Genome-wide screening reveals essential roles for HOX genes and imprinted genes during caudal neurogenesis of human embryonic stem cells.

Mapping the essential pathways for neuronal differentiation can uncover new therapeutics and models for neurodevelopmental disorders. We thus utilized a genome-wide loss-of-function library in haploid human embryonic stem cells, differentiated into caudal neuronal cells. We show that essential genes for caudal neurogenesis are enriched for secreted and membrane proteins and that a large group of neurological conditions, including neurodegenerative disorders, manifest early neuronal phenotypes.

Extramatrical mycelial biomass is mediated by fine root mass and ectomycorrhizal fungal community composition across tree species.

In many ecosystems, a large fraction of gross primary production is invested in mycorrhiza. Ectomycorrhizal (ECM) mycelium is involved in regulating soil carbon and nutrient cycling. However, little is known about how mycelial biomass, production and turnover differ depending on ECM fungal community composition and associated tree species.

Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose.

The 'assimilates inhibition hypothesis' posits that accumulation of nonstructural carbohydrates (NSCs) in leaves reduces leaf net photosynthetic rate, thus internally regulating photosynthesis. Experimental work provides equivocal support mostly under controlled conditions without identifying a particular NSC as involved in the regulation. We combined 3-yr in situ leaf gas exchange observations (natural dynamics) in the upper crown of mature Betula pendula simultaneously with measurements of concentrations of sucrose, hexoses (glucose and fructose), and starch, and similar measurements during several one-day shoot girdling (perturbation dynamics).

Partitioning seasonal stem carbon dioxide efflux into stem respiration, bark photosynthesis, and transport-related flux in Scots pine.

Stem CO2 efflux is an important component of the carbon balance in forests. The efflux is considered to principally reflect the net result of two dominating and opposing processes: stem respiration and stem photosynthesis. In addition, transport of CO2 in xylem sap is thought to play an appreciable role in affecting the net flux.

The killifish germline regulates longevity and somatic repair in a sex-specific manner.

Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history.

The killifish germline regulates longevity and somatic repair in a sex-specific manner.

Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history.

Hyposensitive canopy conductance renders ecosystems vulnerable to meteorological droughts.

Increased meteorological drought intensity with rising atmospheric demand for water (hereafter vapor pressure deficit [VPD]) increases the risk of tree mortality and ecosystem dysfunction worldwide. Ecosystem-scale water-use strategy is increasingly recognized as a key factor in regulating drought-related ecosystem responses. However, the link between water-use strategy and ecosystem vulnerability to meteorological droughts is poorly established.

Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.

Transcription factor (TF) binding to genomic DNA elements constitutes one of the key mechanisms that regulates gene expression program in cells. Both consensus and nonconsensus DNA sequence elements influence the recognition specificity of TFs. Based on the analysis of experimentally determined c-Myc binding preferences to genomic DNA, here we statistically predict that certain repetitive, nonconsensus DNA symmetry elements can relatively reduce TF-DNA binding preferences.

Esrrb is a cell-cycle-dependent associated factor balancing pluripotency and XEN differentiation.

Cell cycle and differentiation decisions are linked; however, the underlying principles that drive these decisions are unclear. Here, we combined cell-cycle reporter system and single-cell RNA sequencing (scRNA-seq) profiling to study the transcriptomes of embryonic stem cells (ESCs) in the context of cell-cycle states and differentiation. By applying retinoic acid, to G1 and G2/M ESCs, we show that, while both populations can differentiate toward epiblast stem cells (EpiSCs), only G2/M ESCs could differentiate into extraembryonic endoderm cells.

Contrasting responses of woody and grassland ecosystems to increased CO as water supply varies.

Experiments show that elevated atmospheric CO (eCO) often enhances plant photosynthesis and productivity, yet this effect varies substantially and may be climate sensitive. Understanding if, where and how water supply regulates CO enhancement is critical for projecting terrestrial responses to increasing atmospheric CO and climate change. Here, using data from 14 long-term ecosystem-scale CO experiments, we show that the eCO enhancement of annual aboveground net primary productivity is sensitive to annual precipitation and that this sensitivity differs between woody and grassland ecosystems.

The response of coarse root biomass to long-term CO enrichment and nitrogen application in a maturing Pinus taeda stand with a large broadleaved component.

Elevated atmospheric CO (eCO ) typically increases aboveground growth in both growth chamber and free-air carbon enrichment (FACE) studies. Here we report on the impacts of eCO and nitrogen amendment on coarse root biomass and net primary productivity (NPP) at the Duke FACE study, where half of the eight plots in a 30-year-old loblolly pine (Pinus taeda, L.) plantation, including competing naturally regenerated broadleaved species, were subjected to eCO (ambient, aCO plus 200 ppm) for 15-17 years, combined with annual nitrogen amendments (11.

CloneSeq - Single-cell clonal 3D culture and analysis protocol.

This CloneSeq protocol combines clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing to resolve the limited sensitivity of single-cell approaches. CloneSeq can reveal rare subpopulations and support cellular stemness. CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging clonal enhanced sensitivity.

Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings.

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood.

Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans.

During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes.

H3K27Ac modification and gene expression in psoriasis.

Background: Numerous alterations in gene expression have been described in psoriatic lesions compared to uninvolved or healthy skin. However, the mechanisms which induce this altered expression remain unclear. Epigenetic modifications play a key role in regulating genes' expression.

CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones.

Single-cell assays have revealed the importance of heterogeneity in many biological systems. However, limited sensitivity is a major hurdle for uncovering cellular variation. To overcome it, we developed CloneSeq, combining clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing (RNA-seq).

How tree species, tree size, and topographical location influenced tree transpiration in northern boreal forests during the historic 2018 drought.

Trees in northern latitude ecosystems are projected to experience increasing drought stress as a result of rising air temperatures and changes in precipitation patterns in northern latitude ecosystems. However, most drought-related studies on high-latitude boreal forests (>50°N) have been conducted in North America, with few studies quantifying the response in European and Eurasian boreal forests. Here, we tested how daily whole-tree transpiration (Q, Liters day ) and Q normalized for mean daytime vapor pressure deficit (Q , Liters day kPa ) were affected by the historic 2018 drought in Europe.

Delineating the heterogeneity of matrix-directed differentiation toward soft and stiff tissue lineages via single-cell profiling.

Mesenchymal stromal/stem cells (MSCs) form a heterogeneous population of multipotent progenitors that contribute to tissue regeneration and homeostasis. MSCs assess extracellular elasticity by probing resistance to applied forces via adhesion, cytoskeletal, and nuclear mechanotransducers that direct differentiation toward soft or stiff tissue lineages. Even under controlled culture conditions, MSC differentiation exhibits substantial cell-to-cell variation that remains poorly characterized.

DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation.

In mammals, cellular identity is defined through strict regulation of chromatin modifications and DNA methylation that control gene expression. Methylation of cytosines at CpG sites in the genome is mainly associated with suppression; however, the reason for enhancer-specific methylation is not fully understood. We used sequential ChIP-bisulfite-sequencing for H3K4me1 and H3K27ac histone marks.

Limited vertical CO2 transport in stems of mature boreal Pinus sylvestris trees.

Several studies have suggested that CO2 transport in the transpiration stream can considerably bias estimates of root and stem respiration in ring-porous and diffuse-porous tree species. Whether this also happens in species with tracheid xylem anatomy and lower sap flow rates, such as conifers, is currently unclear. We infused 13C-labelled solution into the xylem near the base of two 90-year-old Pinus sylvestris L.

TrypOx, a Novel Eukaryotic Homolog of the Redox-Regulated Chaperone Hsp33 in .

ATP-independent chaperones are widespread across all domains of life and serve as the first line of defense during protein unfolding stresses. One of the known crucial chaperones for bacterial survival in a hostile environment (e.g.

Estimating canopy gross primary production by combining phloem stable isotopes with canopy and mesophyll conductances.

Gross primary production (GPP) is a key component of the forest carbon cycle. However, our knowledge of GPP at the stand scale remains uncertain, because estimates derived from eddy covariance (EC) rely on semi-empirical modelling and the assumptions of the EC technique are sometimes not fully met. We propose using the sap flux/isotope method as an alternative way to estimate canopy GPP, termed GPP , at the stand scale and at daily resolution.

Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins.

Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful.

Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry.

Transcription factor (TF) recognition is dictated by the underlying DNA motif sequence specific for each TF. Here, we reveal that DNA sequence repeat symmetry plays a central role in defining TF-DNA-binding preferences. In particular, we find that different TFs bind similar symmetry patterns in the context of different developmental layers.