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Social Science & Medicine (1982) May 2024Service restrictions refer to temporary or permanent bans of individuals from a program or an organization's services, and are widely used in emergency shelter systems....
Service restrictions refer to temporary or permanent bans of individuals from a program or an organization's services, and are widely used in emergency shelter systems. Limited research exists on how service restrictions unfold and their impacts on people experiencing homelessness. This qualitative study used in-depth interviews with timeline mapping to examine the antecedents and consequences of service restrictions from emergency shelters among people experiencing homelessness in two cities in Ontario, Canada. A total of 49 people experiencing homelessness who had been restricted from an emergency shelter program in the past year were recruited and included in the study analysis. A pragmatic and integrative approach was used for data analysis that involved the development of meta-matrices to identify prominent and divergent perspectives and experiences with regard to service restriction antecedents and consequences. Study findings underscored that service restrictions were often the result of violence and aggression, primarily between service users. There were regional differences in other service restriction reasons, including substance use and possession. Service restrictions affected the shelter status of almost all participants, with many subsequently experiencing unsheltered homelessness, and cycling through institutional health, social, and criminal justice services (i.e., institutional circuitry). Other health and social consequences included substance use relapses and hospitalizations; cold-related injuries due to post-restriction unsheltered homelessness; suicidality; food insecurity; diminished contact with support network and connections; and intense feelings of anger, fear, and hopelessness. Overall, the study findings advance our understanding of the role of homeless services in pathways into unsheltered homelessness and institutional circuitry, which raise critical questions about how to mitigate the harms associated with service restrictions, while concurrently facilitating safety and upholding the rights of people experiencing homelessness and emergency shelter staff.
Topics: Humans; Ill-Housed Persons; Female; Ontario; Male; Qualitative Research; Adult; Emergency Shelter; Middle Aged
PubMed: 38574591
DOI: 10.1016/j.socscimed.2024.116831 -
Blood Cancer Discovery May 2024Clonal hematopoiesis (CH) is the expansion of somatically mutated cells in the hematopoietic compartment of individuals without hematopoietic dysfunction. Large CH...
UNLABELLED
Clonal hematopoiesis (CH) is the expansion of somatically mutated cells in the hematopoietic compartment of individuals without hematopoietic dysfunction. Large CH clones (i.e., >2% variant allele fraction) predispose to hematologic malignancy, but CH is detected at lower levels in nearly all middle-aged individuals. Prior work has extensively characterized CH in peripheral blood, but the spatial distribution of hematopoietic clones in human bone marrow is largely undescribed. To understand CH at this level, we developed a method for spatially aware somatic mutation profiling and characterized the bone marrow of a patient with polycythemia vera. We identified the complex clonal distribution of somatic mutations in the hematopoietic compartment, the restriction of somatic mutations to specific subpopulations of hematopoietic cells, and spatial constraints of these clones in the bone marrow. This proof of principle paves the way to answering fundamental questions regarding CH spatial organization and factors driving CH expansion and malignant transformation in the bone marrow.
SIGNIFICANCE
CH occurs commonly in humans and can predispose to hematologic malignancy. Although well characterized in blood, it is poorly understood how clones are spatially distributed in the bone marrow. To answer this, we developed methods for spatially aware somatic mutation profiling to describe clonal heterogeneity in human bone marrow. See related commentary by Austin and Aifantis, p. 139.
Topics: Humans; Bone Marrow; Clonal Hematopoiesis; Mutation; Polycythemia Vera; Clone Cells; Hematopoietic Stem Cells
PubMed: 38421682
DOI: 10.1158/2643-3230.BCD-23-0110 -
Frontiers in Plant Science 2023High temperatures present a formidable challenge to the cultivation of hot pepper, profoundly impacting not only vegetative growth but also leading to flower and fruit...
High temperatures present a formidable challenge to the cultivation of hot pepper, profoundly impacting not only vegetative growth but also leading to flower and fruit abscission, thereby causing a significant reduction in yield. To unravel the intricate genetic mechanisms governing heat tolerance in hot pepper, an F population was developed through the crossing of two distinct genotypes exhibiting contrasting heat tolerance characteristics: DLS-161-1 (heat tolerant) and DChBL-240 (heat susceptible). The F population, along with the parental lines, was subjected to comprehensive phenotyping encompassing diverse morphological, physiological, and biochemical heat-related traits under high temperature conditions (with maximum temperature ranging from 31 to 46.5°C and minimum temperature from 15.4 to 30.5°C). Leveraging the Illumina Nova Seq-6000 platform, Double digest restriction-site associated DNA sequencing (ddRAD-seq) was employed to generate 67.215 Gb data, with subsequent alignment of 218.93 million processed reads against the reference genome of . Subsequent variant calling and ordering resulted in 5806 polymorphic SNP markers grouped into 12 LGs. Further QTL analysis identified 64 QTLs with LOD values ranging from 2.517 to 11.170 and explained phenotypic variance ranging from 4.05 to 19.39%. Among them, 21 QTLs, explaining more than 10% phenotypic variance, were identified as major QTLs controlling 9 morphological, 3 physiological, and 2 biochemical traits. Interestingly, several QTLs governing distinct parameters were found to be colocalized, suggesting either a profound correlation between the QTLs regulating these traits or their significant genomic proximity. In addition to the QTLs, we also identified 368380 SSR loci within the identified QTL regions, dinucleotides being the most abundant type (211,381). These findings provide valuable insights into the genetics of heat tolerance in hot peppers. The identified QTLs and SSR markers offer opportunities to develop heat-tolerant varieties, ensuring better crop performance under high-temperature conditions.
PubMed: 37692444
DOI: 10.3389/fpls.2023.1232800 -
BioRxiv : the Preprint Server For... Jun 2024Among dozens of known epigenetic marks, naturally occurring phosphorothioate (PT) DNA modifications are unique in replacing a non-bridging phosphate oxygen with...
Among dozens of known epigenetic marks, naturally occurring phosphorothioate (PT) DNA modifications are unique in replacing a non-bridging phosphate oxygen with redox-active sulfur and function in prokaryotic restriction-modification and transcriptional regulation. Interest in PTs has grown due to the widespread distribution of the , and genes among bacteria and archaea, as well as the discovery of PTs in 5-10% of gut microbes. Efforts to map PTs in complex microbiomes using existing next-generation and direct sequencing technologies have failed due to poor sensitivity. Here we developed PT-seq as a high-sensitivity method to quantitatively map PTs across genomes and metagenomically identify PT-containing microbes in complex genomic mixtures. Like other methods for mapping PTs in individual genomes, PT-seq exploits targeted DNA strand cleavage at PTs by iodine, followed by sequencing library construction using ligation or template switching approaches. However, PT-specific sequencing reads are dramatically increased by adding steps to heat denature the DNA, block pre-existing 3'-ends, fragment DNA after T-tailing, and enrich iodine-induced breaks using biotin-labeling and streptavidin beads capture. Iterative optimization of the sensitivity and specificity of PT-seq is demonstrated with individual bacteria and human fecal DNA.
PubMed: 38895297
DOI: 10.1101/2024.06.03.597111 -
BMC Genomics Apr 2024Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on...
BACKGROUND
Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored.
RESULTS
Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected.
CONCLUSIONS
Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
Topics: Base Composition; Genomics; Animals; Introns; Genome; Exons; Genetic Loci; Genome Size; Plants; DNA, Intergenic
PubMed: 38664648
DOI: 10.1186/s12864-024-10312-3 -
Entropy (Basel, Switzerland) Nov 2023Deep Unfolding Networks (DUNs) serve as a predominant approach for Compressed Sensing (CS) reconstruction algorithms by harnessing optimization. However, a notable...
Deep Unfolding Networks (DUNs) serve as a predominant approach for Compressed Sensing (CS) reconstruction algorithms by harnessing optimization. However, a notable constraint within the DUN framework is the restriction to single-channel inputs and outputs at each stage during gradient descent computations. This constraint compels the feature maps of the proximal mapping module to undergo multi-channel to single-channel dimensionality reduction, resulting in limited feature characterization capabilities. Furthermore, most prevalent reconstruction networks rely on single-scale structures, neglecting the extraction of features from different scales, thereby impeding the overall reconstruction network's performance. To address these limitations, this paper introduces a novel CS reconstruction network termed the Multi-channel and Multi-scale Unfolding Network (MMU-Net). MMU-Net embraces a multi-channel approach, featuring the incorporation of Adap-SKConv with an attention mechanism to facilitate the exchange of information between gradient terms and enhance the feature map's characterization capacity. Moreover, a Multi-scale Block is introduced to extract multi-scale features, bolstering the network's ability to characterize and reconstruct the images. Our study extensively evaluates MMU-Net's performance across multiple benchmark datasets, including Urban100, Set11, BSD68, and the UC Merced Land Use Dataset, encompassing both natural and remote sensing images. The results of our study underscore the superior performance of MMU-Net in comparison to existing state-of-the-art CS methods.
PubMed: 38136459
DOI: 10.3390/e25121579 -
Biochimica Et Biophysica Acta.... Jun 2024N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly...
N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly understood. Here, we characterized the synchronization of m6A modifications and placental functions by mapping the m6A methylome in human placentas (n = 3, each trimester), revealing that the dynamic patterns of m6A were associated with gene expression homeostasis and different biological pathways in placental development. Then, we generated trophoblast-specific knockout mice of Wtap, a critical component of methyltransferase complex, and demonstrated that Wtap was essential for trophoblast proliferation, placentation and perinatal growth. Further in vitro experiments which includes cell viability assays and series molecular binding assays demonstrated that WTAP-m6A-IGF2BP3 axis regulated the RNA stability and translation of Anillin (ANLN) and VEGFA, promoting trophoblast proliferation and secretion. Dysregulation of this regulatory axis was observed in placentas from pregnancies with fetal growth restriction (FGR) or preeclampsia, revealing the pathogenic effects of imbalanced m6A modifications. Therefore, our findings provide novel insights into the functions and regulatory mechanisms of m6A modifications in placental development and placental-related gestational diseases.
PubMed: 38866113
DOI: 10.1016/j.bbadis.2024.167290 -
Cold Spring Harbor Protocols May 2024Inverse polymerase chain reaction (PCR) is a method designed to amplify a segment of DNA for which only a portion of the sequence is known. The method consists of...
Inverse polymerase chain reaction (PCR) is a method designed to amplify a segment of DNA for which only a portion of the sequence is known. The method consists of circularizing the DNA fragment by self-ligation and performing PCR with primers annealing inside the known sequence but pointing away from each other (hence the technique is also called "inside-out PCR"). Here we describe how inverse PCR can be used to identify the site of transposon insertion in the bacterial chromosome. This protocol, implemented here with a class of transposons generating reporter gene fusions, involves (i) preparing genomic DNA from the strain harboring the unknown insertion, (ii) cleaving the genomic DNA with a restriction enzyme, (iii) performing a ligation reaction under conditions favoring circularization of the DNA fragments, and (iv) performing inverse PCRs with inside-out primers annealing near either or both termini of the transposon. This last step results in the amplification of the chromosomal sequences immediately adjacent to the transposon, which can then be identified by Sanger sequencing. The protocol can be performed in parallel on several strains providing an effective and economic way for rapidly identifying multiple transposon insertion sites.
Topics: DNA Transposable Elements; Polymerase Chain Reaction; Sequence Analysis, DNA; DNA, Bacterial; Mutagenesis, Insertional; DNA Primers
PubMed: 37188521
DOI: 10.1101/pdb.prot108197 -
Zhongguo Dang Dai Er Ke Za Zhi =... Mar 2024To explore the value of functional magnetic resonance imaging (MRI) techniques, including intravoxel incoherent motion (IVIM), T1 mapping, and T2 mapping, in assessing...
OBJECTIVES
To explore the value of functional magnetic resonance imaging (MRI) techniques, including intravoxel incoherent motion (IVIM), T1 mapping, and T2 mapping, in assessing the microstructural and perfusion changes in the kidneys of rats with intrauterine growth restriction (IUGR).
METHODS
An IUGR rat model was established through a low-protein diet during pregnancy. Offspring from pregnant rats on a low-protein diet were randomly divided into an IUGR 8-week group and an IUGR 12-week group, while offspring from pregnant rats on a normal diet were divided into a normal 8-week group and a normal 12-week group (=8 for each group). The apparent diffusion coefficient (ADC), true diffusion coefficient (D), pseudo-diffusion coefficient (D), perfusion fraction (f), T1 value, and T2 value of the renal cortex and medulla were compared, along with serum creatinine and blood urea nitrogen levels among the groups.
RESULTS
The D value in the renal medulla was higher in the IUGR 12-week group than in the IUGR 8-week group, and the D value in the renal medulla was lower in the IUGR 12-week group than in both the normal 12-week group and the IUGR 8-week group (<0.05). The T1 value in the renal medulla was higher than in the cortex in the IUGR 8-week group, and the T1 value in the renal medulla was higher in the IUGR 12-week group than in both the IUGR 8-week group and the normal 12-week group, with the cortical T1 value in the IUGR 12-week group also being higher than that in the normal 12-week group (<0.05). The T2 values in the renal medulla were higher than those in the cortex across all groups (<0.05). There were no significant differences in the T2 values of either the cortex or medulla among the groups (>0.05). There were no significant differences in serum creatinine and blood urea nitrogen levels among the groups (>0.05). Glomerular hyperplasia and hypertrophy without significant fibrotic changes were observed in the IUGR 8-week group, whereas glomerular atrophy, cystic stenosis, and interstitial inflammatory infiltration and fibrosis were seen in the IUGR 12-week group.
CONCLUSIONS
IVIM MRI can be used to assess and dynamically observe the microstructural and perfusion damage in the kidneys of IUGR rats. MRI T1 mapping can be used to evaluate kidney damage in IUGR rats, and the combination of MRI T1 mapping and T2 mapping can further differentiate renal fibrosis in IUGR rats.
Topics: Animals; Female; Rats; Creatinine; Diffusion Magnetic Resonance Imaging; Fetal Growth Retardation; Kidney; Magnetic Resonance Imaging; Perfusion; Pregnancy
PubMed: 38557382
DOI: 10.7499/j.issn.1008-8830.2309004 -
BMC Genomics Aug 2023For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading...
BACKGROUND
For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either 'sensitive' or 'robust' individuals during the 28-day observation period.
RESULTS
We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly.
CONCLUSION
According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs.
Topics: Animals; Quantitative Trait Loci; Chromosome Mapping; Perciformes; Chromosomes; Genomics; Polymorphism, Single Nucleotide; Genetic Linkage
PubMed: 37558985
DOI: 10.1186/s12864-023-09513-z