Dietary Interventions in Inflammatory Bowel Disease

Inflammatory bowel disease, which primarily includes ulcerative colitis and Crohn’s disease, is a group of chronic diseases of the gastrointestinal tract. Mainly affecting young people, it is characterized by periods of exacerbation and remission. In recent years, there has been an increase in the prevalence of inflammatory bowel disease worldwide, including Poland. The potential impact of nutrition and selected dietary components that are directly or indirectly involved in the pathogenesis of intestinal lesions in IBD is not fully clear. Evaluating the impact of diet on the course of IBD is very complex due to the fact that regardless of a dietary model adopted, each one is based on consumption of many different food groups which affect one another. However, the growing need to produce dietary recommendations for these patients has prompted the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) to develop nutrition guidelines for the patients. The present paper characterizes the dietary models most commonly discussed in research studies and their potential impact on IBD activity.     

The First Examples of [3+2] Cycloadditions with the Participation of (E)-3,3,3-Tribromo-1-Nitroprop-1-Ene

The first examples of [3+2] cycloaddition reactions between 3,3,3-tribromo-1-nitroprop-1-ene (TBMN) were explored on the basis of experimental and theoretical approaches. It was found that reactions involving TBMN and diarylnitrones realized with full regio- and stereoselectivity lead to respective 3,4-cis-4,5-trans-4-nitroisoxazolidines. The regioselecticity and the molecular mechanism of title processes was analyzed on the basis of the advanced DFT computational study.     

Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry

RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq’s integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry coupled with surface-induced dissociation and molecular dynamics simulations to disentangle the arrangement of the CTDs and their impact on the stability of Escherichia coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding.

Many RNA-binding proteins (RBPs) contain intrinsically disordered regions (IDRs) (1) with overlapping functions that have been difficult to disentangle. For example, IDRs may augment specific RNA recognition, connect different RNA-binding modules, and enable the assembly of liquid condensates, while also serving as targets for posttranslational modification (2–4). The heterogeneous and dynamic structures of IDRs make their interactions especially challenging to quantify, and their functions in most RBPs remain poorly understood.Hfq is a bacterial Sm protein that binds small noncoding RNA (sRNA) and chaperones sRNA regulation of complementary messenger RNAs (mRNAs) (5) (Fig. 1). Deletion of Hfq results in pleiotropic effects, including maladaptive responses to stress and decreased virulence (6). The well-folded core of the Hfq hexamer assembles into a symmetric ring that binds U- and A-rich sequence motifs in sRNA and mRNA substrates (7). Conserved arginine patches on the outer rim of the hexamer also bind RNA and are essential for its chaperone activity (8, 9).Open in a separate windowFig. 1.Role of Hfq’s CTDs in sRNA regulation. Hfq chaperones the annealing of sRNAs with their target mRNAs, but it is not known how binding of RNAs occurs when the core of Hfq is occluded by many disordered CTDs. Although the acidic tips of the CTDs (red) can interact with basic patches on the rim (blue) (11), the organization and collective behavior of the CTDs is unknown.Escherichia coli Hfq also has intrinsically disordered C-terminal domains (CTDs) that extend outward from the core of the hexamer (10). Each monomer containing 102 residues contributes a 37-amino-acid (aa) CTD, creating a crowded zone of disordered polypeptide around the protein. This ring-shaped organization, which is unlike disordered regions in other RBPs, raises the possibility that the Hfq CTDs act together rather than individually.The CTD conformations of E. coli Hfq have never been fully resolved. Nevertheless, NMR chemical shift perturbations and molecular dynamics (MD) simulations determined that the CTDs interact with the rim of the hexamer (12). Additionally, unassigned electron density in a crystal structure of Hfq bound to RydC sRNA suggested that the CTDs make distributed contacts with the protein–RNA surface (13). These results aligned with the earlier observation that the CTDs (residues 65 to 102) stabilize the Hfq hexamer (14) and contribute to its function (15–20). We found that semiconserved acidic residues at the C terminus mimic nucleic acid, competing with RNA for binding to the rim (11, 21, 22). Competition with the CTDs can result in preferential dissociation of nonspecific RNA and retention of specific RNA ligands. More recently, it was shown that the bases and the tips of the CTDs interact synergistically with particular Hfq surfaces, leading to different effects depending on the RNA ligand (23).Because of their intrinsic disorder and sixfold symmetry, how the CTDs organize around Hfq stabilizing the hexamer is still unknown. Additionally, it is not known if each CTD acts locally and independently, or if the six CTDs act together to accommodate or displace an incoming RNA (Fig. 1). Moreover, the energetic contributions of individual CTDs to RNA binding have been almost impossible to quantify.We addressed these challenges by using native mass spectrometry (nMS) coupled with surface-induced dissociation (SID) (Fig. 2A and SI Appendix, Fig. S1A). In nMS, the protein complex is exchanged into a volatile electrolyte, allowing transfer of the intact native complex to the gas phase (24). After ionization, collision of the precursor ion with a surface (nMS-SID) dissociates the complex into product ions that provide information about the stabilities of the noncovalent interfaces within the complex and their molecular organization (25). This method has been used to characterize the stability, structure, and assembly pathways of many protein complexes, including RBPs and membrane proteins (26–28). Although nMS does not reveal atomic detail, it is uniquely capable of resolving mixtures of complexes by mass and shape. Yet, despite its promise for discovery, nMS-SID studies of large biomolecular complexes typically require customized instrumentation (SI Appendix, Fig. S1A).Open in a separate windowFig. 2.Disordered CTDs stabilize Hfq. (A) nMS-SID dissociates the Hfq hexamer precursor ions into oligomers that retain the connectivity of the native protein. Fragments are separated according to their arrival time after traversing an ion mobility cell (see also SI Appendix, Fig. S1 and Table S1). (B and C) Energy-resolved mass spectrum of (B) HfqΔCTD and (C) Hfq, showing the fraction of each fragment at different CE. The CE are corrected for the mass of the CTDs (SI Appendix, Eq. S1). Reported fractions are the sum of the intensities of each dissociation product normalized by the total intensity of all products. Symbols report the average of three replicates. Some SEs are smaller than the symbols. Solid lines represent a linear interpolation of the data. (D and E) Percentage of each oligomer (pentamer, tetramer, trimer, dimer, or monomer) in the dissociation products, as a function of the remaining hexamer fraction for (D) HfqΔCTD and (E) Hfq. Errors are the spread of the ERMS curves, normalized by the total dissociated fraction and converted to a percentage. Colored as in B and C. Solid lines are a visual guide. (F and G) Surface-induced unfolding (SIU) of (F) HfqΔCTD and (G) Hfq. Extended ions arrive later than compact ions. Color scale, fraction of hexamer; dashed vertical lines, CE at the transition from compact to extended protein, at which the hexamer fractions are ∼0.2 and ∼0.7, respectively.Here, by using nMS-SID and all-atom MD simulations, we show that the six disordered CTDs of apo Hfq form extensive interactions that connect and stabilize the entire hexamer. When RNA binds any subunit of Hfq, these stabilizing interactions are disrupted throughout the hexamer. Taken together, our results show how disordered regions can integrate RNA–protein interactions across a multisubunit chaperone.     

Rheological Properties of Sodium Carboxymethylcellulose Solutions in Dihydroxy Alcohol/Water Mixtures

The aim of the research presented in this paper was to determine the effect of dihydroxy alcohols on the rheological properties of sodium carboxymethylcellulose (Na-CMC) solutions with different degrees of substitution and different average molecular masses. Rheological measurements were carried out with a rotational rheometer in continuous and oscillatory flows. Two dihydroxy alcohols were used in the study: butane-1,3-diol and propane-1,2-diol. The concentration of Na-CMC in the solutions was 1.6% and 2.2%, while the concentration of the dihydroxy alcohols ranged from 10% to 60%. The measurements show that the viscoelastic properties of Na-CMC solutions are strongly linked to the type of solvent used. The application of low-substituted high-molecular-mass Na-CMC makes it possible to obtain fluids with the properties of weak physical gels. On the other hand, the dissolution of Na-CMC with a high degree of substitution (>1) and low molecular mass in dihydroxy alcohol/water mixtures yields a viscoelastic fluid. Based on oscillatory measurements, increasing concentrations of polyhydroxy alcohols in Na-CMC solutions were found to induce an increase in the strength of the network structure. At the same concentrations of polyhydroxy alcohols in solutions containing butane-1,3-diol, a stronger network structure is formed compared to solutions containing propane-1,2-diol. The rheological measurement results presented in this paper may be useful in the formulation of drug carriers and cosmetics in which rheological properties are a significant factor.     

Methods for studying the zebrafish brain: past,present and future

The zebrafish (Danio rerio) is one of the most promising new model organisms. The increasing popularity of this amazing small vertebrate is evident from the exponentially growing numbers of research articles, funded projects and new discoveries associated with the use of zebrafish for studying development, brain function, human diseases and screening for new drugs. Thanks to the development of novel technologies, the range of zebrafish research is constantly expanding with new tools synergistically enhancing traditional techniques. In this review we will highlight the past and present techniques which have made, and continue to make, zebrafish an attractive model organism for various fields of biology, with a specific focus on neuroscience.     

The PD-1/PD-L1 Inhibitory Pathway is Altered in Primary Glomerulonephritides

The pathogenesis of primary proliferative and non-proliferative glomerulonephritides (PGN and NPGN) is still not fully understood, however, current evidence suggests that most cases of PGN and NPGN are the results of immunologic response to different etiologic agents that activates various biological processes leading to glomerular inflammation and injury. Programmed cell death protein 1 (PD-1) is the major inhibitory receptor regulating T cell exhaustion. The aim of this study was to evaluate the frequencies of PD-1-positive and PD-ligand 1 (PD-L1)-positive T and B lymphocytes in patients with NPGN and PGN in relation to clinical parameters for the first time. The study included peripheral blood (PB) samples from 20 newly diagnosed PGN and NPGN patients. The control group comprised of 20 healthy age- and sex-matched subjects. The viable PB lymphocytes underwent labelling with fluorochrome-conjugated monoclonal antibodies anti-PD-1 and anti-PD-L1, and were analyzed using a flow cytometer. The frequencies of CD4⁺/PD1⁺ T lymphocytes, CD8⁺/PD1⁺ T lymphocytes, and CD19⁺/PD-1⁺ B lymphocytes in the PGN group exceeded values obtained both in the NPGN group, and the control group. Alteration of PD-1/PD-L1 pathway may be involved in poorer prognosis, as patients with PGN are characterized by higher frequencies of PD-1-positive and PD-L1-positive T and B lymphocytes than patients with NPGN. Our results suggest that deregulation of PD-1/PD-L1 axis may contribute to the PGN and NPGN pathogenesis. High percentages of lymphocytes with PD-1 and PD-L1 expression may be related to the continuous T-cell activation and development of glomerular inflammation and injury.

     

Effects of 12-week supervised treadmill training on spatio-temporal gait parameters in patients with claudication

The purpose of the study was to evaluate selected temporal and spatial gait parameters in patients with intermittent claudication after completion of 12-week supervised treadmill walking training. The study included 36 patients (26 males and 10 females) aged: mean 64 (SD 7.7) with intermittent claudication. All patients were tested on treadmill (Gait Trainer, Biodex). Before the programme and after its completion, the following gait biomechanical parameters were tested: step length (cm), step cycle (cycle/s), leg support time (%), coefficient of step variation (%) as well as pain-free walking time (PFWT) and maximal walking time (MWT) were measured. Training was conducted in accordance with the current TASC II guidelines. After 12 weeks of training, patients showed significant change in gait biomechanics consisting in decreased frequency of step cycle (p?p?p?p?p?p?>?0.05).

• Implications for Rehabilitation

• Twelve-week treadmill walking training programme may lead to significant improvement of temporal and spatial gait parameters in patients with intermittent claudication.

• Twelve-week treadmill walking training programme may lead to significant improvement of pain-free walking time and maximum walking time in patients with intermittent claudication.