High-resolution Sequence Research Articles

Association Analysis Between Intratumoral and Peritumoral MRI Radiomics Features and Overall Survival of Neoadjuvant Therapy in Rectal Cancer.

The use of peritumoral features to determine the survival time of patients with rectal cancer (RC) is still imprecise. To explore the correlation between intratumoral, peritumoral and combined features, and overall survival (OS). Retrospective. One hundred sixty-six RC patients (53 women, 113 men; average age: 55 ± 12 years) who underwent radical resection after neoadjuvant therapy. 3 T; T2WI sagittal, T1WI axial, T2WI axial with fat suppression, and high-resolution T2WI axial sequences, enhanced T1WI axial and sagittal sequences with fat suppression. Radiologist A segmented 166 patients, and radiologist B randomly segmented 30 patients. Intratumoral and peritumoral features were extracted, and features with good stability (ICC ≥0.75) were retained through intra-observer analysis. Seven classifiers, including Logistic Regression (LR), Support Vector Machine (SVM), K-Nearest Neighbors (KNN), Random Forest (RF), Extremely randomized trees (ET), eXtreme Gradient Boosting (XGBoost), and LightGBM (LGBM), were applied to select the classifier with the best performance. Next, the Rad-score of best classifier and the clinical features were selected to establish the models, thus, nomogram was built to identify the association with 1-, 3-, and 5-year OS. LASSO, regression analysis, ROC, DeLong method, Kaplan-Meier curve. P < 0.05 indicated a significant difference. Only Node (irregular tumor nodules in the surrounding mesentery) and ExtraMRF (lymph nodes outside the perirectal mesentery) were significantly different in 20 clinical features. Twelve intratumoral, 3 peritumoral, and 14 combined features related to OS were selected. LR, SVM, and RF classier showed the best efficacy in the intratumoral, peritumoral, and combined model, respectively. The combined model (AUC = 0.954 and 0.821) had better survival association than the intratumoral model (AUC = 0.833 and 0.813) and the peritumoral model (AUC = 0.824 and 0.687). The proposed peritumoral model with radiomics features may serve as a tool to improve estimated survival time. 3 TECHNICAL EFFICACY: Stage 4.

Fast and High-Resolution T2 Mapping Based on Echo Merging Plus k-t Undersampling with Reduced Refocusing Flip Angles (TEMPURA) as Methods for Human Renal MRI.

To develop a highly accelerated multi-echo spin-echo method, TEMPURA, for reducing the acquisition time and/or increasing spatial resolution for kidney T2 mapping. TEMPURA merges several adjacent echoes into one k-space by either combining independent echoes or sharing one echo between k-spaces. The combined k-space is reconstructed based on compressed sensing theory. Reduced flip angles are used for the refocusing pulses, and the extended phase graph algorithm is used to correct the effects of indirect echoes. Two sequences were developed: a fast breath-hold sequence; and a high-resolution sequence. The performance was evaluated prospectively on a phantom, 16 healthy subjects, and two patients with different types of renal tumors. The fast TEMPURA method reduced the acquisition time from 3-5 min to one breath-hold (18 s). Phantom measurements showed that fast TEMPURA had a mean absolute percentage error (MAPE) of 8.2%, which was comparable to a standardized respiratory-triggered sequence (7.4%), but much lower than a sequence accelerated by purely k-t undersampling (21.8%). High-resolution TEMPURA reduced the in-plane voxel size from 3 × 3 to 1 × 1 mm2, resulting in improved visualization of the detailed anatomical structure. In vivo T2 measurements demonstrated good agreement (fast: MAPE = 1.3%-2.5%; high-resolution: MAPE = 2.8%-3.3%) and high correlation coefficients (fast: R = 0.85-0.98; high-resolution: 0.82-0.96) with the standardized method, outperforming k-t undersampling alone (MAPE = 3.3-4.5%, R = 0.57-0.59). TEMPURA provides fast and high-resolution renal T2 measurements. It has the potential to improve clinical throughput and delineate intratumoral heterogeneity and tissue habitats at unprecedented spatial resolution.

MR-Neurography of the facial nerve in parotid tumors: intra-parotid nerve visualization and surgical correlation.

One of the most severe complications in surgery of parotid tumors is facial palsy. Imaging of the intra-parotid facial nerve is challenging due to small dimensions. Our aim was to assess, in patients with parotid tumors, the ability of high-resolution 3D double-echo steady-state sequence with water excitation (DE3D-WE) (1) to visualize the extracranial facial nerve and its tracts, (2) to evaluate their relationship to the parotid lesion and (3) to compare MRI and surgical findings. A retrospective study was conducted including all patients with parotid tumors, who underwent MRI from April 2022 to December 2023.Two radiologists independently reviewed DE3D-WE images, assessing quality of visualization of the facial nerve bilaterally and localizing the nerve's divisions in relation to the tumor. MRI data were compared with surgical findings. Forty consecutive patients were included (M:F = 22:18; mean age 56.3 ± 17.4years). DE3D-WE could excellently visualize the nerve main trunk and the temporofacial division in all cases. The cervicofacial branch was visible in 99% of cases and visibility was good. Distal divisions were displayed in 34% of cases with a higher visibility on the tumor side (p < 0.05). Interrater agreement was high (weighted kappa 0.94 ± 0.01 [95% CI 0.92-0.97]). Compared to surgery accuracy of MRI in localizing the nerve was 100% for the main trunk, 96% for the temporofacial and 89% for the cervicofacial branches. Facial nerve MR-neurography represents a reliable tool. DE3D-WE can play an important role in surgical planning of patients with parotid tumors, reducing the risk of nerve injury.

Prevalence of Anterior Inferior Cerebellar Artery Vascular Loop in Cerebellopontine Angle With Three-Dimensional Constructive Interference in Steady State (CISS) Sequence MRI.

Background The cerebellopontine angle (CPA) cistern houses vital neurovascular structures such as cranial nerves V, VII, and VIII and the anterior inferior cerebellar artery (AICA), often leading to neurovascular compression syndromes due to its complex anatomy. Although vascular compression is a recognized cause of certain neuralgias, its association with otologic symptoms such as tinnitus, hearing loss, and dizziness remains uncertain. Hence, this study aims to determine the prevalence of the AICA vascular loop in the CPA cistern on MRI in patients with asymptomatic audiovestibular symptoms. Methodology Adult patients who underwent MRI, including the posterior fossa's high-resolution volumetric T2 sequence (three-dimensional constructive interference in steady state (3D-CISS)), were assessed. Patients with a history of audiovestibular symptoms (tinnitus/dizziness/vertigo/sensorineural hearing loss), intracranial tumor, vascular lesions, intracranial surgery, brain radiation therapy, traumatic brain injury, poor image quality, and MRI scans without 3D-CISS sequences were excluded. Two radiologists independently reviewed 114 (228 sides) MRI studies for the vascular loop of AICA in the CPA cistern and the extension of the AICA loop into the ipsilateral internal acoustic meatus which was graded by Chavda's classification. Results The prevalence of vascular loop of AICA in the CPA cistern was as high as 47.6% in asymptomatic patients. Grade I Chavda vascular loop was the most common type followed by type II, with type III being the least common type. Conclusions Knowledge regarding the high prevalence of the AICA loop in the asymptomatic population and the lack of significant correlation between the presence of the AICA loop and otovestibular symptoms should be considered in preoperative planning for decompression procedures.

Sulcal Morphometry Predicts Mild Cognitive Impairment Conversion to Alzheimer's Disease.

Being able to differentiate mild cognitive impairment (MCI) patients who would eventually convert (MCIc) to Alzheimer's disease (AD) from those who would not (MCInc) is a key challenge for prognosis. This study aimed to investigate the ability of sulcal morphometry to predict MCI progression to AD, dedicating special attention to an accurate identification of sulci. Twenty-five AD patients, thirty-seven MCI and twenty-five healthy controls (HC) underwent a brain-MR protocol (1.5T scanner) including a high-resolution T1-weighted sequence. MCI patients underwent a neuropsychological assessment at baseline and were clinically re-evaluated after a mean of 2.3 years. At follow-up, 12 MCI were classified as MCInc and 25 as MCIc. Sulcal morphometry was investigated using the BrainVISA framework. Consistency of sulci across subjects was ensured by visual inspection and manual correction of the automatic labelling in each subject. Sulcal surface, depth, length, and width were retrieved from 106 sulci. Features were compared across groups and their classification accuracy in predicting MCI conversion was tested. Potential relationships between sulcal features and cognitive scores were explored using Spearman's correlation. The width of sulci in the temporo-occipital region strongly differentiated between each pair of groups. Comparing MCIc and MCInc, the width of several sulci in the bilateral temporo-occipital and left frontal areas was significantly altered. Higher width of frontal sulci was associated with worse performances in short-term verbal memory and phonemic fluency. Sulcal morphometry emerged as a strong tool for differentiating HC, MCI, and AD, demonstrating its potential prognostic value for the MCI population.

Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters

Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unravel the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA reveals co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity uncovers that head-to-head interactions between replication and transcription machinery result in 60% DSB contribution to the head-on compared to 40% for co-directional. Taken together we reveal TTR as a fragile class and show how the linear interaction between transcription and replication impacts genome stability.

Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing.

The update of the draft genome assembly of sea urchin, Hemicentrotus pulcherrimus, which is widely studied in East Asia as a model organism of early development, was performed using Oxford nanopore long-read sequencing. The updated assembly provided ~600-Mb genome sequences divided into 2,163 contigs with N50 = 516 kb. BUSCO completeness score and transcriptome model mapping ratio (TMMR) of the present assembly were obtained as 96.5% and 77.8%, respectively. These results were more continuous with higher resolution than those by the previous version of H. pulcherrimus draft genome, HpulGenome_v1, where the number of scaffolds = 16,251 with a total of ~100 Mb, N50 = 143 kb, BUSCO completeness score = 86.1%, and TMMR = 55.4%. The obtained genome contained 36,055 gene models that were consistent with those in other echinoderms. Additionally, two tandem repeat sequences of early histone gene locus containing 47 copies and 34 copies of all histone genes, and 185 of the homologous sequences of the interspecifically conserved region of the Ars insulator, ArsInsC, were obtained. These results provide further advance for genome-wide research of development, gene regulation, and intranuclear structural dynamics of multicellular organisms using H. pulcherrimus.

Therapeutic effect and mechanism of Jingfang Granules on acute lung injury based on intestinal flora and fecal metabolomics

This study aims to elucidate the therapeutic effect and mechanism of Jingfang Granules on acute lung injury, and to investigate the regulatory effect of Jingfang Granules on the metabolic disorders of endogenous metabolites in feces and the homeostasis of intestinal microbiota in acute lung injury, mice were randomly divided into a sham group, a model group, and a Jingfang Granules group. After modeling, the mice were continuously administered for 6 days. Using ultra-high performance liquid chromatography quadrupole/electrostatic field orbital trap high-resolution mass spectrometry(UHPLC-HESI-QE-Orbitrap-MS/MS) metabolomics technology and 16S rRNA high-throughput sequencing technology, changes in endogenous small molecule substances and gut microbiota in mouse intestines were determined, and potential biomarkers were identified. The results showed that Jingfang Granules can regulate 11 biomarkers, including L-glutamic acid, succinic acid, arachidonic acid, linoleic acid, linolenic acid, phenylalanine, sphingosine, 2-hydroxy-2-methyl butyric acid, pyruvate, tryptophan, and palmitic acid. Metabolic pathway analysis was conducted on these 11 biomarkers using the online software MetaboAnalyst, identifying potential major metabolic pathways. Among them, a total of 10 metabolic pathways are closely related to the treatment of acute lung injury with Jingfang Granules, including alanine, aspartate and glutamate metabolism, aminoacyl-tRNA biosynthesis, citrate cycle(TCA cycle), alyoxylate and dicarboxylate metabolism, arginine and proline metabolism, linoleic acid metabolism and linolenic acid metabolism, nitrogen metabolism, D-glutamine and D-gluta-matemetabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism. The results of gut microbiota showed significant differences in bacteria, mainly including Bacteroides, Akkermansia, Lachnospiraceae＿NK4A136＿group, Lachnochlostridium, and Klebsiella. Spearman analysis confirms that Akkermansia and Lachnospiraceae＿NK4A136＿group is a significant positive correlation between the abundance of succinic acid, arachidonic acid, linolenic acid, linoleic acid, butyric acid, and pyruvate in the group; Bacteroides, Klebsiella, Lachnochlostrium are significantly positively correlated with the abundance of L-glutamic acid, phenylalanine, and sphingosine. The above results indicate that the therapeutic effect of Jingfang Granules on acute lung injury is achieved by improving the imbalance of gut microbiota in mice with acute lung injury, balancing the metabolism of alanine, biosynthesis of aminoacyl tRNA, aspartic acid, glutamate, tricarboxylic acid cycle, biosynthesis of phenylalanine, tyrosine, tryptophan, and metabolism of linoleic acid.

Ancient DNA and osteological analyses of a unique paleo-archive reveal Early Holocene faunal expansion into the Scandinavian Arctic.

Paleo-archives are essential for our understanding of species responses to climate warming, yet such archives are extremely rare in the Arctic. Here, we combine morphological analyses and bulk-bone metabarcoding to investigate a unique chronology of bone deposits sealed in the high-latitude Storsteinhola cave system (68°50' N 16°22' E) in Norway. This deposit dates to a period of climate warming from the end of the Late Glacial [~13 thousand calibrated years before the present (ka cal B.P.)] to the Holocene thermal maximum (~5.6 ka cal B.P.). Paleogenetic analyses allow us to exploit the 1000s of morphologically unidentifiable bone fragments resulting in a high-resolution sequence with 40 different taxa, including species not previously found here. Our record reveals borealization in both the marine and terrestrial environments above the Arctic Circle as a naturally recurring phenomenon in past periods of warming, providing fundamental insights into the ecosystem-wide responses that are ongoing today.

3D balanced SSFP UTE MRI for multiple contrasts whole brain imaging.

This study aimed to develop a new high-resolution MRI sequence for the imaging of the ultra-short transverse relaxation time (uT2) components in the brain, while simultaneously providing proton density (PD) contrast for reference and quantification. The sequence combines low flip angle balanced SSFP (bSSFP) and UTE techniques, together with a 3D dual-echo rosette k-space trajectory for readout. The expected image contrast was evaluated by simulations. A study cohort of six healthy volunteers and eight multiple sclerosis (MS) patients was recruited to test the proposed sequence. Subtraction between two TEs was performed to extract uT2 signals. In addition, conventional longitudinal relaxation time (T1) weighted, T2-weighted, and PD-weighted MRI sequences were also acquired for comparison. Typical PD-contrast was found in the second TE images, while uT2 signals were selectively captured in the first TE images. The subtraction images presented signals primarily originating from uT2 components, but only if the first TE is short enough. Lesions in the MS subjects showed hyperintense signals in the second TE images but were hypointense signals in the subtraction images. The lesions had significantly lower signal intensity in subtraction images than normal white matter (WM), which indicated a reduction of uT2 components likely associated with myelin. 3D isotropic sub-millimeter (0.94 mm) spatial resolution images were acquired with the novel bSSFP UTE sequence within 3 min. It provided easy extraction of uT2 signals and PD-contrast for reference within a single acquisition.

High-Resolution Free-Breathing Automated Quantitative Myocardial Perfusion by Cardiovascular Magnetic Resonance for the Detection of Functionally Significant Coronary Artery Disease.

Current assessment of myocardial ischaemia from stress perfusion cardiovascular magnetic resonance (SP-CMR) largely relies on visual interpretation. This study investigated the use of high-resolution free-breathing SP-CMR with automated quantitative mapping in the diagnosis of coronary artery disease (CAD). Diagnostic performance was evaluated against invasive coronary angiography (ICA) with fractional flow reserve (FFR) measurement. Seven-hundred and three patients were recruited for SP-CMR using the research sequence at 3 Tesla. Of those receiving ICA within 6 months, 80 patients either had FFR measurement, or identification of a chronic total occlusion (CTO) with inducible perfusion defects seen on SP-CMR. Myocardial blood flow (MBF) maps were automatically generated in-line on the scanner following image acquisition at hyperaemic stress and rest, allowing myocardial perfusion reserve (MPR) calculation. 75 coronary vessels assessed by FFR, and 28 vessels with CTO were evaluated at both segmental and coronary territory level. Coronary territory stress MBF and MPR were reduced in FFR-positive (≤ 0.80) regions (median stress MBF: 1.74 [0.90-2.17] ml/min/g; MPR: 1.67 [1.10-1.89]) compared with FFR-negative regions (stress MBF: 2.50 [2.15-2.95] ml/min/g; MPR 2.35 [2.06-2.54] p < 0.001 for both). Stress MBF ≤ 1.94 ml/min/g and MPR ≤ 1.97 accurately detected FFR-positive CAD on a per-vessel basis (area under the curve: 0.85 and 0.96 respectively; p < 0.001 for both). A novel scanner-integrated high-resolution free-breathing SP-CMR sequence with automated in-line perfusion mapping is presented which accurately detects functionally significant CAD.

Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data

Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high-resolution single-cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to “tipping points” whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single-cell transcriptomics data to infer the stability and gene regulatory networks (GRNs) along cell lineages. Our method uses the unspliced and spliced counts from single-cell RNA sequencing data and cell ordering along lineage trajectories to train an RNA splicing multivariate model, from which cell-state stability along the lineage is inferred based on spectral analysis of the model’s Jacobian matrix. Moreover, the model infers the RNA cross-species interactions resulting in GRNs and their variation along the cell lineage. When applied to epithelial-mesenchymal transition in ovarian and lung cancer-derived cell lines, our model predicts a saddle-node transition between the epithelial and mesenchymal states passing through an unstable, intermediate cell state. Furthermore, we show that the underlying GRN controlling epithelial-mesenchymal transition rearranges during the transition, resulting in denser and less modular networks in the intermediate state. Overall, our method represents a flexible tool to study cell lineages with a combination of theory-driven modeling and single-cell transcriptomics data.

Single-cell RNA-seq reveals keratinocyte and fibroblast heterogeneity and their crosstalk via epithelial-mesenchymal transition in psoriasis

The pathogenesis of psoriasis, a chronic inflammatory autoimmune skin disease with a high global prevalence, remains unclear. We performed a high-resolution single-cell RNA sequencing analysis of 94,759 cells from 13 samples, including those from psoriasis model mice and wild-type mice. We presented a single-cell atlas of the skin of imiquimod-induced mice with psoriasis and WT mice, especially the heterogeneity of keratinocytes and fibroblasts. More interestingly, we discovered that special keratinocyte subtypes and fibroblast subtypes could interact with each other through epithelial–mesenchymal transition and validated the results with drug verification. Moreover, we conducted a tentative exploration of the potential pathways involved and revealed that the IL-17 signalling pathway may be the most relevant pathway. Collectively, we revealed the full-cycle landscape of key cells associated with psoriasis and provided a more comprehensive understanding of the pathogenesis of psoriasis.

50 Effects of cottonseed supplementation on the rumen microbiota of parasite-challenged meat goats

Abstract Cotton serves as a vital economic driver within the agricultural sector of Mississippi. The seeds of cotton are rich in fat and protein content, making them a cost-effective alternative to soybean meal and other expensive protein sources. Additionally, cottonseed is the primary source of gossypol, a phenolic compound with significant potential for natural parasite control. The rumen microbiota, a diverse community of microorganisms, has a pivotal role in nutrient digestion and detoxification. However, the impact of cottonseed on rumen microbial ecosystems remains largely unexplored. The aim of this study is to investigate the effects of cottonseed supplementation on the rumen microbiota of meat goats with and without the challenge of parasites. Forty female weaned Boer × Spanish crossed meat goats were assigned to one of the four treatments (n = 10 per treatment) in a 2 × 2 factorial design consisting of control group (CON), parasite challenge group (P), cottonseed supplementation (0.5% body weight) without parasite challenge group (CS-NP), and CS supplementation with parasite challenge group (CS-P). The parasite challenge was performed with a dose of 4,000 infective third-stage larvae of Haemonchus contortus per animal. After 25 d following the first dose, the treatments were applied for 10 wk. The goats were slaughtered at the end of the experiment, and rumen digesta samples were collected for microbiota analysis using high-resolution full-length 16S rRNA gene amplicon sequencing. The results revealed that the parasite challenge significantly reduced the number of bacterial species in the rumen (P = 0.032), regardless of cottonseed supplement. Anaeromassilibacillus senegalensis, which has been isolated from kwashiorkor (severe protein malnutrition) patient, Hungateiclostridium aldrichii, and Mogibacterium diversum were enriched in rumen of P group, while Anaerocella delicata and the rumen lipolytic organism Anaerovibrio lipolyticus were reduced compared with the CON group [linear discriminant analysis (LDA) scores &amp;gt; 3.6]. Cottonseed supplementation did not affect the number of bacterial species in the rumen of parasite-challenged goats, but it did lead to an increase of Anaerovibrio lipolyticus (P = 0.008) and a reduction of Anaeromassilibacillus senegalensis (P = 0.007). Moreover, cottonseed supplementation tended to increase the number of bacterial species in the rumen of meat goats without parasite challenge (P = 0.08) and increased the relative abundance of butyrate-producing bacteria such as Pseudobutyrivibrio xylanivorans and Intestinimonas butyriciproducens, along with the butanol-producing bacteria Clostridium saccharoperbutylacetonicum (LDA scores &amp;gt; 2). Conversely, cottonseed supplementation inhibited cellulolytic bacteria Fibrobacter succinogenes, polysaccharide-degrading bacteria Butyrivibrio proteoclasticus, and several Prevotella species, including P. oris, P. loescheii, P. copri, and P. albensis (LDA score &amp;gt; 2). In conclusion, parasite challenge affects the rumen microbial diversity and certain bacterial species that utilize protein and lipids, and cottonseed supplementation partially restores the altered rumen microbial ecosystem of the parasite-challenged meat goats.

Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia.

Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.

A high-resolution sequence stratigraphic framework for the eastern Ellis Bay Formation, Canada: A record of Hirnantian sea-level change

Anticosti Island (Québec, Canada) contains one of the thickest Ordovician/Silurian boundary sections in the world, providing a fossiliferous and well-preserved record of the Late Ordovician mass extinction; however, the absence of a comprehensive correlation framework for the island prevents the full incorporation of data from across Anticosti into a global understanding of the extinction event. Here, we combine sedimentological, stratigraphic, and chemostratigraphic data to develop a sequence stratigraphic framework for the Ellis Bay and lowermost Becscie formations along the northeastern shore of Anticosti Island. These formations record six fourth-order (∼100−400 k.y.) depositional sequences bounded by regionally traceable unconformities. Evidence of subaerial weathering and exposure at many of these unconformities is subtle and has long gone unrecognized, which highlights the complexity of correlation in this and other stratigraphically thin icehouse records. Quartz pebble lags that mantle these surfaces punctuate the otherwise fine-grained, mixed carbonate−siliciclastic strata of the Ellis Bay Formation and provide the means to trace unconformities across localities; these surfaces are also marked by depleted carbon isotopic values, meteoric cement, microkarst, and incised valleys. This sequence stratigraphic framework provides the first correlation framework for exposures from the eastern end of this classic Ordovician/Silurian boundary section, and thus enables the integration of paleobiological, stratigraphic, and geochemical data into a basin-wide perspective of the Late Ordovician mass extinction. Critically, comparison to sequence stratigraphic frameworks from coeval sections suggests that other regions may be incomplete at the level of the fourth-order cycles recorded on Anticosti Island and may contain similarly cryptic unconformities.

5-Chloro-2'-deoxycytidine Induces a Distinctive High-Resolution Mutational Spectrum of Transition Mutations In Vivo.

The biomarker 5-chlorocytosine (5ClC) appears in the DNA of inflamed tissues. Replication of a site-specific 5ClC in a viral DNA genome results in C → T mutations, which is consistent with 5ClC acting as a thymine mimic in vivo. Direct damage of nucleic acids by immune-cell-derived hypochlorous acid is one mechanism by which 5ClC could appear in the genome. A second, nonmutually exclusive mechanism involves damage of cytosine nucleosides or nucleotides in the DNA precursor pool, with subsequent utilization of the 5ClC deoxynucleotide triphosphate as a precursor for DNA synthesis. The present work characterized the mutagenic properties of 5ClC in the nucleotide pool by exposing cells to the nucleoside 5-chloro-2'-deoxycytidine (5CldC). In both Escherichia coli and mouse embryonic fibroblasts (MEFs), 5CldC in the growth media was potently mutagenic, indicating that 5CldC enters cells and likely is erroneously incorporated into the genome from the nucleotide pool. High-resolution sequencing of DNA from MEFs derived from the gptΔ C57BL/6J mouse allowed qualitative and quantitative characterization of 5CldC-induced mutations; CG → TA transitions in 5'-GC(Y)-3' contexts (Y = a pyrimidine) were dominant, while TA → CG transitions appeared at a much lower frequency. The high-resolution mutational spectrum of 5CldC revealed a notable similarity to the Catalogue of Somatic Mutations in Cancer mutational signatures SBS84 and SBS42, which appear in human lymphoid tumors and in occupationally induced cholangiocarcinomas, respectively. SBS84 is associated with the expression of activation-induced cytidine deaminase (AID), a cytosine deaminase associated with inflammation, as well as immunoglobulin gene diversification during antibody maturation. The similarity between the spectra of AID activation and 5CldC could be coincidental; however, the administration of 5CldC did induce some AID expression in MEFs, which have no inherent expression of its gene. In summary, this work shows that 5CldC induces a distinct pattern of mutations in cells. Moreover, that pattern resembles human mutational signatures induced by inflammatory processes, such as those triggered in certain malignancies.

Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi.

The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem-mofettes or natural CO2 springs caused by geological CO2 exhalations-are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, "stress tolerant" taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.IMPORTANCEArbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.

Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens

This study aims to use spatial transcriptomics to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3 muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified. Sequence reads were aligned to the chicken reference genome (Galgal6) and mapped to histological images. Unsupervised K-means clustering and Seurat integrative analysis differentiated histologic features and their specific gene expression pattern, including lipid laden macrophages (LLM), unaffected myofibers, myositis and vasculature. In particular, LLM exhibited reprogramming of lipid metabolism with up-regulated lipid transporters and genes in peroxisome proliferator-activated receptors pathway, possibly through P. Moreover, overexpression of fatty acid binding protein 5 could enhance fatty acid uptake in adjacent veins. In myositis regions, increased expression of cathepsins may play a role in muscle homeostasis and repair by mediating lysosomal activity and apoptosis. A better knowledge of different cell-type interactions at early stages of WB is essential in developing a comprehensive understanding.

Management of Spontaneous Spinal CSF Leaks Using Noninvasive Dynamic MR Neurography: A Case Series

AbstractSpontaneous spinal cerebrospinal fluid (CSF) leak presents with orthostatic headache and may lead to formation of subdural collection. Invasive magnetic resonance imaging or computed tomography myelography is routinely used to detect these leaks. Noninvasive dynamic magnetic resonance neurography can also detect these leaks and confirm its resolution post treatment. It includes three-dimensional NerveView, a high-resolution short-tau inversion recovery sequence for better visualization of spinal nerves and leak sites. This article showcases the diagnostic and therapeutic journey of three patients with spontaneous spinal CSF leak all of whom were diagnosed with dynamic magnetic resonance neurography and treated successfully with autologous targeted epidural blood patch. In one case, epidural blood patch was repeated after 2 months for recurrence of the leak.