Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree.

Principles of assembly reveal a periodic table of protein complexes.

Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways.

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Single-cell RNA-sequencing (scRNA-seq) facilitates identification of new cell types and gene regulatory networks as well as dissection of the kinetics of gene expression and patterns of allele-specific expression. However, to facilitate such analyses, separating biological variability from the high level of technical noise that affects scRNA-seq protocols is vital. Here we describe and validate a generative statistical model that accurately quantifies technical noise with the help of external RNA spike-ins.

High-flux table-top soft x-ray source driven by sub-2-cycle, CEP stable, 1.85-μm 1-kHz pulses for carbon K-edge spectroscopy.

We report on the first table-top high-flux source of coherent soft x-ray radiation up to 400 eV, operating at 1 kHz. This source covers the carbon K-edge with a beam brilliance of (4.3±1.

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

Embryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state.

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

Protein families evolve functional variation by accumulating point mutations at functionally important amino acid positions. Homologs in the LacI/GalR family of transcription regulators have evolved to bind diverse DNA sequences and allosteric regulatory molecules. In addition to playing key roles in bacterial metabolism, these proteins have been widely used as a model family for benchmarking structural and functional prediction algorithms.

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

Background: Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell surface markers. Recent studies have identified significant cellular heterogeneities in the HSC compartment with subsets of HSCs displaying lineage bias.

European Adder bites in dogs in southern Germany. A retrospective study over a 6.5-year period.

Objective: In some regions of Germany dogs are presented to the veterinarian due to a snake bite, especially during the summer. These patients often show multiple clinical and laboratory deviations. Without a significant history diagnosis is commonly difficult.

Computational assignment of cell-cycle stage from single-cell transcriptome data.

The transcriptome of single cells can reveal important information about cellular states and heterogeneity within populations of cells. Recently, single-cell RNA-sequencing has facilitated expression profiling of large numbers of single cells in parallel. To fully exploit these data, it is critical that suitable computational approaches are developed.

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.

The lineage factor Foxp3 is essential for the development and maintenance of regulatory T cells, but little is known about the mechanisms involved. Here, we demonstrate that an N-terminal proline-rich interaction region is crucial for Foxp3's function. Subdomains within this key region link Foxp3 to several independent mechanisms of transcriptional regulation.

The technology and biology of single-cell RNA sequencing.

The differences between individual cells can have profound functional consequences, in both unicellular and multicellular organisms. Recently developed single-cell mRNA-sequencing methods enable unbiased, high-throughput, and high-resolution transcriptomic analysis of individual cells. This provides an additional dimension to transcriptomic information relative to traditional methods that profile bulk populations of cells.

An atlas of mouse CD4(+) T cell transcriptomes.

Background: CD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of several effector subtypes that exhibit distinct functions. The transcriptional mechanisms that underlie the specific functional identity of CD4(+) T cells are not fully understood.

Spatiotemporal isolation of attosecond soft X-ray pulses in the water window.

Attosecond pulses at photon energies that cover the principal absorption edges of the building blocks of materials are a prerequisite for time-resolved probing of the triggering events leading to electronic dynamics such as exciton formation and annihilation. We demonstrate experimentally the isolation of individual attosecond pulses at the carbon K-shell edge (284 eV) in the soft X-ray water window with pulse duration below 400 as and with a bandwidth supporting a 30-as pulse duration. Our approach is based on spatiotemporal isolation of long-wavelength-driven harmonics and validates a straightforward and scalable approach for robust and reproducible attosecond pulse isolation.

Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

Proteins assemble into complexes with diverse quaternary structures. Although most heteromeric complexes of known structure have even stoichiometry, a significant minority have uneven stoichiometry--that is, differing numbers of each subunit type. To adopt this uneven stoichiometry, sequence-identical subunits must be asymmetric with respect to each other, forming different interactions within the complex.

Computational and analytical challenges in single-cell transcriptomics.

The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has already led to profound new discoveries in biology, ranging from the identification of novel cell types to the study of global patterns of stochastic gene expression. Alongside the technological breakthroughs that have facilitated the large-scale generation of single-cell transcriptomic data, it is important to consider the specific computational and analytical challenges that still have to be overcome. Although some tools for analysing RNA-seq data from bulk cell populations can be readily applied to single-cell RNA-seq data, many new computational strategies are required to fully exploit this data type and to enable a comprehensive yet detailed study of gene expression at the single-cell level.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Recent technical developments have enabled the transcriptomes of hundreds of cells to be assayed in an unbiased manner, opening up the possibility that new subpopulations of cells can be found. However, the effects of potential confounding factors, such as the cell cycle, on the heterogeneity of gene expression and therefore on the ability to robustly identify subpopulations remain unclear. We present and validate a computational approach that uses latent variable models to account for such hidden factors.

Strong-field plasmonic photoemission in the mid-IR at <1 GW/cm² intensity.

We investigated nonlinear photoemission from plasmonic films with femtosecond, mid-infrared pulses at 3.1 μm wavelength. Transition between regimes of multi-photon-induced and tunneling emission is demonstrated at an unprecedentedly low intensity of <1 GW/cm(2).

Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators.

Structure, dynamics, assembly, and evolution of protein complexes.

The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes.

[Smoke inhalation in dogs and cats - a retrospective study over 5.5 years].

Objective: Particularly during household fires, inhalation of hot air and smoke, and the formation of carboxyhaemoglobin and cyanide lead to respiratory tract and lung injury in small animals. Additionally, oxygenation is impaired in most cases. The aim of this retrospective study was to analyse smoke exposure, physical examination findings and clinical pathology results as well as their course in dogs and cats presented after smoke inhalation.

[Heatstroke in dogs in southern Germany. A retrospective study over a 5.5-year period].

Objective: Heatstroke is a life-threating emergency in dogs. The aim of this retrospective study was to analyse the sources of heat stroke in dogs, predisposing and prognostic factors, results of physical examination and clinical pathology as well as the course of this condition and appropriate treatment.

Material And Methods: Patient histories of 12 dogs diagnosed with heat stroke over a 5.

Protein flexibility facilitates quaternary structure assembly and evolution.

The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes.

Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.

T helper 2 (Th2) cells regulate helminth infections, allergic disorders, tumor immunity, and pregnancy by secreting various cytokines. It is likely that there are undiscovered Th2 signaling molecules. Although steroids are known to be immunoregulators, de novo steroid production from immune cells has not been previously characterized.