On the Low-Pressure Hysteresis (LPH) in Gas Sorption Isotherms of Porous Carbons.

This study investigates the origin of low-pressure hysteresis (LPH) in the adsorption and desorption of three different probe molecules: carbon dioxide, nitrogen, and argon, across various adsorption temperatures (from cryogenic to room temperature), and within five different carbon materials: synthetic carbons (pristine and one post-synthetically oxidized) and natural coal. Significant attention is dedicated to elucidating LPH in oxidized samples outgassed at various temperatures (120-350 °C). Experimental results show that insufficient outgassing temperature can lead to unreliable data due to artificial LPH and significantly underestimated textural properties, primarily caused by porosity blockage from substances like moisture. Conversely, in samples where heteroatoms have a stabilizing effect on texture, such as natural coal, careful consideration of outgassing temperature is crucial due to the risk of thermal degradation. Other factors contributing to LPH are adsorption temperature, and especially, kinetic limitations at cryogenic temperatures for cellulose-based carbons. Minor factors responsible for LPH are the physical state of the sample (monolith vs powder) and the flexibility of the porous system, both studied by carbon dioxide sorption. This study constitutes an important piece in the evaluation of LPH, providing practical recommendations and underlining the importance of experimental design, with implications for further research in this complex field.

A New Member of the Metal-Porphyrin Frameworks Family: Structure, Physicochemical Properties, Hydrogen and Carbon Dioxide Adsorption.

A novel holmium-based porous metal-porphyrin framework, {(H3 O+ )[Ho(H2 TPPS)]- ⋅ 4H2 O}n (denoted as UPJS-17), was synthesised by hydrothermal reaction. Structural analysis reveals, that UPJS-17 has a three-dimensional open framework. The framework is negatively charged and the negative charge is compensated by hydronium cation. The compound showed no N2 adsorption but the Ar, CO2 and H2 . From the argon adsorption, the surface area of ~150 m2 g-1 was determined. Carbon dioxide adsorption was measured at various temperatures (0, 10, 20, 30 and 40 °C) and the compound showed the highest adsorption capacity (at 0 °C) of 7.0 wt % of CO2 . From the carbon dioxide adsorption isotherms the isosteric heat of 56,5 kJ mol-1 was determined. Hydrogen adsorption was studied at -196 °C with hydrogen uptake of 2.1 wt % at 1 bar.

A novel SATB1 protein isoform with different biophysical properties.

Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1's mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.

Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8+ T cells.

The networks of transcription factors (TFs) that control intestinal-resident memory CD8+ T (TRM) cells, including multipotency and effector programs, are poorly understood. In this work, we investigated the role of the TF Bcl11b in TRM cells during infection with Listeria monocytogenes using mice with post-activation, conditional deletion of Bcl11b in CD8+ T cells. Conditional deletion of Bcl11b resulted in increased numbers of intestinal TRM cells and their precursors as well as decreased splenic effector and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors, with no major alterations in their programs. Bcl11b-/- TRM cells had altered transcriptional programs, with diminished expression of multipotent/multifunctional (MP/MF) program genes, including Tcf7, and up-regulation of the effector program genes, including Prdm1. Bcl11b also limits the expression of Ahr, another TF with a role in intestinal CD8+ TRM cell differentiation. Deregulation of TRM programs translated into a poor recall response despite TRM cell accumulation in the intestine. Reduced expression of MP/MF program genes in Bcl11b-/- TRM cells was linked to decreased chromatin accessibility and a reduction in activating histone marks at these loci. In contrast, the effector program genes displayed increased activating epigenetic status. These findings demonstrate that Bcl11b is a frontrunner in the tissue residency program of intestinal memory cells upstream of Tcf1 and Blimp1, promoting multipotency and restricting the effector program.

Sr(II) and Ba(II) Alkaline Earth Metal-Organic Frameworks (AE-MOFs) for Selective Gas Adsorption, Energy Storage, and Environmental Application.

Two new alkaline earth metal-organic frameworks (AE-MOFs) containing Sr(II) (UPJS-15) or Ba(II) (UPJS-16) cations and extended tetrahedral linker (MTA) were synthesized and characterized in detail (UPJS stands for University of Pavol Jozef Safarik). Single-crystal X-ray analysis (SC-XRD) revealed that the materials are isostructural and, in their frameworks, one-dimensional channels are present with the size of ~11 × 10 Å2. The activation process of the compounds was studied by the combination of in situ heating infrared spectroscopy (IR), thermal analysis (TA) and in situ high-energy powder X-ray diffraction (HE-PXRD), which confirmed the stability of compounds after desolvation. The prepared compounds were investigated as adsorbents of different gases (Ar, N2, CO2, and H2). Nitrogen and argon adsorption measurements showed that UPJS-15 has SBET area of 1321 m2 g-1 (Ar) / 1250 m2 g-1 (N2), and UPJS-16 does not adsorb mentioned gases. From the environmental application, the materials were studied as CO2 adsorbents, and both compounds adsorb CO2 with a maximum capacity of 22.4 wt.% @ 0 °C; 14.7 wt.% @ 20 °C and 101 kPa for UPJS-15 and 11.5 wt.% @ 0°C; 8.4 wt.% @ 20 °C and 101 kPa for UPJS-16. According to IAST calculations, UPJS-16 shows high selectivity (50 for CO2/N2 10:90 mixture and 455 for CO2/N2 50:50 mixture) and can be applied as CO2 adsorbent from the atmosphere even at low pressures. The increased affinity of materials for CO2 was also studied by DFT modelling, which revealed that the primary adsorption sites are coordinatively unsaturated sites on metal ions, azo bonds, and phenyl rings within the MTA linker. Regarding energy storage, the materials were studied as hydrogen adsorbents, but the materials showed low H2 adsorption properties: 0.19 wt.% for UPJS-15 and 0.04 wt.% for UPJS-16 @ -196 °C and 101 kPa. The enhanced CO2/H2 selectivity could be used to scavenge carbon dioxide from hydrogen in WGS and DSR reactions. The second method of applying samples in the area of energy storage was the use of UPJS-15 as an additive in a lithium-sulfur battery. Cyclic performance at a cycling rate of 0.2 C showed an initial discharge capacity of 337 mAh g-1, which decreased smoothly to 235 mAh g-1 after 100 charge/discharge cycles.

Artifacts and misinterpretations in gas physisorption measurements and characterization of porous solids.

This contribution provides a critical review of gas physisorption in the textural characterization of porous solids, with the focus on the artifacts in experimental data that lead to serious misinterpretation of the results derived from the analysis of adsorption isotherms. Apart from the problems related to the determination and interpretation of the BET area, we paid particular attention to the issues associated with the determination of pore size distribution; for example, the choice of the correct branch of the hysteresis loop and the network effects. Pitfalls in the analyses using either the classical macroscopic or the advanced microscopic (DFT, GCMC) methodology are addressed. The ultimate aim is to provide guidance for proper calculations and correct interpretation of physisorption data.

Carbonaceous Materials Porosity Investigation in a Wet State by Low-Field NMR Relaxometry.

The porosity of differently wetted carbonaceous material with disordered mesoporosity was investigated using low-field 1H NMR relaxometry. Spin−spin relaxation (relaxation time T2) was measured using the CPMG pulse sequence. We present a non-linear optimization method for the conversion of relaxation curves to the distribution of relaxation times by using non-specialized software. Our procedure consists of searching for the number of components, relaxation times, and their amplitudes, related to different types of hydrogen nuclei in the sample wetted with different amounts of water (different water-to-carbon ratio). We found that a maximum of five components with different relaxation times was sufficient to describe the observed relaxation. The individual components were attributed to a tightly bounded surface water layer (T2 up to 2 ms), water in small pores especially supermicropores (2 < T2 < 7 ms), mesopores (7 < T2 < 20 ms), water in large cavities between particles (20−1500 ms), and bulk water surrounding the materials (T2 > 1500 ms). To recalculate the distribution of relaxation times to the pore size distribution, we calculated the surface relaxivity based on the results provided by additional characterization techniques, such as thermoporometry (TPM) and N2/−196 °C physisorption.

The 3D enhancer network of the developing T cell genome is shaped by SATB1.

Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.

Carbon dioxide and hydrogen adsorption study on surface-modified HKUST-1 with diamine/triamine.

The present article intended to study the influence of post-synthetic modification with ethylenediamine (en, diamine) and diethylenetriamine (deta, triamine) within the coordinatively unsaturated sites (CUSs) of HKUST-1 on carbon dioxide and hydrogen storage. The as-sythesized adsorbent was solvent-exchanged and subsequently post-synthetically modified with di-/triamines as sources of amine-based sorption sites due to the increased CO2 storage capacity. It is known that carbon dioxide molecules have a high affinity for amine groups, and moreover, the volume of amine molecules itself reduces the free pore volume in HKUST-1, which is the driving force for increasing the hydrogen storage capacity. Different concentrations of amines were used for modification of HKUST-1, through which materials with different molar ratios of HKUST-1 to amine: 1:0.05; 1:0.1; 1:0.25; 1:0.5; 1:0.75; 1:1; 1:1.5 were synthesized. Adsorption measurements of carbon dioxide at 0 °C up to 1 bar have shown that the compounds can adsorb large amounts of carbon dioxide. In general, deta-modified samples showed higher adsorbed amounts of CO2 compared to en-modified materials, which can be explained by the higher number of amine groups within the deta molecule. With an increasing molar ratio of amines, there was a decrease in wt.% CO2. The maximum storage capacity of CO2 was 22.3 wt.% for HKUST-1: en/1:0.1 and 33.1 wt.% for HKUST-1: deta/1:0.05 at 0 °C and 1 bar. Hydrogen adsorption measurements showed the same trend as carbon dioxide, with the maximum H2 adsorbed amounts being 1.82 wt.% for HKUST-1: en/1:0.1 and 2.28 wt.% for HKUST-1: deta/1:0.05 at - 196 °C and 1 bar.

HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells.

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

Activation of a Cryptic Manumycin-Type Biosynthetic Gene Cluster of Saccharothrix espanaensis DSM44229 by Series of Genetic Manipulations.

(1) Background: Manumycins are small actinomycete polyketides with prominent cancerostatic and immunosuppressive activities via inhibition of various eukaryotic enzymes. Their overall activity towards human cells depends on the structural variability of both their polyketide chains, mainly the upper one. In our genetic screening project to find novel producers of anti-inflammatory manumycins, the strain Saccharothrix espanaensis DSM44229 was identified as containing a novel manumycin-type biosynthetic gene cluster (BGC). (2) Methods: The biosynthetic genes appeared to be silent under all assayed laboratory conditions. Several techniques were used to activate the BGC, including: (i) heterologous expression in various hosts, (ii) overexpression of putative pathway-specific regulatory genes, and (iii) overexpression of a bottleneck cyclizing aminolevulinate synthase gene in both natural and heterologous producers. (3) Results: Multiple novel manumycin-type compounds were produced at various levels by genetically-modified strains, sharing a tetraene lower chain structure with a colabomycin subgroup of manumycins, but possessing much shorter and saturated upper chains. (4) Conclusions: A cryptic manumycin-type BGC was successfully activated by genetic means to gain production of novel manumycin-type compounds for future comparative activity assays. Heterologously produced compounds were identical to those found after final activation of the BGC in the original strain, proving the intactness of the cloned BGC.

SATB1-mediated chromatin landscape in T cells.

The regulatory circuits that define developmental decisions of thymocytes are still incompletely resolved. SATB1 protein is predominantly expressed at the CD4+CD8+cell stage exerting its broad transcription regulation potential with both activatory and repressive roles. A series of post-translational modifications and the presence of potential SATB1 protein isoforms indicate the complexity of its regulatory potential. The most apparent mechanism of its involvement in gene expression regulation is via the orchestration of long-range chromatin loops between genes and their regulatory elements. Multiple SATB1 perturbations in mice uncovered a link to autoimmune diseases while clinical investigations on cancer research uncovered that SATB1 has a promoting role in several types of cancer and can be used as a prognostic biomarker. SATB1 is a multivalent tissue-specific factor with a broad and yet undetermined regulatory potential. Future investigations on this protein could further uncover T cell-specific regulatory pathways and link them to (patho)physiology.

The role of the oxygen functional groups in adsorption of copper (II) on carbon surface.

The effect of carbon surface oxidation on the adsorption of Cu(II) ions from aqueous solution was studied in order to explain the role of the oxygen functional groups in the binding of copper ions. Pristine carbonaceous adsorbent was oxidized to a various extent of oxygen uptake (Fenton-like oxidation < persulphate in H2SO4 < H2O2 in HNO3). Equilibrium adsorption tests were performed in acetate buffer at pH ≈ 5. The results show that the adsorption capacity of pristine adsorbent is expectable low (~0.1 mmol g-1). The oxidized samples adsorb Cu(II) at a considerably higher level of ~1.4 mmol g-1 despite the degree of surface oxidation. Analysis of the surface groups (FTIR, TPD) and surface charge (zeta potential) of used adsorbents and their Cu(II) saturated counterpart lead to the finding that Cu(II) ions are mostly bonded by complexation with the dissociated carboxylic groups (partly formed by anhydrides hydrolysis) probably in the form of Cu(Ac)+ formed in the acetate buffer. The extent of dissociation is given by equilibrium pH during the adsorption and does not depend on the total amount of the surface groups. Thus, the content of active sites and consequently adsorption capacity is independent on the degree of oxidation when pH is kept constant. The results indicate that even moderate oxidation treatment of carbonaceous materials can produce highly effective adsorbents for Cu(II) immobilization.

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities.

Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used for phylogenetic analyses of unrelated taxa. The part of single-copy gene encoding the second largest subunit of RNA polymerase II (rpb2) was thus compared with first spacer of ITS as an alternative marker for the analysis of fungal communities in spruce forest topsoil, and their applicability was tested on a comprehensive mock community. In soil, rpb2 exhibited broad taxonomic coverage of the entire fungal tree of life including basal fungal lineages. The gene exhibited sufficient variation for the use in phylogenetic analyses and taxonomic assignments, although it amplifies also paralogues. The fungal taxon spectra obtained with rbp2 region and ITS1 corresponded, but sequence abundance differed widely, especially in the basal lineages. The proportions of OTU counts and read counts of major fungal groups were close to the reality when rpb2 was used as a molecular marker while they were strongly biased towards the Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic placement of rbp2 sequences is currently more difficult than that of the ITS sequences, its discriminative power, quantitative representation of community composition and suitability for phylogenetic analyses represent significant advantages.

Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques.

A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike "classical" primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of "classical" ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers.