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Placenta Dec 2023In-vivo measurements of placental structure and function have the potential to improve prediction, diagnosis, and treatment planning for a wide range of pregnancy...
INTRODUCTION
In-vivo measurements of placental structure and function have the potential to improve prediction, diagnosis, and treatment planning for a wide range of pregnancy complications, such as fetal growth restriction and pre-eclampsia, and hence inform clinical decision making, ultimately improving patient outcomes. MRI is emerging as a technique with increased sensitivity to placental structure and function compared to the current clinical standard, ultrasound.
METHODS
We demonstrate and evaluate a combined diffusion-relaxation MRI acquisition and analysis pipeline on a sizable cohort of 78 normal pregnancies with gestational ages ranging from 15 + 5 to 38 + 4 weeks. Our acquisition comprises a combined T2*-diffusion MRI acquisition sequence - which is simultaneously sensitive to oxygenation, microstructure and microcirculation. We analyse our scans with a data-driven unsupervised machine learning technique, InSpect, that parsimoniously identifies distinct components in the data.
RESULTS
We identify and map seven potential placental microenvironments and reveal detailed insights into multiple microstructural and microcirculatory features of the placenta, and assess their trends across gestation.
DISCUSSION
By demonstrating direct observation of micro-scale placental structure and function, and revealing clear trends across pregnancy, our work contributes towards the development of robust imaging biomarkers for pregnancy complications and the ultimate goal of a normative model of placental development.
Topics: Pregnancy; Humans; Female; Placenta; Microcirculation; Diffusion Magnetic Resonance Imaging; Fetal Growth Retardation; Magnetic Resonance Imaging; Placentation
PubMed: 37952367
DOI: 10.1016/j.placenta.2023.11.002 -
Genes Dec 2023Standard cytogenetic techniques (chromosomal banding analysis-CBA, and fluorescence in situ hybridization-FISH) show limits in characterizing complex chromosomal...
Standard cytogenetic techniques (chromosomal banding analysis-CBA, and fluorescence in situ hybridization-FISH) show limits in characterizing complex chromosomal rearrangements and structural variants arising from two or more chromosomal breaks. In this study, we applied optical genome mapping (OGM) to fully characterize two cases of complex chromosomal rearrangements at high resolution. In case 1, an acute myeloid leukemia (AML) patient showing chromothripsis, OGM analysis was fully concordant with classic cytogenetic techniques and helped to better refine chromosomal breakpoints. The OGM results of case 2, a patient with non-Hodgkin lymphoma, were only partially in agreement with previous cytogenetic analyses and helped to better define clonal heterogeneity, overcoming the bias related to clonal selection due to cell culture of cytogenetic techniques. In both cases, OGM analysis led to the identification of molecular markers, helping to define the pathogenesis, classification, and prognosis of the analyzed patients. Despite extensive efforts to study hematologic diseases, standard cytogenetic methods display unsurmountable limits, while OGM is a tool that has the power to overcome these limitations and provide a cytogenetic analysis at higher resolution. As OGM also shows limits in defining regions of a repetitive nature, combining OGM with CBA to obtain a complete cytogenetic characterization would be desirable.
Topics: Humans; In Situ Hybridization, Fluorescence; Karyotyping; Chromosome Aberrations; Cytogenetic Analysis; Restriction Mapping
PubMed: 38137002
DOI: 10.3390/genes14122180 -
GigaByte (Hong Kong, China) 2023While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read...
While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance accessibility and comparison, we have developed a BAC restriction map database. Using information from the National Center for Biotechnology Information's cloneDB FTP site, we constructed a database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of the available restriction enzymes. Along with the database, we generated a set of Python functions to reconstruct the database and more easily access the information within. This data is valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.
PubMed: 37753479
DOI: 10.46471/gigabyte.93 -
STAR Protocols Jun 2024Dinoflagellate genomes often are very large and difficult to assemble, which has until recently precluded their analysis with modern functional genomic tools. Here, we...
Dinoflagellate genomes often are very large and difficult to assemble, which has until recently precluded their analysis with modern functional genomic tools. Here, we present a protocol for mapping three-dimensional (3D) genome organization in dinoflagellates and using it for scaffolding their genome assemblies. We describe steps for crosslinking, nuclear lysis, denaturation, restriction digest, ligation, and DNA shearing and purification. We then detail procedures sequencing library generation and computational analysis, including initial Hi-C read mapping and 3D-DNA scaffolding/assembly correction. For complete details on the use and execution of this protocol, please refer to Marinov et al..
Topics: Dinoflagellida; Genome, Protozoan; Genomics; Chromosome Mapping; Sequence Analysis, DNA
PubMed: 38483898
DOI: 10.1016/j.xpro.2024.102941 -
Gait & Posture Sep 2023Toe-walking is one of the most common gait deviations (due to soleus and/or gastrocnemius muscle contractures), compromising the first (heel rocker) and second (ankle...
BACKGROUND
Toe-walking is one of the most common gait deviations (due to soleus and/or gastrocnemius muscle contractures), compromising the first (heel rocker) and second (ankle rocker) of the foot during walking. The aim of this study is to evaluate the effect of emulated artificially gastrocnemius and soleus contractures on the first and second rocker during walking.
METHOD
An exoskeleton was built to emulate contractures of the bilateral gastrocnemius and soleus muscles. Ten healthy participants were recruited to walk under the following conditions: without emulated contractures or with bilateral emulated contractures at 0°,10°, 20° and 30° of plantarflexion of the soleus or gastrocnemius in order to create an artificial restriction of dorsiflexion ankle movement. A linear regression from the ankle plantar-dorsiflexion angle pattern was performed on 0-5 % of the gait cycle (first rocker) and on 12-31 % of the gait cycle (second rocker) to compute the slope of the curve. The proportion of participants with the presence of the first and second rocker was then computed. A Statistical Parametric Mapping (SPM) analysis assessed the kinematic variations among different degrees of emulated contractures.
FINDINGS
The first and second rockers are completely absent from 10° of plantarflexion emulated contracture. The data indicate there was a non-linear shift of the gait pattern of the ankle kinematics and an important shift toward plantarflexion values with the loss of the rockers.
INTERPRETATION
This study suggests that toe-walking in the experimental simulation situation is not necessarily due to a high emulated contracture level and can occur with a small emulated contracture by an adaptation choice. This study may improve interpretation of clinical gait analysis and shows that the link between the level of gastrocnemius/soleus emulated contracture and progression of toe-walking (increased plantarflexion during gait) is not linear.
Topics: Humans; Gait; Muscle, Skeletal; Walking; Contracture; Ankle Joint; Movement Disorders; Toes; Biomechanical Phenomena
PubMed: 37523808
DOI: 10.1016/j.gaitpost.2023.07.285 -
Placenta Jun 2024The congenital condition gastroschisis is associated with delayed villous development and placental malperfusion, suggesting placental involvement. This study uses RNA...
The congenital condition gastroschisis is associated with delayed villous development and placental malperfusion, suggesting placental involvement. This study uses RNA sequencing to compare the placental transcriptome in pregnancies with and without gastroschisis. 180 coding genes were differentially expressed, mapping to multiple gene ontology pathways. Altered placental gene expression may represent fetal signalling to the placenta, and these changes could contribute to the pathogenesis of gastroschisis and associated morbidities, including fetal growth restriction.
PubMed: 38870840
DOI: 10.1016/j.placenta.2024.06.001 -
PLoS Computational Biology May 2024The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+)....
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools-a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.
Topics: Software; Chromosomes; Computational Biology; Humans; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing; Chromosome Mapping
PubMed: 38809952
DOI: 10.1371/journal.pcbi.1012164 -
Ultramicroscopy Nov 2023A method for the reciprocal space treatment of high-resolution transmission electron microscopy (HR-TEM) and high-resolution scanning transmission electron microscopy...
A method for the reciprocal space treatment of high-resolution transmission electron microscopy (HR-TEM) and high-resolution scanning transmission electron microscopy (HR-STEM) images has been developed. Named "Absolute strain" (AbStrain), it allows for quantification and mapping of interplanar distances and angles, displacement fields and strain tensor components with reference to a user-defined Bravais lattice and with their corrections from the image distortions specific to HR-TEM and HR-STEM imaging. We provide the corresponding mathematical formalism. AbStrain goes beyond the restriction of the existing method known as geometric phase analysis by enabling direct analysis of the area of interest without the need for reference lattice fringes of a similar crystal structure on the same field of view. In addition, for the case of a crystal composed of two or more types of atoms, each with its own sub-structure constraint, we developed a method named "Relative displacement" for extracting sub-lattice fringes associated to one type of atom and measuring atomic columns displacements associated to each sub-structure with reference to a Bravais lattice or to another sub-structure. The successful application of AbStrain and Relative displacement to HR-STEM images of functional oxide ferroelectric heterostructures is demonstrated.
PubMed: 37329809
DOI: 10.1016/j.ultramic.2023.113778 -
Integrated Environmental Assessment and... Apr 2024This study evaluates the knowledge structure of microplastic pollution and its effects on the aquatic food chain. The presence of microplastics has seriously harmed the... (Review)
Review
This study evaluates the knowledge structure of microplastic pollution and its effects on the aquatic food chain. The presence of microplastics has seriously harmed the ecosystem. Through bibliometric analysis, 216 journal publications were retrieved from the Web of Science (WoS) from 2008 to 2023 (April), with no restriction in the time frame. Applying bibliographic coupling and co-word analysis, the emerging, current, and future themes of microplastic pollution are presented. Three research streams are derived from bibliographic coupling, centralized on the source of microplastic pollution and its impact. At the same time, research streams from co-word analysis are associated with overcoming the issue of microplastics in the ecosystem. This study's implications suggest three main principles to mitigate microplastic issues: (1) educating the public on the impact of microplastic pollution, (2) implementing holistic regulations and policies, and (3) developing treatment strategies through conventional, innovative, and hybrid approaches. Microplastic pollution is a global concern, requiring a holistic and comprehensive approach to overcome it. This review is the first to present a scientific mapping of the microplastics literature, which is a fundamental basis for future research on microplastic pollution and its impact on the ecosystem. Integr Environ Assess Manag 2024;00:1-12. © 2024 SETAC.
PubMed: 38593234
DOI: 10.1002/ieam.4930 -
MBio Jan 2024Autophagy is a process used by cells to recycle organelles and macromolecules and to eliminate intracellular pathogens. Previous studies have shown that some stains of...
Autophagy is a process used by cells to recycle organelles and macromolecules and to eliminate intracellular pathogens. Previous studies have shown that some stains of are resistant to autophagy-dependent growth restriction, while others are highly susceptible. Although it is known that autophagy-mediated control requires activation by interferon gamma, the basis for why parasite strains differ in their susceptibility is unknown. Our findings indicate that susceptibility involves at least five unlinked parasite genes on different chromosomes, including several secretory proteins targeted to the parasite-containing vacuole and exposed to the host cell cytosol. Our findings reveal that susceptibility to autophagy-mediated growth restriction relies on differential recognition of parasite proteins exposed at the host-pathogen interface, thus identifying a new mechanism for cell-autonomous control of intracellular pathogens.
Topics: Animals; Humans; Toxoplasma; Parasites; Proteins; Vacuoles; Autophagy; Protozoan Proteins
PubMed: 38095418
DOI: 10.1128/mbio.02595-23