Can N2 O emissions offset the benefits from soil organic carbon storage?

To respect the Paris agreement targeting a limitation of global warming below 2°C by 2100, and possibly below 1.5°C, drastic reductions of greenhouse gas emissions are mandatory but not sufficient. Large-scale deployment of other climate mitigation strategies is also necessary. Among these, increasing soil organic carbon (SOC) stocks is an important lever because carbon in soils can be stored for long periods and land management options to achieve this already exist and have been widely tested. However, agricultural soils are also an important source of nitrous oxide (N2 O), a powerful greenhouse gas, and increasing SOC may influence N2 O emissions, likely causing an increase in many cases, thus tending to offset the climate change benefit from increased SOC storage. Here we review the main agricultural management options for increasing SOC stocks. We evaluate the amount of SOC that can be stored as well as resulting changes in N2 O emissions to better estimate the climate benefits of these management options. Based on quantitative data obtained from published meta-analyses and from our current level of understanding, we conclude that the climate mitigation induced by increased SOC storage is generally overestimated if associated N2 O emissions are not considered but, with the exception of reduced tillage, is never fully offset. Some options (e.g. biochar or non-pyrogenic C amendment application) may even decrease N2 O emissions.

Loss of genomic integrity induced by lysosphingolipid imbalance drives ageing in the heart.

Cardiac dysfunctions dramatically increase with age. Revealing a currently unknown contributor to cardiac ageing, we report the age-dependent, cardiac-specific accumulation of the lysosphingolipid sphinganine (dihydrosphingosine, DHS) as an evolutionarily conserved hallmark of the aged vertebrate heart. Mechanistically, the DHS-derivative sphinganine-1-phosphate (DHS1P) directly inhibits HDAC1, causing an aberrant elevation in histone acetylation and transcription levels, leading to DNA damage. Accordingly, the pharmacological interventions, preventing (i) the accumulation of DHS1P using SPHK2 inhibitors, (ii) the aberrant increase in histone acetylation using histone acetyltransferase (HAT) inhibitors, (iii) the DHS1P-dependent increase in transcription using an RNA polymerase II inhibitor, block DHS-induced DNA damage in human cardiomyocytes. Importantly, an increase in DHS levels in the hearts of healthy young adult mice leads to an impairment in cardiac functionality indicated by a significant reduction in left ventricular fractional shortening and ejection fraction, mimicking the functional deterioration of aged hearts. These molecular and functional defects can be partially prevented in vivo using HAT inhibitors. Together, we report an evolutionarily conserved mechanism by which increased DHS levels drive the decline in cardiac health.

Detection of RNA-DNA binding sites in long noncoding RNAs.

Long non-coding RNAs (lncRNAs) can act as scaffolds that promote the interaction of proteins, RNA, and DNA. There is increasing evidence of sequence-specific interactions of lncRNAs with DNA via triple-helix (triplex) formation. This process allows lncRNAs to recruit protein complexes to specific genomic regions and regulate gene expression. Here we propose a computational method called Triplex Domain Finder (TDF) to detect triplexes and characterize DNA-binding domains and DNA targets statistically. Case studies showed that this approach can detect the known domains of lncRNAs Fendrr, HOTAIR and MEG3. Moreover, we validated a novel DNA-binding domain in MEG3 by a genome-wide sequencing method. We used TDF to perform a systematic analysis of the triplex-forming potential of lncRNAs relevant to human cardiac differentiation. We demonstrated that the lncRNA with the highest triplex-forming potential, GATA6-AS, forms triple helices in the promoter of genes relevant to cardiac development. Moreover, down-regulation of GATA6-AS impairs GATA6 expression and cardiac development. These data indicate the unique ability of our computational tool to identify novel triplex-forming lncRNAs and their target genes.

The missing-VP effect in readers of English as a second language.

English sentences with double center-embedded clauses are read faster when they are made ungrammatical by removing one of the required verb phrases. This phenomenon is known as the missing-VP effect. German and Dutch speakers do not experience the missing-VP effect when reading their native language, but they do when reading English as a second language (L2). We investigate whether the missing-VP effect when reading L2 English occurs in native Dutch speakers because their knowledge of English is similar to that of native English speakers (the high exposure account), or because of the difficulty of L2 reading (the low proficiency account). In an eye-tracking study, we compare the size of the missing-VP effect between native Dutch and native English participants, and across native Dutch participants with varying L2 English proficiency and exposure. Results provide evidence for both accounts, suggesting that both native-like knowledge of English and L2 reading difficulty play a role.

Increase of cystathionine-γ-lyase (CSE) during late wound repair: Hydrogen sulfide triggers cytokeratin 10 expression in keratinocytes.

The gaseous mediators nitric oxide (NO), carbon monoxide (CO) and lately also hydrogen sulfide (H2S) have been described to contribute to the interplay of protein type- and lipid mediators in the regulation of wound healing. In particular, the recently reported role of H2S in skin repair remains largely unresolved. Therefore we assessed the expressional kinetics of potential H2S-producing enzymes during undisturbed skin repair: the cystathionine-γ-lyase (CSE), the cystathionine-ß-synthase (CBS) and the 3-mercaptopyruvate sulfurtransferase (MPST). All three enzymes were not transcriptionally induced upon wounding and remained silent through the acute inflammatory and proliferative phase of skin repair. By contrast, CSE expression started to increase significantly at the later stages of healing, when cellular proliferation ceases within the granulation tissue and neoepidermis. The importance of H2S production in late healing phases was supported by a strong induction of otherwise not-induced CBS to complement the loss of CSE function in CSE-deficient mice. Immunohistochemistry revealed hair follicle keratinocytes and basal keratinocytes of the neo-epidermis covering the wound area as sources of CSE expression. Subsequent in vitro studies implicated a role of CSE-derived H2S for keratinocyte differentiation: the H2S-donor GYY4137 markedly increased the Ca2+-triggered expression of the early keratinocyte differentiation markers cytokeratin 10 (CK10) and involucrin (IVN) in cultured human keratinocytes. Here, GYY4137-derived H2S strongly enhanced CK10 expression by increasing the binding of RNA polymerase II to the CK10 promoter.

Judgements about double-embedded relative clauses differ between languages.

When the middle verb phrase is removed from an English double-embedded sentence, the remainder of the sentence is read faster in spite of the ungrammaticality. It has been shown that this "missing-VP effect" is reversed in German and Dutch. The current study demonstrates that the same cross-linguistic difference holds for sentences judgments: Native speakers consider English double-embedded sentences more comprehensible and acceptable when the middle verb phrase is removed, whereas the same is not the case in Dutch. This interaction between language and grammaticality also appears in a within-subjects replication that tests Dutch native speakers in both languages. These results, in combination with earlier findings, give rise to a hybrid account according to which the missing-VP effect is caused by properties of the language as well as properties of working memory.

A heterogeneous Ly-6B2+ leukocyte population consists of yet undescribed iNOS-expressing cell types in murine skin wounds.

The gaseous mediator nitric oxide (NO) is a central regulatory molecule during the inflammatory phase of cutaneous tissue repair. The inducible NO-synthase (iNOS) represents the main isoform of the three NO producing enzymes at the wound site. In particular, keratinocytes and macrophages are described as main sources of iNOS-derived NO in skin wounds. Here we provide experimental evidence that Ly-6B2+ leukocytes are an additional cellular source of iNOS-derived NO in wounds. As wound iNOS protein expression temporally coincides with both macrophage and neutrophil infiltration, we used immunohistochemistry (IHC) and fluorescence-activated cell sorting (FACS) to address iNOS expression in both macrophages and neutrophil subsets. IHC analyses excluded F4/80+ macrophages as iNOS producers, but indicated Ly-6G/C (Gr-1)+ neutrophils to express iNOS in wound granulation tissue. A subsequent FACS-based analysis from cellular wound tissue preparations revealed an iNOS-expressing fraction of Ly-6B2-determined leukocytes that consisted of Ly-6G+ and Ly-6G- cells, meaning that mainly mature neutrophils (Ly-6B2+/Ly-6G+) as well as inflammatory monocytes (Ly-6B2+/Ly-6G-) are dominant iNOS-expressing cell types in the developing granulation tissue of acute wounds.

Prediction During Natural Language Comprehension.

The notion of prediction is studied in cognitive neuroscience with increasing intensity. We investigated the neural basis of 2 distinct aspects of word prediction, derived from information theory, during story comprehension. We assessed the effect of entropy of next-word probability distributions as well as surprisal A computational model determined entropy and surprisal for each word in 3 literary stories. Twenty-four healthy participants listened to the same 3 stories while their brain activation was measured using fMRI. Reversed speech fragments were presented as a control condition. Brain areas sensitive to entropy were left ventral premotor cortex, left middle frontal gyrus, right inferior frontal gyrus, left inferior parietal lobule, and left supplementary motor area. Areas sensitive to surprisal were left inferior temporal sulcus ("visual word form area"), bilateral superior temporal gyrus, right amygdala, bilateral anterior temporal poles, and right inferior frontal sulcus. We conclude that prediction during language comprehension can occur at several levels of processing, including at the level of word form. Our study exemplifies the power of combining computational linguistics with cognitive neuroscience, and additionally underlines the feasibility of studying continuous spoken language materials with fMRI.

Climate change mitigation through livestock system transitions.

Livestock are responsible for 12% of anthropogenic greenhouse gas emissions. Sustainable intensification of livestock production systems might become a key climate mitigation technology. However, livestock production systems vary substantially, making the implementation of climate mitigation policies a formidable challenge. Here, we provide results from an economic model using a detailed and high-resolution representation of livestock production systems. We project that by 2030 autonomous transitions toward more efficient systems would decrease emissions by 736 million metric tons of carbon dioxide equivalent per year (MtCO2e⋅y(-1)), mainly through avoided emissions from the conversion of 162 Mha of natural land. A moderate mitigation policy targeting emissions from both the agricultural and land-use change sectors with a carbon price of US$10 per tCO2e could lead to an abatement of 3,223 MtCO2e⋅y(-1). Livestock system transitions would contribute 21% of the total abatement, intra- and interregional relocation of livestock production another 40%, and all other mechanisms would add 39%. A comparable abatement of 3,068 MtCO2e⋅y(-1) could be achieved also with a policy targeting only emissions from land-use change. Stringent climate policies might lead to reductions in food availability of up to 200 kcal per capita per day globally. We find that mitigation policies targeting emissions from land-use change are 5 to 10 times more efficient--measured in "total abatement calorie cost"--than policies targeting emissions from livestock only. Thus, fostering transitions toward more productive livestock production systems in combination with climate policies targeting the land-use change appears to be the most efficient lever to deliver desirable climate and food availability outcomes.

Recessive cardiac phenotypes in induced pluripotent stem cell models of Jervell and Lange-Nielsen syndrome: disease mechanisms and pharmacological rescue.

Jervell and Lange-Nielsen syndrome (JLNS) is one of the most severe life-threatening cardiac arrhythmias. Patients display delayed cardiac repolarization, associated high risk of sudden death due to ventricular tachycardia, and congenital bilateral deafness. In contrast to the autosomal dominant forms of long QT syndrome, JLNS is a recessive trait, resulting from homozygous (or compound heterozygous) mutations in KCNQ1 or KCNE1. These genes encode the α and ß subunits, respectively, of the ion channel conducting the slow component of the delayed rectifier K(+) current, IKs. We used complementary approaches, reprogramming patient cells and genetic engineering, to generate human induced pluripotent stem cell (hiPSC) models of JLNS, covering splice site (c.478-2A>T) and missense (c.1781G>A) mutations, the two major classes of JLNS-causing defects in KCNQ1. Electrophysiological comparison of hiPSC-derived cardiomyocytes (CMs) from homozygous JLNS, heterozygous, and wild-type lines recapitulated the typical and severe features of JLNS, including pronounced action and field potential prolongation and severe reduction or absence of IKs. We show that this phenotype had distinct underlying molecular mechanisms in the two sets of cell lines: the previously unidentified c.478-2A>T mutation was amorphic and gave rise to a strictly recessive phenotype in JLNS-CMs, whereas the missense c.1781G>A lesion caused a gene dosage-dependent channel reduction at the cell membrane. Moreover, adrenergic stimulation caused action potential prolongation specifically in JLNS-CMs. Furthermore, sensitivity to proarrhythmic drugs was strongly enhanced in JLNS-CMs but could be pharmacologically corrected. Our data provide mechanistic insight into distinct classes of JLNS-causing mutations and demonstrate the potential of hiPSC-CMs in drug evaluation.

Inhibition of cyclooxygenase-1 and -2 activity in keratinocytes inhibits PGE2 formation and impairs vascular endothelial growth factor release and neovascularisation in skin wounds.

Inhibition of cyclooxygenase (Cox) enzymatic activity by non-steroidal anti-inflammatory drugs (NSAIDs) provides the molecular basis of analgesia following wounding or surgery. This study investigated the role of Cox activity in the regulation of vascular endothelial growth factor (VEGF) expression in keratinocytes and the formation of new blood vessels in acute wounds in mice. To this end, human HaCaT keratinocytes were stimulated with epidermal growth factor (EGF). EGF increased Cox-1 mRNA in the presence of the constitutively expressed Cox-1 protein in keratinocytes. EGF coinduced Cox-2 and VEGF165 mRNA and protein expression and an accumulation of prostaglandin E2 (PGE2 ) in cell culture supernatants. Inhibition of Cox isozyme activity by Cox-1 and -2 siRNA or ibuprofen reduced PGE2 and VEGF165 release from keratinocytes. In a mouse model of excisional wound healing, Cox-2 and VEGF165 expression were colocalized in the granulation tissue of acute wounds. Oral treatment of mice with the Cox-1 and -2 inhibitor diclofenac was associated with reduced levels of VEGF165 protein and an impaired blood vessel formation in acute wound tissue. In summary, our data suggest that a reduction of PGE2 -triggered VEGF165 protein expression in wound keratinocytes is likely to contribute to the observed impairment of wound neovascularisation upon Cox inhibition.

Reservoir computing and the Sooner-is-Better bottleneck.

Prior language input is not lost but integrated with the current input. This principle is demonstrated by "reservoir computing": Untrained recurrent neural networks project input sequences onto a random point in high-dimensional state space. Earlier inputs can be retrieved from this projection, albeit less reliably so as more input is received. The bottleneck is therefore not "Now-or-Never" but "Sooner-is-Better."

FGF signalling inhibits neural induction in human embryonic stem cells.

Human embryonic stem cells (hESCs) can exit the self-renewal programme, through the action of signalling molecules, at any given time and differentiate along the three germ layer lineages. We have systematically investigated the specific roles of three signalling pathways, TGFß/SMAD2, BMP/SMAD1, and FGF/ERK, in promoting the transition of hESCs into the neuroectoderm lineage. In this context, inhibition of SMAD2 and ERK signalling served to cooperatively promote exit from hESC self-renewal through the rapid downregulation of NANOG and OCT4. In contrast, inhibition of SMAD1 signalling acted to maintain SOX2 expression and prevent non-neural differentiation via HAND1. Inhibition of FGF/ERK upregulated OTX2 that subsequently induced the neuroectodermal fate determinant PAX6, revealing a novel role for FGF2 in indirectly repressing PAX6 in hESCs. Combined inhibition of the three pathways hence resulted in highly efficient neuroectoderm formation within 4 days, and subsequently, FGF/ERK inhibition promoted rapid differentiation into peripheral neurons. Our study assigns a novel, biphasic role to FGF/ERK signalling in the neural induction of hESCs, which may also have utility for applications requiring the rapid and efficient generation of peripheral neurons.

Uptake of neutrophil-derived Ym1 protein distinguishes wound macrophages in the absence of interleukin-4 signaling in murine wound healing.

The determination of regenerative wound-healing macrophages as alternatively activated macrophages is currently questioned by the absence of IL-4 in wound tissue. Yet, murine wound tissue expressed high levels of Ym1 (chitinase 3-like 3), an established marker of the IL-4-induced alternatively activated macrophage phenotype. Ym1 was expressed in wound neutrophils but not in macrophages. Initially, Ym1-free wound-healing macrophages, invading from the wound margins, became gradually positive for the protein in the absence of IL-4 signaling and Stat6 activation, as they entered the neutrophil-populated wound regions. IL-4 failed to induce Ym1 protein in ex vivo-cultured wound tissue explants containing wound-healing macrophages. Recombinant Ym1 protein was selectively taken up by macrophages but not by keratinocytes and endothelial cells. Cultured macrophages lost the ability to take up the recombinant protein when four highly conserved residues and the 70-amino acid small α+ß domain essential for Ym1 function were removed. The data suggest that the IL-4/Stat6-independent presence of Ym1 protein in wound-healing macrophages is of exogenous origin, with Ym1 taken up from wound neutrophils as the cellular source. The data suggest that in situ determination of wound-healing macrophages, often defined by Ym1, might not essentially describe an IL-4-dependent macrophage phenotype. Consequently, wound-healing macrophages should not be classified by the established categories of the well-accepted but simplified paradigm of M1/M2 macrophage activation.

Deregulated unfolded protein response in chronic wounds of diabetic ob/ob mice: a potential connection to inflammatory and angiogenic disorders in diabetes-impaired wound healing.

Type-2 diabetes mellitus (T2D) represents an important metabolic disorder, firmly connected to obesity and low level of chronic inflammation caused by deregulation of fat metabolism. The convergence of chronic inflammatory signals and nutrient overloading at the endoplasmic reticulum (ER) leads to activation of ER-specific stress responses, the unfolded protein response (UPR). As obesity and T2D are often associated with impaired wound healing, we investigated the role of UPR in the pathologic of diabetic-impaired cutaneuos wound healing. We determined the expression patterns of the three UPR branches during normal and diabetes-impaired skin repair. In healthy and diabetic mice, injury led to a strong induction of BiP (BiP/Grp78), C/EBP homologous protein (CHOP) and splicing of X-box-binding protein (XBP)1. Diabetic-impaired wounds showed gross and sustained induction of UPR associated with increased expression of the pro-inflammatory chemokine macrophage inflammatory protein (MIP)2 as compared to normal healing wounds. In vitro, treatment of RAW264.7 macrophages with tunicamycin, and subsequently stimulation with lipopolysaccharide (LPS) and interferon (IFN)-γ enhances MIP2 mRNA und protein expression compared to proinflammatory stimulation alone. However, LPS/IFNγ induced vascular endothelial growth factor (VEGF) production was blunted by tunicamycin induced-ER stress. Hence, UPR is activated following skin injury, and functionally connected to the production of proinflammatory mediators. In addition, prolongation of UPR in diabetic non-healing wounds aggravates ER stress and weakens the angiogenic phenotype of wound macrophages.

Rapid hierarchical assembly of medium-size DNA cassettes.

Synthetic biology applications call for efficient methods to generate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of multiple plasmids encoding individual genes. Multiple methods have been proposed to achieve this goal. Here, we describe a novel protocol that allows one-step cloning of up to four gene-size DNA fragments, followed by a second assembly of these concatenated sequences into large circular DNA. The protocols described here comprise a simple, cheap and fast solution for routine construction of cassettes with up to 10 gene-size components.

Communicative efficiency in multimodal language directed at children and adults.

The ecology of human communication is face to face. In these contexts, speakers dynamically modify their communication across vocal (e.g., speaking rate) and gestural (e.g., cospeech gestures related in meaning to the content of speech) channels while speaking. What is the function of these adjustments? Here we ask whether speakers dynamically make these adjustments to increase communicative success, and decrease cognitive effort while speaking. We assess whether speakers modulate word durations and produce iconic (i.e., imagistically evoking properties of referents) gestures depending on the predictability of each word they utter. Predictability is operationalized as surprisal and computed from computational language models trained on corpora of child-directed, or adult-directed language. Using data from a novel corpus (Ecological Language Corpus) of naturalistic interactions between adult-child (aged 3-4), and adult-adult, we show that surprisal predicts speakers' multimodal adjustments and that some of these effects are modulated by whether the comprehender is a child or an adult. Thus, communicative efficiency applies generally across vocal and gestural communicative channels not being limited to structural properties of language or vocal modality. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Perspectives on Fracture Liaison Service in Austria: clinical and economic considerations.

Osteoporosis is a widespread disease and affects over 500,000 people in Austria. Fragility fractures are associated with it and represent not only an individual problem for the patients, but also an enormous burden for the healthcare system. While trauma surgery care is well provided in Vienna, there is an enormous treatment gap in secondary prevention after osteoporotic fracture. Systematic approaches such as the Fracture Liaison Service (FLS) aim to identify patients with osteoporosis after fracture, to clarify diagnostically, to initiate specific therapy, and to check therapy adherence. The aim of this article is to describe the practical implementation and operational flow of an already established FLS in Vienna. This includes the identification of potential FLS inpatients, the diagnostic workup, and recommendations for an IT solution for baseline assessment and follow-up of FLS patients. We summarize the concept, benefits, and limitations of FLS and provide prospective as well as clinical and economic considerations for a city-wide FLS, managed from a central location. Future concepts of FLS should include artificial intelligence for vertebral fracture detection and simple IT tools for the implementation of FLS in the outpatient sector.

A modified TALEN-based system for robust generation of knock-out human pluripotent stem cell lines and disease models.

BACKGROUND: Transcription activator-like effector nucleases (TALENs) have emerged as a tool for enabling targeted gene editing and disruption in difficult systems, such as human pluripotent stem cells (hPSCs). The modular architecture of TAL effectors theoretically enables targeting of any genomic locus and several cloning systems for custom TALEN assembly have recently been established. However, there is a lack of versatile TALEN expression systems applicable to hPSCs. RESULTS: Here, we extend an existing TALE assembly system by a dual set of expression vectors for efficient application of TALEN technology in hPSCs. This is characterized by improved TALEN architecture as well as antibiotic resistance and fluorescent reporter cassettes, thus enabling enrichment for transfected cells. Improved functionality of the combined system was demonstrated by targeted disruption of the HPRT1 gene to create isogenic disease models of Lesch-Nyhan-Syndrome. Using female hPSCs, homozygous disruption of HPRT1 occurred at efficiencies of up to 15%. Differentiating isogenic knock-out cells both into central nervous system (CNS) as well as into sensory-like neurons recapitulated previously described phenotypes based on patient-specific induced PSCs and extended these findings to non-CNS neurons, respectively. CONCLUSION: The combined vector system allows for flexible and affordable generation of knock-out hPSCs lines, thus enabling investigation of developmental processes as well as the generation of isogenic disease models without the need for patient material.

Reading time data for evaluating broad-coverage models of English sentence processing.

We make available word-by-word self-paced reading times and eye-tracking data over a sample of English sentences from narrative sources. These data are intended to form a gold standard for the evaluation of computational psycholinguistic models of sentence comprehension in English. We describe stimuli selection and data collection and present descriptive statistics, as well as comparisons between the two sets of reading times.