We describe a case of severe neonatal anemia with kernicterus caused by compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. ...This is the first described case of a KLF1-null human. The phenotype of severe nonspherocytic hemolytic anemia, jaundice, hepatosplenomegaly, and marked erythroblastosis is more severe than that present in congenital dyserythropoietic anemia type IV as a result of dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found that human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell-cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control, and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis.
•Complete loss of KLF1 function is compatible with life but results in severe nonspherocytic hemolytic anemia and kernicterus.•Human KLF1 regulates most aspects of red cell biology.
A flexible metal‐organic framework selectively sorbs para‐ (pX) over meta‐xylene (mX) by synergic restructuring around pX coupled with generation of unused void space upon mX loading. The nature of ...the structural change suggests more generally that flexible structures which are initially mismatched in terms of fit and capacity to the preferred guest are strong candidates for effective molecular separations.
Nobody′s perfect: The metal‐organic framework Ce(HTCPB) is structurally mismatched to both the para and meta isomers of xylene. It restructures synergically around the para isomer to give a high‐quality structural and functional fit, but rearrangement around the meta isomer requires larger host distortions and gives a poorer fit than in the para case. This “off‐target” host thus has high selectivity for the sorption of para‐ over meta‐xylene.
This article explores questions on perceptions of the location of the 'Midwest', a contested vernacular region of the United States. We created a custom online survey with R's web framework Shiny, in ...which participants were presented with a blank web map and asked to 'draw' their definition of the Midwest. Instead of simply describing the aggregated results, we employ machine learning algorithms - Naive Bayes, Random Forest and Categorical Boosting - in an attempt to classify users into groups, with a focus on the features that most effectively separate responses. We also demonstrate a way to engineer features from a single spatial response question and provide an implementation through a small R package. Furthermore, we discuss misclassified observations and suggest some driving factors in the construction of regional perception. This research is important not only for its contribution to perceptual regions but also for the approach, which could be applied to place-based survey analysis more broadly.
The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost ...exclusively on protein-coding transcripts. However, recent transcriptome analyses show that the mammalian genome contains thousands of long noncoding RNAs (ncRNAs), many of which appear to be expressed in a developmentally regulated manner. The functions of these remain untested. To identify ncRNAs involved in ES cell biology, we used a custom-designed microarray to examine the expression profiles of mouse ES cells differentiating as embryoid bodies (EBs) over a 16-d time course. We identified 945 ncRNAs expressed during EB differentiation, of which 174 were differentially expressed, many correlating with pluripotency or specific differentiation events. Candidate ncRNAs were identified for further characterization by an integrated examination of expression profiles, genomic context, chromatin state, and promoter analysis. Many ncRNAs showed coordinated expression with genomically associated developmental genes, such as Dlx1, Dlx4, Gata6, and Ecsit. We examined two novel developmentally regulated ncRNAs, Evx1as and Hoxb5/6as, which are derived from homeotic loci and share similar expression patterns and localization in mouse embryos with their associated protein-coding genes. Using chromatin immunoprecipitation, we provide evidence that both ncRNAs are associated with trimethylated H3K4 histones and histone methyltransferase MLL1, suggesting a role in epigenetic regulation of homeotic loci during ES cell differentiation. Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery.
Thermodynamic and materials considerations were made for some two- and three-step thermochemical cycles to split water using solar-thermal processing. The direct thermolysis of water to produce H
2 ...using solar-thermal processing is unlikely in the near term due to ultra-high-temperature requirements exceeding
3000
K
and the need to separate H
2 from O
2 at these temperatures. However, several lower temperature
(<2500
K)
thermochemical cycles including ZnO/Zn, Mn
2O
3/MnO, substituted iron oxide, and the sulfur–iodine route (S–I) provide an opportunity for high-temperature solar-thermal development. Although zirconia-based materials are well suited for metal oxide routes in terms of chemical compatibility at these temperatures, thermal shock issues are a major concern for solar-thermal applications. Hence, efforts need to be directed towards methods for designing reactors to eliminate thermal shock (ZrO
2 based) or that use graphite (very compatible in terms of temperature and thermal shock) with designs that prevent contact of chemical species with graphite materials at high temperatures. Fluid-wall reactor configurations where inert gases provide a blanket to protect the graphite wall appear promising in this regard, but their use will impact process efficiency. For the case of S–I up to
1800
K
, silicon carbide appears to be a suitable material for the high-temperature H
2SO
4 dissociation. There is a need for a significant amount of work to be done in the area of high-temperature solar-thermal reactor engineering to develop thermochemical water splitting processes.
Abstract
Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of dCas9-based activation systems. To counter this, we create an ...improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). We show that TETact demethylation-coupled activation is able to induce transcription of suppressed genes, both individually and simultaneously in cells, and has utility across a number of cell types. Furthermore, we show that TETact can effectively reactivate embryonic haemoglobin genes in non-erythroid cells. We anticipate that TETact will expand the existing CRISPR toolbox and be valuable for functional studies, genetic screens and potential therapeutics.
Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a ...challenge to uncover their functions.
We present a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan. We applied our pipeline to a mouse Klf1 knockout dataset, and discussed the plausible functions of the novel lncRNAs we detected by differential expression analysis. We identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type and Klf1 knockout conditions.
Our method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type and Klf1 knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
The paper contributes a general dynamical formulation and numerical solution procedure for studying nonlinear and three-dimensional dynamics of Kirchhoff rods. Target applications include the dynamic ...formation of DNA loops and supercoils as well as loops (hockles) in marine cables. The formulation accommodates non-homogeneous and non-isotropic inextensible rods both with and without coupling of tension and torsion. The utility of this formulation is illustrated by studying the dynamics and quasi-static response of a clamped–clamped rod subject to compression and/or twist. For slow loading rates, the computed quasi-static responses converge to published equilibrium solutions for a benchmark problem. As loading rates increase, new behaviors are observed including hysteresis in the neighborhood of equilibrium bifurcations. The addition of chirality in the form of tension–torsion coupling has a pronounced influence on the computed looped geometries. This finding has implications for DNA loops formed by DNA–protein binding as well as loop formation in helically wound wire and synthetic cables.
Mouse hematopoietic tissues contain abundant tissue-resident macrophages that support immunity, hematopoiesis, and bone homeostasis. A systematic strategy to characterize macrophage subsets in mouse ...bone marrow (BM), spleen, and lymph node unexpectedly reveals that macrophage surface marker staining emanates from membrane-bound subcellular remnants associated with unrelated cells. Intact macrophages are not present within these cell preparations. The macrophage remnant binding profile reflects interactions between macrophages and other cell types in vivo. Depletion of CD169+ macrophages in vivo eliminates F4/80+ remnant attachment. Remnant-restricted macrophage-specific membrane markers, cytoplasmic fluorescent reporters, and mRNA are all detected in non-macrophage cells including isolated stem and progenitor cells. Analysis of RNA sequencing (RNA-seq) data, including publicly available datasets, indicates that macrophage fragmentation is a general phenomenon that confounds bulk and single-cell analysis of disaggregated hematopoietic tissues. Hematopoietic tissue macrophage fragmentation undermines the accuracy of macrophage ex vivo molecular profiling and creates opportunity for misattribution of macrophage-expressed genes to non-macrophage cells.
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•Genuine macrophages are absent from hematopoietic tissue single-cell preparations•Fragmented remnants of macrophages containing cytoplasm adhere to other cells•Macrophage remnants convolute hematopoietic tissue flow cytometry analysis•Remnant-derived macrophage-RNA is misattributed to other cells in RNA-seq data
Millard et al. demonstrate intact macrophages are absent in hematopoietic tissue single-cell suspensions as they are disrupted during preparation. Macrophage remnants containing membrane and intracellular contents remain attached to other cells within the suspensions. This results in misassignment of macrophage identity and misattribution of macrophage-expressed genes.
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