Cohesin composition and dosage independently affect early development in zebrafish.

Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed "cohesinopathies" are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Here we show that zebrafish rad21 or stag2b mutants independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2b mutants have narrower notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA-sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2b, but not rad21 mutants. Our results suggest that mutations altering the quantity versus composition of cohesin have independent developmental consequences, with implications for the understanding and management of cohesinopathies.

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging.

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Genome-wide analysis of early vascular tunic repair and regeneration for Botrylloides digenesis reveals striking similarities to human wound healing.

The early stages of regeneration after injury are similar to those of wound healing. The ascidian Botrylloides diegensis can regenerate an entire adult from a small fragment of vascular tunic following the removal of all zooids in an injury-induced regeneration model. We investigated the molecular and cellular changes following injury to determine the differences between the healing process and the initiation of whole-body regeneration (WBR). We conducted transcriptome analysis at specific time points during regeneration and wound healing to identify differentially expressed genes (DEGs) and the unique biological processes associated with each state. Our findings revealed 296 DEGs at 10 h post-injury (hpi), with 71 highly expressed in healed tissue and 225 expressed during the WBR process. These DEGs were predicted to play roles in tissue reorganization, integrin signaling, extracellular matrix organization, and the innate immune system. Pathway analysis of the upregulated genes in the healed tunic indicated functional enrichment related to tissue repair, as has been observed in other species. Additionally, we examined the cell types in the tunic and ampullae in both tissue states using histology and in situ hybridization for six genes identified by transcriptome analysis. We observed strong mRNA expression in cells within the WBR tunic, and in small RNA-positive granules near the tunic edge. We hypothesized that many of these genes function in the compaction of the ampullae tunic, which is a pivotal process for WBR and dormancy in B. diegensis, and in an immune response. These findings establish surprising similarities between ascidian regeneration and human wound healing, emphasizing the potential for future investigations into human regenerative and repair mechanisms. This study provides valuable insights into the gene sets specifically activated during regeneration compared to wound healing, shedding light on the divergent activities of these processes.

Interactions between root hairs and the soil microbial community affect the growth of maize seedlings.

Root hairs are considered important for rhizosphere formation, which affects root system functioning. Through interactions with soil microorganisms mediated by root exudation, root hairs may affect the phenotypes and growth of young plants. We tested this hypothesis by integrating results from two experiments: (1) a factorial greenhouse seedling experiment with Zea mays B73-wt and its root-hairless mutant, B73-rth3, grown in live and autoclaved soil, quantifying 15 phenotypic traits, seven growth rates, and soil microbiomes and (2) a semi-hydroponic system quantifying root exudation of maize genotypes. Possibly as compensation for lacking root hairs, B73-rth3 seedlings allocated more biomass to roots and grew slower than B73-wt seedlings in live soil, whereas B73-wt seedlings grew slowest in autoclaved soil, suggesting root hairs can be costly and their benefits were realized with more complete soil microbial assemblages. There were substantial differences in root exudation between genotypes and in rhizosphere versus non-rhizosphere microbiomes. The microbial taxa enriched in the presence of root hairs generally enhanced growth compared to taxa enriched in their absence. Our findings suggest the root hairs' adaptive value extends to plant-microbe interactions mediated by root exudates, affecting plant phenotypes, and ultimately, growth.

Process-oriented models of leaf senescence are biased towards the mean: Impacts on model performance and future projections.

The timing of leaf senescence in deciduous trees influences carbon uptake and the resources available for tree growth, defense, and reproduction. Therefore, simulated biosphere-atmosphere interactions and, eventually, estimates of the biospheric climate change mitigation potential are affected by the accuracy of process-oriented leaf senescence models. However, current leaf senescence models are likely to suffer from a bias towards the mean (BTM). This may lead to overly flat trends, whereby errors would increase with increasing difference from the average timing of leaf senescence, ultimately distorting model performance and projected future shifts. However, such effects of the BTM on model performance and future shifts have rarely been investigated. We analyzed >17 × 106 past dates and >49 × 106 future shifts of leaf senescence simulated by 21 process-oriented models that had been calibrated with >45,000 observations from Central Europe for three major European tree species. The surmised effects on model performance and future shifts occurred in all 21 models, revealing strong model-specific BTM. In general, the models performed only slightly better than a null model that just simulates the average timing of leaf senescence. While standard comparisons of model performance favored models with stronger BTM, future shifts of leaf senescence were smaller when projected by models with weaker BTM. Overall, the future shifts for 2090-2099 relative to 1990-1999 increased by an average of 13-14 days after correcting for the BTM. In conclusion, the BTM substantially affects simulations by state-of-the-art leaf senescence models, which compromises model comparisons and distorts projections of future shifts. Smaller shifts result from flatter trends associated with stronger BTM. Therefore, smaller shifts according to models with weaker BTM illustrate the considerable uncertainty in current leaf senescence projections. It is likely that state-of-the-art projections of future biosphere behavior under global change are distorted by erroneous leaf senescence models.

Cryopreserved bone flaps from decompressive craniectomies: a microbiological analysis.

PURPOSE: Surgical site infection (SSI) is a serious complication after cranioplasty. Due to the relatively frequent occurrence of post-cranioplasty SSI, the utility of autologous bone flap swab cultures surrounding cryopreservation as a reliable predictor has been the subject of an ongoing debate. This bicentric study aims to contribute to this topic by conducting an in-depth analysis of bone flaps obtained via decompressive craniectomies. This study had three major aims: assessments of 1) bacterial contamination of bone flaps after decompressive craniotomy, 2) impact of cryoconservation on contamination rates and 3) potential effectiveness of anti-infective treatment to reduce the germ load prior to cranioplasty. METHODS: Cryopreserved bone flaps from two centers were used. Microbiological cultivations of swabs prior to and after cryopreservation were taken and assessed for aerobic and anaerobic growth over a 14-day incubation period. Additionally, in a subset of bone flaps, swab testing was repeated after thorough rinsing with an anti-infectant (octenidine-phenoxyethanol) followed by saline. RESULTS: All 63 bone flaps (patients median age at surgery: 59 years) were obtained via decompressive craniectomies. Swabs done prior to cryopreservation revealed a 54% infection rate with Propionibacterium acnes being the most common microorganism in 65% of those cases. After thorough disinfection of the preserved bone flaps, all but one case showed no bacterial growth in swab testing. Furthermore, no relevant risk factors for bacterial contamination could be identified. CONCLUSION: This retrospective study showed the common presence of bacterial growth in cryopreserved bone flaps before and after freezing. Rinsing with octenidine-phenoxyethanol and saline effectively prevented bacterial growth in a notable percentage of cases, suggesting a potential strategy to reduce contamination. However, persistent bacterial growth in some cases underscores the need for further research to optimize antiseptic measures during autologous cranioplasty.

BackWards - Unveiling the brain's topographic organization of paraspinal sensory input.

Cortical reorganization and its potential pathological significance are being increasingly studied in musculoskeletal disorders such as chronic low back pain (CLBP) patients. However, detailed sensory-topographic maps of the human back are lacking, and a baseline characterization of such representations, reflecting the somatosensory organization of the healthy back, is needed before exploring potential sensory map reorganization. To this end, a novel pneumatic vibrotactile stimulation method was used to stimulate paraspinal sensory afferents, while studying their cortical representations in unprecedented detail. In 41 young healthy participants, vibrotactile stimulations at 20 Hz and 80 Hz were applied bilaterally at nine locations along the thoracolumbar axis while functional magnetic resonance imaging (fMRI) was performed. Model-based whole-brain searchlight representational similarity analysis (RSA) was used to investigate the organizational structure of brain activity patterns evoked by thoracolumbar sensory inputs. A model based on segmental distances best explained the similarity structure of brain activity patterns that were located in different areas of sensorimotor cortices, including the primary somatosensory and motor cortices and parts of the superior parietal cortex, suggesting that these brain areas process sensory input from the back in a "dermatomal" manner. The current findings provide a sound basis for testing the "cortical map reorganization theory" and its pathological relevance in CLBP.

Structure-Property Relationships of Short Chain (Mixed) Cellulose Esters Synthesized in a DMSO/TMG/CO2 Switchable Solvent System.

Increasing environmental pollution and petroleum resource depletion are important indicators for the necessary and inevitable replacement of fossil-based polymeric materials with more sustainable counterparts. Hence, the development of bio-based materials from renewable resources, such as cellulose, is of great importance. Herein, we introduce a rapid and homogeneous microwave assisted synthesis of high molecular weight (59 kDa ≤ Mn ≤ 116 kDa) short chain (mixed) cellulose esters (CEs) with variable acyl side chain length (2 ≤ C ≤ 8) by using a DMSO/TMG/CO2 switchable solvent system. Accordingly, (mixed) CEs were synthesized by implementing tetramethylguanidine (TMG) into a switchable solvent system (DMSO/TMG/CO2), followed by in-depth structural characterization via IR, 1H NMR, 13C NMR, and SEC. Examination of the structure-property relationships revealed a decrease in the glass transition temperature (177 °C ≤ Tg ≤ 204 °C), an increase in surface hydrophobicity, i.e., water contact angle (WCA) (65° ≤ WCA ≤ 98°), and a decrease of Young's modulus (7.51 MPa ≤ E ≤ 13.6 MPa), with longer alkyl side chains.

In the back of your mind: Cortical mapping of paraspinal afferent inputs.

Topographic organisation is a hallmark of vertebrate cortex architecture, characterised by ordered projections of the body's sensory surfaces onto brain systems. High-resolution functional magnetic resonance imaging (fMRI) has proven itself as a valuable tool to investigate the cortical landscape and its (mal-)adaptive plasticity with respect to various body part representations, in particular extremities such as the hand and fingers. Less is known, however, about the cortical representation of the human back. We therefore validated a novel, MRI-compatible method of mapping cortical representations of sensory afferents of the back, using vibrotactile stimulation at varying frequencies and paraspinal locations, in conjunction with fMRI. We expected high-frequency stimulation to be associated with differential neuronal activity in the primary somatosensory cortex (S1) compared with low-frequency stimulation and that somatosensory representations would differ across the thoracolumbar axis. We found significant differences between neural representations of high-frequency and low-frequency stimulation and between representations of thoracic and lumbar paraspinal locations, in several bilateral S1 sub-regions, and in regions of the primary motor cortex (M1). High-frequency stimulation preferentially activated Brodmann Area (BA) regions BA3a and BA4p, whereas low-frequency stimulation was more encoded in BA3b and BA4a. Moreover, we found clear topographic differences in S1 for representations of the upper and lower back during high-frequency stimulation. We present the first neurobiological validation of a method for establishing detailed cortical maps of the human back, which might serve as a novel tool to evaluate the pathological significance of neuroplastic changes in clinical conditions such as chronic low back pain.

Sustainable One-Pot Cellulose Dissolution and Derivatization via a Tandem Reaction in the DMSO/DBU/CO2 Switchable Solvent System.

New sustainable concepts have to be developed to overcome the increasing problems of resource availability. Cellulose derivatives with tunable material properties are promising biobased alternatives to existing petroleum-derived polymeric materials. However, the chemical modification of cellulose is very challenging, often requiring harsh conditions and complex solubilization or activation steps. More sustainable procedures toward novel cellulose derivatives are therefore of great interest. Herein, we describe a novel concept combining two approaches, (i) tandem catalysis and (ii) cellulose derivatization, by applying a single catalyst for three transformations in the DMSO/DBU/CO2 switchable solvent system. Cellulose was functionalized with four different biobased isothiocyanates, which were formed in situ via a catalytic sulfurization of isocyanides with elemental sulfur, preventing the exposure and handling of the isothiocyanates. The degree of substitution of the formed O-cellulose thiocarbamates was shown to be controllable in a range of 0.52-2.16 by varying the equivalents of the reactants. All obtained products were analyzed by ATR-IR, 1H, 13C, and 31P NMR spectroscopy as well as size exclusion chromatography, elemental analysis, differential scanning calorimetry, and thermal gravimetric analysis. Finally, the tandem reaction approach was shown to be beneficial in terms of efficiency as well as sustainability compared to a stepwise synthesis. Recycling ratios ranging from 79.1% to 95.6% were obtained for the employed components, resulting in an E-factor of 2.95 for the overall process.

Cohesin facilitates zygotic genome activation in zebrafish.

At zygotic genome activation (ZGA), changes in chromatin structure are associated with new transcription immediately following the maternal-to-zygotic transition (MZT). The nuclear architectural proteins cohesin and CCCTC-binding factor (CTCF) contribute to chromatin structure and gene regulation. We show here that normal cohesin function is important for ZGA in zebrafish. Depletion of the cohesin subunit Rad21 delays ZGA without affecting cell cycle progression. In contrast, CTCF depletion has little effect on ZGA, whereas complete abrogation is lethal. Genome-wide analysis of Rad21 binding reveals a change in distribution from pericentromeric satellite DNA and other locations, including the miR-430 locus (the products of which are responsible for maternal transcript degradation), to genes, as embryos progress through the MZT. After MZT, a subset of Rad21 binding overlaps the pioneer factor Pou5f3, which activates early expressed genes. Rad21 depletion disrupts the formation of nucleoli and RNA polymerase II foci, suggestive of global defects in chromosome architecture. We propose that Rad21/cohesin redistribution to active areas of the genome is key to the establishment of chromosome organization and the embryonic developmental program.

Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels.

Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage.

Sustainable Fatty Acid Modification of Cellulose in a CO2-Based Switchable Solvent and Subsequent Thiol-Ene Modification.

Searching for more sustainable materials as an alternative to petroleum-based products is of increasing interest due to different environmental issues. Cellulose and fatty acids are two very promising candidates for biobased material design. Herein, we report a sustainable synthesis of fatty acid cellulose esters (FACEs) via transesterification of cellulose with methyl-10-undecenoate in a CO2-based switchable solvent system. FACEs with a degree of substitution between 0.70 and 1.97 were synthesized by simple variation of reaction parameters and characterized in detail. Subsequently, a FACE with a degree of substitution (DS) of 0.70 was modified via thiol-ene reaction, demonstrating an efficient and versatile method to tune the structure and properties of the new cellulose derivatives. Films were produced from each sample via solvent casting, and their mechanical properties were examined using tensile tests. Elastic moduli (E) ranging from 90 to 635 MPa and elongations at break between 2 and 23% were observed, depending on the DS of the FACE and the type of thiol employed for the modification. Finally, contact angle measurements confirmed an increase in the surface hydrophobicity (75-91°) for the thiol-ene-modified samples.

Fully Renewable Non-Isocyanate Polyurethanes via the Lossen Rearrangement.

In this work, a straightforward and efficient synthesis approach to renewable non-isocyanate polyurethanes (NIPUs) is described. For this purpose, suitable and renewable carbamate monomers, possessing two double bonds, are synthesized from hydroxamic fatty acid derivatives via the Lossen rearrangement in a one-step synthesis, and sustainable dithiols are synthesized from dialkenes derived from renewable feedstock (i.e., limonene and 1,4-cyclohexadiene). Subsequently, the comonomers are polymerized with the highly efficient thiol-ene reaction to produce NIPUs with Mn values up to 26 kg mol-1 bearing thioether linkages. The main side product of the Lossen rearrangement, a symmetric urea, can also be polymerized in the same fashion. Important in the view of sustainability, the monomer mixture can also be used directly, without separation. The obtained polymers are characterized by NMR, attenuated total reflection-infrared spectroscopy, differential scanning calorimetry, and size exclusion chromatography.

Synthesis and Encapsulation of Uniform Star-Shaped Block-Macromolecules.

Linear uniform oligomers synthesized via a two-step iterative cycle are postmodified with uniform octaethylene glycol monomethyl ether and finally coupled via azide-alkyne cycloaddition to yield uniform star-shaped block macromolecules with a mass ranging from 10 to 14 kDa. Each of the molecules is carefully characterized by NMR, electrospray ionization mass spectrometry (ESI-MS), and size exclusion chromatography (SEC) to underline their purity as well as their uniformity. The obtained star-shaped macromolecules are investigated in their ability to encapsulate dye molecules by carrying out qualitative solid-liquid phase transfer experiments.

A Practical and Efficient Synthesis of Uniform Conjugated Rod-Like Oligomers.

Herein, a more practical and efficient synthesis protocol for the preparation of uniform rod-like oligo(1,4-phenylene ethynylene)s (OPE)s is presented. Applying an iterative reaction cycle consisting of a decarboxylative coupling reaction and a saponification of an alkynyl carboxylic ester, a uniform pentamer is obtained in ten steps with 14% overall yield. The copper-free conditions prevent homocoupling until the trimer stage, resulting in a significantly easier work-up of the products. Homocoupling is observed from the tetramer stage on, but a simple variation of the work-up procedure also yields the uniform tetramer and pentamer. A thorough comparison with the commonly used and described Sonogashira approach reveals that with the new presented strategy, OPEs can be built in similar overall yield, but easier purification and in a quarter of the time. All oligomers are fully characterized by proton and carbon nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), size-exclusion chromatography (SEC), and infrared spectroscopy (IR).

Synthesis of Passerini-3CR Polymers and Assembly into Cytocompatible Polymersomes.

The versatility of the Passerini three component reaction (Passerini-3CR) is herein exploited for the synthesis of an amphiphilic diblock copolymer, which self-assembles into polymersomes. Carboxy-functionalized poly(ethylene glycol) methyl ether is reacted with AB-type bifunctional monomers and tert-butyl isocyanide in a single process via Passerini-3CR. The resultant diblock copolymer (P1) is obtained in good yield and molar mass dispersity and is well tolerated in model cell lines. The Passerini-3CR versatility and reproducibility are shown by the synthesis of P2, P3, and P4 copolymers. The ability of the Passerini P1 polymersomes to incorporate hydrophilic molecules is verified by loading doxorubicin hydrochloride in P1DOX polymersomes. The flexibility of the synthesis is further demonstrated by simple post-functionalization with a dye, Cyanine-5 (Cy5). The obtained P1-Cy5 polymersomes rapidly internalize in 2D cell monolayers and penetrate deep into 3D spheroids of MDA-MB-231 triple-negative breast cancer cells. P1-Cy5 polymersomes injected systemically in healthy mice are well tolerated and no visible adverse effects are seen under the conditions tested. These data demonstrate that new, biodegradable, biocompatible polymersomes having properties suitable for future use in drug delivery can be easily synthesized by the Passerini-3CR.

Fatty Acids and their Derivatives as Renewable Platform Molecules for the Chemical Industry.

Oils and fats of vegetable and animal origin remain an important renewable feedstock for the chemical industry. Their industrial use has increased during the last 10 years from 31 to 51 million tonnes annually. Remarkable achievements made in the field of oleochemistry in this timeframe are summarized herein, including the reduction of fatty esters to ethers, the selective oxidation and oxidative cleavage of C-C double bonds, the synthesis of alkyl-branched fatty compounds, the isomerizing hydroformylation and alkoxycarbonylation, and olefin metathesis. The use of oleochemicals for the synthesis of a great variety of polymeric materials has increased tremendously, too. In addition to lipases and phospholipases, other enzymes have found their way into biocatalytic oleochemistry. Important achievements have also generated new oil qualities in existing crop plants or by using microorganisms optimized by metabolic engineering.

Modification of Starch via the Biginelli Multicomponent Reaction.

An efficient and straightforward modification of starch using renewable and commercially available aromatic aldehydes (benzaldehyde, vanillin, and p-anisaldehyde) and urea via the Biginelli multicomponent reaction is reported in this work. First, starch acetoacetate (SAA) with a degree of substitution ranging from 1.4 to 2.5, depending on the reaction time or the molar ratio of reactants, is prepared. SAA is then modified with different aromatic aldehydes and urea via the Biginelli reaction. The modified products are characterized by ATR-IR, NMR, and gel permeation chromatography (GPC). The processability of the products is also investigated using a hot press instrument, revealing that glycerol is a suitable and renewable plasticizer for the Biginelli products.

Progress Toward Sustainable Reversible Deactivation Radical Polymerization.

The recent focus of media and governments on renewability, green chemistry, and circular economy has led to a surge in the synthesis of renewable monomers and polymers. In this review, focussing on renewable monomers for reversible deactivation radical polymerizations (RDRP), it is highlighted that for the majority of the monomers and polymers reported, the claim to renewability is not always accurate. By closely examining the sustainability of synthetic routes and the renewability of starting materials, fully renewable monomers are identified and discussed in terms of sustainability, polymerization behavior, and properties obtained after polymerization. The holistic discussion considering the overall preparation process of polymers, that is, monomer syntheses, origin of starting materials, solvents used, the type of RDRP technique utilized, and the purification method, allows to highlight certain topics which need to be addressed in order to progress toward not only (partially) renewable, but sustainable monomers and polymers using RDRPs.