, was analyzed. RESULTS: Single plate construct stiffness was significantly, incrementally, lower in four-point bending and torsion as working length was extended. Addition of an orthogonal plate resulted in significantly higher bending stiffness for SWL, MWL, and LWL (p < 0.05) and torsional stiffness for MWL and LWL (p < 0.05). Single plate construct strain was significantly, incrementally, higher as working length was extended. Addition of an orthogonal plate significantly lowered strain for SWL, MWL, and LWL constructs (p < 0.01). CONCLUSION: Orthogonal plate application resulted in higher bending and torsional construct stiffness and lower strain over the primary plate in bending in this in vitro model. Working length had an inverse relationship with construct stiffness in bending and torsion and a direct relationship with strain. The inverse effect of working length on construct stiffness was completely mitigated by the application of an orthogonal plate in bending and modified in torsion.

2.
Mol Pharm ; 20(9): 4559-4573, 2023 09 04.
Article En | MEDLINE | ID: mdl-37555521

The enzyme PACE4 has been validated as a promising therapeutic target to expand the range of prostate cancer (PCa) treatments. In recent years, we have developed a potent peptidomimetic inhibitor, namely, compound C23 (Ac-(DLeu)LLLRVK-4-amidinobenzylamide). Like many peptides, C23 suffers from an unfavorable drug-like profile which, despite our efforts, has not yet benefited from the usual SAR studies. Hence, we turned our attention toward a novel formulation strategy, i.e., the use of cyclodextrins (CDs). CDs can benefit compounds through the formation of "host-guest" complexes, shielding the guest from degradation and enhancing biological survival. In this study, a series of ßCD-C23 complexes have been generated and their properties evaluated, including potency toward the enzyme in vitro, a cell-based proliferation assay, and stability in plasma. As a result, a new ßCD-formulated lead compound has been identified, which, in addition to being more soluble and more potent, also showed an improved stability profile.


Cyclodextrins , beta-Cyclodextrins , Male , Humans , Peptides/pharmacology , beta-Cyclodextrins/pharmacology , Cyclodextrins/pharmacology , Cyclodextrins/chemistry
3.
PLoS One ; 18(7): e0288622, 2023.
Article En | MEDLINE | ID: mdl-37463144

Phosphatase and tensin homolog (PTEN) mutation is common in prostate cancer during progression to metastatic and castration resistant forms. We previously reported that loss of PTEN function in prostate cancer leads to increased expression and secretion of the Prorenin Receptor (PRR) and its soluble processed form, the soluble Prorenin Receptor (sPRR). PRR is an essential factor required for proper assembly and activity of the vacuolar-ATPase (V-ATPase). The V-ATPase is a rotary proton pump required for the acidification of intracellular vesicles including endosomes and lysosomes. Acidic vesicles are involved in a wide range of cancer related pathways such as receptor mediated endocytosis, autophagy, and cell signalling. Full-length PRR is cleaved at a conserved consensus motif (R-X-X-R↓) by a member of the proprotein convertase family to generate sPRR, and a smaller C-terminal fragment, designated M8.9. It is unclear which convertase processes PRR in prostate cancer cells and how processing affects V-ATPase activity. In the current study we show that PRR is predominantly cleaved by PACE4, a proprotein convertase that has been previously implicated in prostate cancer. We further demonstrate that PTEN controls PRR processing in mouse tissue and controls PACE4 expression in prostate cancer cells. Furthermore, we demonstrate that PACE4 cleavage of PRR is needed for efficient V-ATPase activity and prostate cancer cell growth. Overall, our data highlight the importance of PACE4-mediated PRR processing in normal physiology and prostate cancer tumorigenesis.


Prostatic Neoplasms , Vacuolar Proton-Translocating ATPases , Animals , Humans , Male , Mice , Proprotein Convertases/metabolism , Prorenin Receptor , Prostatic Neoplasms/genetics , Receptors, Cell Surface/genetics , Receptors, Cell Surface/metabolism , Vacuolar Proton-Translocating ATPases/genetics , Vacuolar Proton-Translocating ATPases/metabolism
4.
J Pers Med ; 13(4)2023 Apr 10.
Article En | MEDLINE | ID: mdl-37109036

BACKGROUND: Non-unions after intramedullary nailing of femoral shaft fractures are a significant problem. Treatment options such as augmenting with plates or exchange nailing have been proposed. The ideal treatment remains controversial. METHODS: Augmentative plating using a 4.5 mm LCP or a 3.2 mm LCP leaving the nail in situ was tested biomechanically and compared to exchange intramedullary nailing in a SawboneTM model of a femoral shaft non-union. RESULTS: The difference of fracture gap motion in axial testing was small. In rotational testing, the exchange nail allowed for the largest amount of motion. The 4.5 mm augmentative plate was the most stable construct in all loading conditions. CONCLUSIONS: Augmentative plating using a 4.5 mm LCP plate while leaving the nail in situ is biomechanically superior to exchange intramedullary nailing. A small fragment 3.2 mm LCP is undersized and does not reduce fracture motion sufficiently in a femoral shaft non-union.

5.
Front Plant Sci ; 14: 1121570, 2023.
Article En | MEDLINE | ID: mdl-37077645

Pollen development, from unicellular microspores to anthesis, is a complex process involving the coordinated specification, differentiation and functions of different cell types. Key to understanding this development is identifying the genes expressed at precise stages of development. However, transcriptomic studies on pollen prior to anthesis are complicated by the inaccessible nature of pollen developing in the anther and the resistant pollen wall. To assist with understanding gene expression during pollen development we have developed a protocol to perform RNA-Seq on pollen isolated from a single anther (SA RNA-Seq). The protocol involves removing pollen from a single anther for analysis and viewing the remaining pollen to determine the developmental stage. The isolated pollen is chemically lysed and mRNA isolated from the lysate using an oligo-dT column before library preparation. Here, we report on the development and testing of our method and the generation of a transcriptome for three stages of pollen development from Arabidopsis (Arabidopsis thaliana) and two stages from male kiwifruit (Actinidia chinensis). This protocol enables the transcriptome of precise developmental stages of pollen to be analyzed, and uses a small number of plants, potentially facilitating studies that require a range of treatments or the analysis of the first generation of transgenic plants.

6.
PLoS One ; 18(3): e0281596, 2023.
Article En | MEDLINE | ID: mdl-36888681

As global awareness, science, and policy interventions for plastic escalate, institutions around the world are seeking preventative strategies. Central to this is the need for precise global time series of plastic pollution with which we can assess whether implemented policies are effective, but at present we lack these data. To address this need, we used previously published and new data on floating ocean plastics (n = 11,777 stations) to create a global time-series that estimates the average counts and mass of small plastics in the ocean surface layer from 1979 to 2019. Today's global abundance is estimated at approximately 82-358 trillion plastic particles weighing 1.1-4.9 million tonnes. We observed no clear detectable trend until 1990, a fluctuating but stagnant trend from then until 2005, and a rapid increase until the present. This observed acceleration of plastic densities in the world's oceans, also reported for beaches around the globe, demands urgent international policy interventions.


Smog , Water Pollutants, Chemical , Water Pollutants, Chemical/analysis , Plastics , Environmental Monitoring , Oceans and Seas , Waste Products/analysis
7.
Mol Ecol Resour ; 23(4): 771-786, 2023 May.
Article En | MEDLINE | ID: mdl-36598115

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.


DNA, Environmental , Porifera , Animals , DNA, Environmental/genetics , Ecosystem , DNA Barcoding, Taxonomic/methods , Environmental Monitoring/methods , Biodiversity , Vertebrates/genetics , Fishes/genetics , Water
8.
Sci Rep ; 12(1): 17489, 2022 10 19.
Article En | MEDLINE | ID: mdl-36261691

Prostate cancer (PCa) is a complex disease progressing from in situ to invasive or metastatic tumors while also being capable of modulating its androgen dependence. Understanding how novel therapies are working across the different stages of the disease is critical for their proper positioning in the spectrum of PCa treatments. The targeting of proprotein convertase PACE4 (Paired basic Amino Acid-Cleaving Enzyme 4) has been proposed as a novel approach to treat PCa. Animal studies performed on LNCaP xenografts, an androgen-dependent model, already yielded positive results. In this study, we tested PACE4 inhibition on JHU-LNCaP-SM, a newly described androgen-independent model, in cell-based and xenograft assays. Like LNCaP, JHU-LNCaP-SM cells express PACE4 and its oncogenic isoform PACE4-altCT. Using isoform-specific siRNAs, downregulation of PACE4-altCT resulted in JHU-LNCaP-SM growth inhibition. Furthermore, JHU-LNCaP-SM responded to the PACE4 pharmacological inhibitor known as C23 in cell-based assays as well as in athymic nude mice xenografts. These data support the efficacy of PACE4 inhibitors against androgen independent PCa thereby demonstrating that PACE4 is a key target in PCa. The JHU-LNCaP-SM cell line represents a model featuring important aspects of androgen-independent PCa, but it also represents a very convenient model as opposed to LNCaP cells for in vivo studies, as it allows rapid screening due to its high implantation rate and growth characteristics as xenografts.


Androgens , Prostatic Neoplasms , Mice , Animals , Male , Humans , Androgens/metabolism , Mice, Nude , Cell Line, Tumor , Prostatic Neoplasms/pathology , Proprotein Convertases/metabolism , Protein Isoforms , Amino Acids, Basic , Cell Proliferation , Receptors, Androgen
9.
Structure ; 30(11): 1518-1529.e5, 2022 11 03.
Article En | MEDLINE | ID: mdl-36108635

Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.


Intracellular Signaling Peptides and Proteins , Single-Domain Antibodies , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Protein Serine-Threonine Kinases/genetics , Single-Domain Antibodies/metabolism , Ubiquitin/metabolism , Ubiquitination
10.
Dev Dyn ; 251(11): 1880-1896, 2022 11.
Article En | MEDLINE | ID: mdl-35809036

BACKGROUND: Limb buds develop as bilateral outgrowths of the lateral plate mesoderm and are patterned along three axes. Current models of proximal to distal patterning of early amniote limb buds suggest that two signals, a distal organizing signal from the apical epithelial ridge (AER, Fgfs) and an opposing proximal (retinoic acid [RA]) act early on pattern this axis. RESULTS: Transcriptional analysis of stage 51 Xenopus laevis hindlimb buds sectioned along the proximal-distal axis showed that the distal region is distinct from the rest of the limb. Expression of capn8.3, a novel calpain, was located in cells immediately flanking the AER. The Wnt antagonist Dkk1 was AER-specific in Xenopus limbs. Two transcription factors, sall1 and zic5, were expressed in distal mesenchyme. Zic5 has no described association with limb development. We also describe expression of two proximal genes, gata5 and tnn, not previously associated with limb development. Differentially expressed genes were associated with Fgf, Wnt, and RA signaling as well as differential cell adhesion and proliferation. CONCLUSIONS: We identify new candidate genes for early proximodistal limb patterning. Our analysis of RA-regulated genes supports a role for transient RA gradients in early limb bud in proximal-to-distal patterning in this anamniote model organism.


Gene Expression Regulation, Developmental , Limb Buds , Animals , Limb Buds/metabolism , Xenopus laevis/genetics , Xenopus laevis/metabolism , Mesoderm/metabolism , Fibroblast Growth Factors/genetics , Fibroblast Growth Factors/metabolism , Tretinoin/metabolism , Extremities , Gene Expression , Ectoderm/metabolism , DNA-Binding Proteins/genetics , Nerve Tissue Proteins/genetics , Xenopus Proteins/genetics , Xenopus Proteins/metabolism
11.
Am J Perinatol ; 2022 Sep 16.
Article En | MEDLINE | ID: mdl-35863371

OBJECTIVE: Prostaglandins (PGs) use for cervical ripening with small for gestational age (SGA) fetuses is controversial since it remains uncertain if use increases the chance of cesarean delivery (CD). We aimed to assess the association between PG use for cervical ripening and mode of delivery between SGA and appropriate for gestational age (AGA) neonates. STUDY DESIGN: Secondary analysis of the Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-Be (nuMoM2b), a prospective observational cohort study of 10,038 nulliparas. We included women undergoing induction with nonanomalous fetuses in the cephalic presentation. Women with >2 cm cervical dilation or prior uterine scar were excluded. We assessed the association of PG use with CD among women with SGA and AGA neonates. SGA was defined as birth weight <10th percentile for gestational age and sex. Multivariable logistic regression was used to adjust for potential confounders and test for interaction. Secondary outcomes included adverse neonatal outcomes, indication for CD, maternal hemorrhage, and chorioamnionitis. RESULTS: Among 2,353 women eligible, PGs were used in 54.8%, SGA occurred in 15.1%, and 35.0% had CD. The association between PG use and CD differed significantly (interaction p = 0.018) for SGA versus AGA neonates; CD occurred more often in SGA neonates exposed to PGs than not (35 vs. 22%, p = 0.009). PG use was not associated with CD among AGA neonates (36 vs. 36%, p = 0.8). This effect remained significant when adjusting for body mass index, race/ethnicity, and cervical dilation. Among SGA neonates, CD for "nonreassuring fetal status" was similar between PG groups. Among SGA neonates, PG use was not associated with adverse neonatal outcomes or postpartum hemorrhage but had a higher rate of chorioamnionitis (7.0 vs. 2.1%, p = 0.048). CONCLUSION: PG use was associated with a higher rate of CD in SGA but not AGA neonates; however, further studies are needed before PG use is discouraged with SGA neonates. KEY POINTS: · PGs are commonly used for cervical ripening.. · PG use was associated with increased risk of cesarean delivery in SGA neonates.. · PG use was not associated with adverse neonatal outcomes..

12.
Sci Transl Med ; 14(644): eabn3971, 2022 05 11.
Article En | MEDLINE | ID: mdl-35544593

Screening with digital breast tomosynthesis (DBT) improves breast cancer detection and reduces false positives. However, currently, no breast cancer risk model takes advantage of the additional information generated by DBT imaging for breast cancer risk prediction. We developed and internally validated a DBT-based short-term risk model for predicting future late-stage and interval breast cancers after negative screening exams. We included the available 805 incident breast cancers and a random sample of 5173 healthy women matched on year of study entry in a nested case-control study from 154,200 multiethnic women, aged 35 to 74, attending DBT screening in the United States between 2014 and 2019. A relative risk model was trained using elastic net logistic regression and nested cross-validation to estimate risks for using imaging features and age. An absolute risk model was developed using derived risks and U.S. incidence and competing mortality rates. Absolute risks, discrimination performance, and risk stratification were estimated in the left-out validation set. The discrimination performance of 1-year risk was 0.82 (95% CI, 0.79 to 0.85) with good calibration (P = 0.7). Using the U.S. Preventive Service Task Force guidelines, 14% of the women were at high risk, 19.6 times higher compared to general risk. In this high-risk group, 76% of stage II and III cancers and 59% of stage 0 cancers were observed (P < 0.01). Using mammographic features generated from DBT screens, our image-based risk prediction model could guide radiologists in selecting women for clinical care, potentially leading to earlier detection and improved prognoses.


Breast Neoplasms , Breast/diagnostic imaging , Breast Neoplasms/diagnostic imaging , Case-Control Studies , Early Detection of Cancer/methods , Female , Humans , Mammography/methods , Sensitivity and Specificity
13.
Alzheimers Dement (N Y) ; 8(1): e12222, 2022.
Article En | MEDLINE | ID: mdl-35505899

Introduction: Ethnicity influences dementia etiology, prognosis, and treatment, while culture shapes help-seeking and care. Despite increasing population diversity in high-income settlement countries, ethnic minorities remain underrepresented in dementia research. We investigated approaches to enhance the recruitment, and consistent collection and analysis of variables relevant to, ethnic minorities in dementia studies to make recommendations for consistent practice in dementia research. Methods: We did a scoping review, searching Embase, PsycINFO, Medline, CENTRAL, and CINAHL between January 1, 2010 and January 7, 2020. Dementia clinical and cohort studies that actively recruited ethnic minorities in high-income countries were included. A steering group of experts developed criteria through which high-quality studies were identified. Results: Sixty-six articles were retrieved (51 observational; 15 experimental). Use of interpreters and translators (n = 17) was the most common method to facilitate participant recruitment. Race and ethnicity (n = 59) were the most common variables collected, followed by information on native language (n = 14), country of birth (n = 9), and length of time in country of settlement (n = 8). Thirty-three studies translated or used a culturally validated instrument. Twenty-three articles conducted subgroup analyses based on ethnicity. Six high-quality studies facilitated inclusion through community engagement, collected information on multiple aspects of ethnic diversity, and adjusted/substratified to analyze the impact of ethnicity on dementia. Discussion: We make recommendations for consistent recruitment, collection, and reporting of variables relating to ethnic and cultural diversity in dementia research.

14.
Sci Rep ; 12(1): 6066, 2022 04 11.
Article En | MEDLINE | ID: mdl-35410344

The proprotein convertase PACE4 has demonstrated value as a viable therapeutic target in prostate cancer (PCa). A novel isoform named PACE4-altCT, which arises in neoplastic lesions, plays an important role in tumor progression and has been validated as a pharmacological target. With the discovery of its overexpression in PCa and the alternative splicing of its pre-RNA to generate an oncogenic C-terminally modified isoform named PACE4-altCT, understanding and validating its value as a potential biomarker is of great interest either from prognostic or targeted therapy intervention. Expression of ERG in LNCaP cells was used to investigate the relationship between ERG expression occurring in PCa cells and PACE4-altCT expression by Western blot and qPCR. Using immunohistochemistry, the expression levels of PACE4 isoforms in patient tissues were investigated and correlated with ERG tumor status and Gleason score. An ELISA method was developed using affinity purified recombinant protein and used for quantitative analysis of plasma concentrations of PACE4-altCT and used for correlation. In contrast with the consensual isoform, PACE4-altCT was only strongly overexpressed in prostate cancer patients, correlated with ERG expression levels. Despite its intracellular retention PACE4-altCT could be detected in the plasma of most patients with prostate cancer, whereas it was only found at low levels in normal patients whereas total plasmatic PACE4 levels did not vary significantly between groups. Our study demonstrates that PACE4-altCT is strongly overexpressed in prostate cancer using both immunohistochemical and ELISA techniques and may have some interesting potential as a biomarker.


Proprotein Convertases/metabolism , Prostatic Neoplasms , Serine Endopeptidases/metabolism , Biomarkers , Cell Line, Tumor , Humans , Male , Prostatic Neoplasms/diagnosis , Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Protein Isoforms/genetics
15.
Viruses ; 14(2)2022 02 10.
Article En | MEDLINE | ID: mdl-35215963

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has wreaked havoc across the globe for the last two years. More than 300 million cases and over 5 million deaths later, we continue battling the first real pandemic of the 21st century. SARS-CoV-2 spread quickly, reaching most countries within the first half of 2020, and New Zealand was not an exception. Here, we describe the first isolation and characterization of SARS-CoV-2 variants during the initial virus outbreak in New Zealand. Patient-derived nasopharyngeal samples were used to inoculate Vero cells and, three to four days later, a cytopathic effect was observed in seven viral cultures. Viral growth kinetics was characterized using Vero and VeroE6/TMPRSS2 cells. The identity of the viruses was verified by RT-qPCR, Western blot, indirect immunofluorescence assays, and electron microscopy. Whole-genome sequences were analyzed using two different yet complementary deep sequencing platforms (MiSeq/Illumina and Ion PGM™/Ion Torrent™), classifying the viruses as SARS-CoV-2 B.55, B.31, B.1, or B.1.369 based on the Pango Lineage nomenclature. All seven SARS-CoV-2 isolates were susceptible to remdesivir (EC50 values from 0.83 to 2.42 µM) and ß-D-N4-hydroxycytidine (molnupiravir, EC50 values from 0.96 to 1.15 µM) but not to favipiravir (>10 µM). Interestingly, four SARS-CoV-2 isolates, carrying the D614G substitution originally associated with increased transmissibility, were more susceptible (2.4-fold) to a commercial monoclonal antibody targeting the spike glycoprotein than the wild-type viruses. Altogether, this seminal work allowed for early access to SARS-CoV-2 isolates in New Zealand, paving the way for numerous clinical and scientific research projects in the country, including the development and validation of diagnostic assays, antiviral strategies, and a national COVID-19 vaccine development program.


COVID-19/epidemiology , Genome, Viral , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Adolescent , Adult , Aged , Animals , Antibodies, Monoclonal/pharmacology , Antiviral Agents , Chlorocebus aethiops , Cohort Studies , Cytopathogenic Effect, Viral , Humans , Middle Aged , New Zealand/epidemiology , SARS-CoV-2/drug effects , SARS-CoV-2/immunology , Vero Cells , Whole Genome Sequencing , Young Adult
16.
Methods Mol Biol ; 2458: 47-62, 2022.
Article En | MEDLINE | ID: mdl-35103961

Bisulfite sequencing is the "gold-standard" technique for DNA methylation analysis. By combining bisulfite sequencing with high-throughput, next-generation sequencing technology, we can document methylation from many thousands of individual reads (equivalent to alleles or "cells"), for multiple target regions and from many samples simultaneously. Here, we describe a next-generation bisulfite-sequencing assay for targeted DNA methylation analysis which offers scope for the simultaneous interrogation of multiple genomic loci across numerous samples.


DNA Methylation , Sulfites , High-Throughput Nucleotide Sequencing/methods , Sequence Analysis, DNA/methods
17.
Methods Mol Biol ; 2458: 301-320, 2022.
Article En | MEDLINE | ID: mdl-35103974

The three-dimensional structure of the genome is highly organized and is an important aspect of gene regulation. Chromatin interactions can be identified using chromosome conformation capture-based techniques, which rely on proximity ligation. Of these techniques, circular chromosome conformation capture sequencing (4C-seq) is used to identify all chromatin interactions occurring with a single chromosomal location (one versus all). Here we describe a 4C-seq protocol that has been optimized for primary adherent cells, for which the first digestion step is inefficient using standard 4C-seq protocols. It can, however, also be applied to other cell or tissue types. This protocol utilizes a standard DNA library preparation method using a commercial kit, and includes a description of the data processing steps.


Chromosomes , High-Throughput Nucleotide Sequencing , Chromatin/genetics , Chromosomes/genetics , Genome , High-Throughput Nucleotide Sequencing/methods , Nucleic Acid Conformation , Sequence Analysis, DNA/methods
18.
J Matern Fetal Neonatal Med ; 35(25): 8462-8471, 2022 Dec.
Article En | MEDLINE | ID: mdl-34582307

BACKGROUND: While neonates with birth weight <10th percentile are at increased risk of morbidity and mortality, most of these are constitutionally small and not at increased risk. There are no current strategies that reliably distinguish constitutionally small neonates from small neonates at the highest risk of morbidity, so additional tools for risk stratification are needed. OBJECTIVE: Our objectives were to identify factors that are independently associated with perinatal morbidity among neonates with birth weight <10th percentile (small for gestational age, SGA) and to create predictive models of perinatal morbidity among SGA neonates based on the timing of information availability. STUDY DESIGN: This secondary analysis of the Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-Be, was a nested case-control study. Participants were prospectively enrolled at eight U.S. centers, with data collection occurring at three standard time points during pregnancy and again after delivery. Our analysis included neonates with birth weights <10th percentile and excluded those with major congenital malformations or suspected or confirmed aneuploidy. The primary outcome was a composite of perinatal morbidity, defined as NICU admission >48 h, NEC, sepsis, RDS, mechanical ventilation, retinopathy of prematurity, seizures, grade 3 or 4 IVH, stillbirth, or death before discharge. Cases were SGA neonates that experienced the primary outcome, and controls were SGA neonates that did not. Maternal factors for potential inclusion in predictive modeling were drawn from a broad list of variables collected as part of the NuMoM2B study, including demographic, anthropometric, clinical, ultrasound, social/behavioral, dietary, and psychological variables. Characteristics that were different in bivariate analysis between cases and controls then underwent further evaluation and refinement. Continuous and multi-category variables were assessed using multiple approaches, including as continuous variables, using standard categories (such as for BMI) as well as empirically-derived cut-points identified by receiver-operating characteristics methodology. The approach for each variable that resulted in the best performance was selected for use in modeling. After variable optimization, multivariable analysis was used to derive prediction models using factors known at mid-pregnancy (Model 1) and delivery (Model 2). RESULTS: Of the original cohort, 865 were eligible and analyzed, with 134 (15.5%) experiencing the primary outcome. After bivariable and multivariable analysis, these variables were included in Model 1: BMI, stress level, diastolic blood pressure, narcotic use (all in 1st trimester), and uterine artery pulsatility index at 16-21 weeks. Model 2 added the following variables to Model 1: preterm delivery, preeclampsia, and suspected fetal growth restriction. When models 1 and 2 were empirically tested and compared to predicted performance to demonstrate calibration, observed morbidity rates approximately followed expected rates within deciles. Models 1 and 2 had respective areas under the receiver-operating characteristic curve of 0.72 (95% CI 0.67-0.76) and 0.84 (0.80-0.88), to predict the composite morbidity. CONCLUSION: Using a deeply phenotyped cohort of nulliparous women, we created two models with the moderate-good prediction of perinatal morbidity among SGA neonates. TRIAL REGISTRATION: clinicaltrials.gov ID: NCT01322529.


Infant, Small for Gestational Age , Ultrasonography, Prenatal , Pregnancy , Infant, Newborn , Infant , Female , Humans , Birth Weight , Gestational Age , Pregnancy Trimester, Third , Case-Control Studies , Fetal Growth Retardation
19.
OTA Int ; 4(4): e152, 2021 Dec.
Article En | MEDLINE | ID: mdl-34765902

OBJECTIVES: To investigate the mechanical properties of cephalomedullary nailing of intertrochanteric OTA/AO 31-A3.1 (reverse oblique) fractures and to test the hypothesis that anatomical reduction and augmentation with cerclage wire produces a more stable construct. METHODS: A standardized fracture model in composite saw bone was created to stimulate an intertrochaneric 31-A3.1 fracture, using a 3D printed cutting guide. Simulated osteosynthesis was performed with 12 femurs divided into anatomically reduced and varus malreduced groups. Each femur was tested with and without cerclage wire augmentation. All femurs were fixed with a 215 mm, 130 degree, 11.5 mm nail. An Instron 8874 biaxial materials testing machine was used to assess the axial stiffness. Cyclic loading consisted of 5000 cycles of sinusoidal combined axial-torsion loading at 3 Hz. Axial load was 100 N to 2000 N and torsion -4.5 Nm to +4.5 Nm. Stiffness was measured before and after cyclic loading. RESULTS: Reduced constructs were stiffer than residual varus constructs. The mean overall fracture stiffness was 508.7 N/mm for reduced constructs and 379.2 N/mm for varus constructs. Removing the cables significantly decreased the fracture stiffness for both constructs (mean difference 60.0 N/mm, 95% CI 7.7-112.3, P = .032). CONCLUSIONS: Anatomical reduction has a dominant effect on facture stiffness. Anatomically reduced fractures are stiffer than varus malreduced fractures. A cerclage wire further improves construct stiffness if anatomical reduction is achieved. Cerclage wiring is less effective if anatomical reduction is not achieved.

20.
Viruses ; 13(11)2021 11 04.
Article En | MEDLINE | ID: mdl-34835031

It has been 20 months since we first heard of SARS-CoV-2, the novel coronavirus detected in the Hubei province, China, in December 2019, responsible for the ongoing COVID-19 pandemic. Since then, a myriad of studies aimed at understanding and controlling SARS-CoV-2 have been published at a pace that has outshined the original effort to combat HIV during the beginning of the AIDS epidemic. This massive response started by developing strategies to not only diagnose individual SARS-CoV-2 infections but to monitor the transmission, evolution, and global spread of this new virus. We currently have hundreds of commercial diagnostic tests; however, that was not the case in early 2020, when just a handful of protocols were available, and few whole-genome SARS-CoV-2 sequences had been described. It was mid-January 2020 when several District Health Boards across New Zealand started planning the implementation of diagnostic testing for this emerging virus. Here, we describe our experience implementing a molecular test to detect SARS-CoV-2 infection, adapting the RT-qPCR assay to be used in a random-access platform (Hologic Panther Fusion® System) in a clinical laboratory, and characterizing the first whole-genome SARS-CoV-2 sequences obtained in the South Island, right at the beginning of the SARS-CoV-2 outbreak in New Zealand. We expect that this work will help us and others prepare for the unequivocal risk of similar viral outbreaks in the future.


COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/virology , Female , Genome, Viral , Humans , Male , New Zealand/epidemiology , Phylogeny , Reproducibility of Results , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Whole Genome Sequencing
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