Simultaneous sequencing of genetic and epigenetic bases in DNA.

DNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Methods widely used to detect epigenetic DNA bases fail to capture common C-to-T mutations or distinguish 5-methylcytosine from 5-hydroxymethylcytosine. We present a single base-resolution sequencing methodology that sequences complete genetics and the two most common cytosine modifications in a single workflow. DNA is copied and bases are enzymatically converted. Coupled decoding of bases across the original and copy strand provides a phased digital readout. Methods are demonstrated on human genomic DNA and cell-free DNA from a blood sample of a patient with cancer. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. Simultaneous, phased reading of genetic and epigenetic bases provides a more complete picture of the information stored in genomes and has applications throughout biomedicine.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment.

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

Cutaneous Ewing Sarcoma Presenting as a Second Primary Malignancy in a Child.

Ewing sarcoma is an EWS-ETS family member-driven malignancy that most commonly arises from bone. Cutaneous Ewing sarcoma is a rare variant which harbors an EWS-ETS family fusion but demonstrates an immunohistochemical staining pattern distinct from classic Ewing tumors. EWSR1 fluorescence in situ hybridization testing interpretation can be challenging in the setting of cutaneous Ewing sarcoma, making an integrated histologic and sequencing approach key for an accurate diagnosis. Here, we report a pediatric patient with a history of neuroblastoma treated with surgery only that developed a cutaneous nodule and was diagnosed with cutaneous Ewing sarcoma as a second primary cancer.

African American polycystic kidney patients receive higher risk kidneys, but do not face increased risk for graft failure or post-transplant mortality.

African Americans (AA) are disproportionately affected by end-stage renal disease (ESRD) and have worse outcomes following renal transplantation. Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic condition leading to ESRD necessitating transplant. We explored this population with respect to race by conducting a retrospective analysis of the UNOS database between 2005 and 2019. Our study included 10,842 (AA n = 1661; non-AA n = 9181) transplant recipients whose primary diagnosis was ADPKD. We further stratified the AA ADPKD population with respect to blood groups (AA blood type B n = 295 vs AA non-B blood type n = 1366), and also compared this cohort to AAs with a diagnosis of DM (n = 16,706) to identify unique trends in the ADPKD population. We analyzed recipient and donor characteristics, generated survival curves, and conducted multivariate analyses. African American ADPKD patients waited longer for transplants (924 days vs 747 days P < .001), and were more likely to be on dialysis (76% vs 62%; p < .001). This same group was also more likely to have AA donors (21% vs 9%; p < .001) and marginally higher KDPI kidneys (0.48 vs 0.45; p < .001). AA race was a risk factor for delayed graft function (DGF), increasing the chance of DGF by 45% (OR 1.45 95% CI 1.26-1.67; p < .001). AA race was not associated with graft failure (HR 1.10 95% CI 0.95-1.28; p = .21) or patient mortality (HR 0.84 95% CI 0.69-1.03; p = .09). Racial disparities exist in the ADPKD population. They should be continually studied and addressed to improve transplant equity.

Pan-Cancer Landscape Analysis Reveals Recurrent KMT2A-MAML2 Gene Fusion in Aggressive Histologic Subtypes of Thymoma.

PURPOSE: Thymomas are epithelial neoplasms that represent the most common thymic tumors in adults. These tumors have been shown to harbor a relatively low mutational burden. As a result, there is a lack of genetic alterations that may be used prognostically or targeted therapeutically for this disease. Here, we describe a recurrent gene rearrangement in type B2 + B3 thymomas. PATIENTS AND METHODS: A single index case of thymoma was evaluated by an RNA-based solid fusion assay. Separately, tissues from 255,008 unique advanced cancers, including 242 thymomas, were sequenced by hybrid capture-based next-generation DNA sequencing/comprehensive genomic profiling of 186 to 406 genes, including lysine methyltransferase 2A (KMT2A) rearrangements, and a portion were evaluated for RNA of 265 genes. We characterized molecular and clinicopathologic features of the pertinent fusion-positive patient cases. RESULTS: We identified 11 patients with thymomas harboring a gene fusion of KMT2A and mastermind-like transcriptional coactivator 2 (MAML2). Fusion breakpoints were identified between exon 8, 9, 10, or 11 of KMT2A and exon 2 of MAML2. Fifty-five percent were men, with a median age of 48 years at surgery (range, 29-69 years). Concurrent genomic alterations were infrequent. The 11 thymomas were of B2 or B3 type histology, with 1 case showing foci of thymic carcinoma. The frequency of KMT2A-MAML2 fusion was 4% of all thymomas (10 of 242) and 6% of thymomas of B2 or B3 histology (10 of 169). CONCLUSION: KMT2A-MAML2 represents the first recurrent fusion described in type B thymoma. The fusion seems to be specific to type B2 and B3 thymomas, the most aggressive histologic subtypes. The identification of this fusion offers insights into the biology of thymoma and may have clinical relevance for patients with disease refractory to conventional therapeutic modalities.

Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California.

Thermus species are widespread in natural and artificial thermal environments. Two new yellow-pigmented strains, L198T and L423, isolated from Little Hot Creek, a geothermal spring in eastern California, were identified as novel organisms belonging to the genus Thermus. Cells are Gram-negative, rod-shaped, and non-motile. Growth was observed at temperatures from 45 to 75 °C and at salinities of 0-2.0% added NaCl. Both strains grow heterotrophically or chemolithotrophically by oxidation of thiosulfate to sulfate. L198T and L423 grow by aerobic respiration or anaerobic respiration with arsenate as the terminal electron acceptor. Values for 16S rRNA gene identity (≤ 97.01%), digital DNA-DNA hybridization (≤ 32.7%), OrthoANI (≤ 87.5%), and genome-to-genome distance (0.13) values to all Thermus genomes were less than established criteria for microbial species. The predominant respiratory quinone was menaquinone-8 and the major cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. One unidentified phospholipid (PL1) and one unidentified glycolipid (GL1) dominated the polar lipid pattern. The new strains could be differentiated from related taxa by ß-galactosidase and ß-glucosidase activity and the presence of hydroxy fatty acids. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic evidence, the novel species Thermus sediminis sp. nov. is proposed, with the type strain L198T (= CGMCC 1.13590T = KCTC XXX).

Reliability of Casting Indices Among Members of an Orthopaedic Surgery Residency.

BACKGROUND: Multiple casting indices have been described to evaluate the adequacy of cast placement in pediatric distal forearm fractures. The aim of this study was to determine the intrarater and interrater reliability of the measurements of 5 common casting indices among members of an orthopaedic surgery residency program. The cast index, 3-point index, gap index, padding index, and Canterbury index were evaluated. METHODS: This was a single-center prospective cohort reliability study that included 12 members of an orthopaedic surgery residency. Participants were placed into 1 of 4 groups by level of training: physician assistants, junior residents, senior residents, and attending orthopaedic surgeons. Twelve radiographs of casted pediatric distal forearm fractures were measured by each participant on 2 separate occasions. Statistical analysis using the intraclass correlation coefficient was used to determine the intrarater and interrater reliability. RESULTS: The cast index was the only casting index to meet our criteria for good intrarater and interrater reliability. CONCLUSION: Continued use of the cast index as a tool to assess pediatric distal forearm cast application is supported by this study. LEVEL OF EVIDENCE: Level 2.

Inter- and intraobserver reliability in the radiographic evaluation of adult flatfoot deformity.

BACKGROUND: Adult acquired flatfoot is a complex deformity with numerous radiographic measurements described to define it. The purpose of this study was to evaluate the inter- and intraobserver reliability of six radiographic measurements using digital and conventional radiographs. MATERIALS AND METHODS: Three digital weightbearing radiographs consisting of anteroposterior, lateral, and hindfoot alignment views were obtained at presentation for 20 consecutive patients. Six radiographic measurements were made for each patient: talus/second metatarsal angle, calcaneal pitch angle, talus/first metatarsal angle, medial cuneiform/fifth metatarsal distance, tibial/calcaneal displacement, and calcaneal angulation. Each radiograph was evaluated on multiple occasions by a senior orthopaedic surgery resident, a junior orthopaedic surgery resident, and a third-year medical student. Inter- and intraobserver reliability was determined using measurements made on digital radiographs. RESULTS: Interobserver reliabilities were 0.830 for talus/second metatarsal angle, 0.948 for calcaneal pitch angle, 0.781 for talus/first metatarsal angle, 0.991 for medial cuneiform/fifth metatarsal distance, 0.870 for tibial/calcaneal displacement, and 0.834 for calcaneal angulation. Interobserver reliability was similar for digital and conventional radiographs, and intraobserver reliability increased with observer experience. CONCLUSION: Adult acquired flatfoot deformity is a complex condition that is difficult to quantify radiographically. The medial cuneiform/fifth metatarsal distance and the calcaneal pitch angle were found to have the highest interobserver reliability. Intraobserver reliability increased with observer experience.

Design of a Real Time FPGA-based Three Dimensional Positioning Algorithm.

We report on the implementation and hardware platform of a real time Statistics-Based Processing (SBP) method with depth of interaction processing for continuous miniature crystal element (cMiCE) detectors using a sensor on the entrance surface design. Our group previously reported on a Field Programmable Gate Array (FPGA) SBP implementation that provided a two dimensional (2D) solution of the detector's intrinsic spatial resolution. This new implementation extends that work to take advantage of three dimensional (3D) look up tables to provide a 3D positioning solution that improves intrinsic spatial resolution. Resolution is most improved along the edges of the crystal, an area where the 2D algorithm's performance suffers. The algorithm allows an intrinsic spatial resolution of ~0.90 mm FWHM in X and Y and a resolution of ~1.90 mm FWHM in Z (i.e., the depth of the crystal) based upon DETECT2000 simulation results that include the effects of Compton scatter in the crystal. A pipelined FPGA implementation is able to process events in excess of 220k events per second, which is greater than the maximum expected coincidence rate for an individual detector. In contrast to all detectors being processed at a centralized host, as in the current system, a separate FPGA is available at each detector, thus dividing the computational load. A prototype design has been implemented and tested using a reduced word size due to memory limitations of our commercial prototyping board.

Gene expression profiling of porokeratosis demonstrates similarities with psoriasis.

BACKGROUND: Porokeratosis (PK) is a clinically heterogeneous entity associated with sharply demarcated, annular, or serpiginous lesions with a hyperkeratotic ridge. This disorder is associated with aberrant keratinocyte differentiation that histologically manifests as a stack of parakeratin termed the cornoid lamella; this structure represents the peripheral hyperkeratotic ridge of clinical lesions. Histologically, the keratinocytes forming the cornoid lamella demonstrate an altered differentiation program. However, the molecular basis of PK remains incompletely understood. METHODS: As a first step in characterizing PK at the molecular level, gene expression profiling was performed on a cornoid lamella isolated from a large, Mibelli-type porokeratotic lesion. As a control, gene expression profiling of peripheral uninvolved epidermis was also performed. The gene expression profile of cornoid lamellar keratinocytes was compared with similar profiles obtained from a psoriatic plaque and cutaneous squamous cell carcinoma. RESULTS: Our study demonstrates a striking similarity between the gene expression profiles of PK and psoriasis. In addition, novel markers of the porokeratotic keratinocytes were identified, including keratin 16, S-100 A8 and A9, and connexin 26. CONCLUSIONS: This study supports the hypothesis that PK is a disorder of hyperproliferative keratinocytes exhibiting similarity at the molecular level to psoriasis. Consequently, some therapeutic modalities efficacious for psoriasis may be of benefit in PK.