Exploring the significance of microbiota metabolites in rheumatoid arthritis: uncovering their contribution from disease development to biomarker potential.

Rheumatoid arthritis (RA) is a multifaceted autoimmune disorder characterized by chronic inflammation and joint destruction. Recent research has elucidated the intricate interplay between gut microbiota and RA pathogenesis, underscoring the role of microbiota-derived metabolites as pivotal contributors to disease development and progression. The human gut microbiota, comprising a vast array of microorganisms and their metabolic byproducts, plays a crucial role in maintaining immune homeostasis.

Approach to Measuring the Effect of PARP1 on RNA Polymerase II Elongation Rates.

The rate of RNA polymerase II (RNAPII) transcriptional elongation plays a critical role in mRNA biogenesis, from transcription initiation to alternative splicing. As RNAPII moves along the DNA, it must read the DNA sequences wrapped up as chromatin. Thus, the structure of chromatin impedes the movement and speed at which RNAPII moves, presenting a crucial regulation to gene expression.

PARP1's Involvement in RNA Polymerase II Elongation: Pausing and Releasing Regulation through the Integrator and Super Elongation Complex.

RNA polymerase elongation along the gene body is tightly regulated to ensure proper transcription and alternative splicing events. Understanding the mechanism and factors critical in regulating the rate of RNA polymerase II elongation and processivity is clearly important. Recently we showed that PARP1, a well-known DNA repair protein, when bound to chromatin, regulates RNA polymerase II elongation.

Evidence Supporting Substrate Channeling between Domains of Human PAICS: A Time-Course Analysis of C-Bicarbonate Incorporation.

Human phosphoribosylaminoimidazole carboxylase phosphoribosylaminoimdiazole succinocarboxamide synthetase (PAICS) is a dual activity enzyme catalyzing two consecutive reactions in purine nucleotide synthesis. Crystallographic structures of recombinant human PAICS suggested the channeling of 4-carboxy-5-aminoimidazole-1-ribose-5'-phosphate (CAIR) between two active sites of PAICS, while a prior work of an avian PAICS suggested otherwise. Here, we present time-course mass spectrometric data supporting the channeling of CAIR between domains of recombinant human PAICS.

PARP1 is a versatile factor in the regulation of mRNA stability and decay.

PARP1 is an abundant nuclear protein with many pleiotropic functions involved in epigenetic and transcriptional controls. Abundance of mRNA depends on the balance between synthesis and decay of a particular transcript. PARP1 binds RNA and its depletion results in increased expression of genes involved in nonsense-mediated decay, suggesting that PARP1 might be involved in mRNA stability.

Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing.

Background: Recently, we showed that PARP1 is involved in cotranscriptional splicing, possibly by bridging chromatin to RNA and recruiting splicing factors. It also can influence alternative splicing decisions through the regulation of RNAPII elongation. In this study, we investigated the effect of PARP1-mediated chromatin changes on RNAPII movement, during transcription and alternative splicing.

Linking kindling to increased glutamate release in the dentate gyrus of the hippocampus through the STXBP5/tomosyn-1 gene.

Introduction: In kindling, repeated electrical stimulation of certain brain areas causes progressive and permanent intensification of epileptiform activity resulting in generalized seizures. We focused on the role(s) of glutamate and a negative regulator of glutamate release, STXBP5/tomosyn-1, in kindling.

Methods: Stimulating electrodes were implanted in the amygdala and progression to two successive Racine stage 5 seizures was measured in wild-type and STXBP5/tomosyn-1 (Tom) animals.

Methodology to Identify Poly-ADP-Ribose Polymerase 1 (PARP1)-mRNA Targets by PAR-CLiP.

There is a long list of important RNA-binding proteins (RBP) involved in different steps of gene expression through posttranscriptional modifications: pre-mRNA splicing, mRNA stabilization, polyadenylation, mRNA export from nucleus to the cytoplasm, and translation. The critical role of RNA-protein interaction necessitates a continuous identification of proteins involved in this process. Here we describe the identification of Poly-ADP-Ribose Polymerase 1 (PARP1) as an RNA binding protein involved in RNA splicing.

Involvement of PARP1 in the regulation of alternative splicing.

Specialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the nucleosomes at exon/intron boundaries of specific genes, suggestive of a role for this enzyme in alternative splicing. Poly (ADP) ribose polymerase has previously been implicated in the PARylation of splicing factors as well as regulation of the histone modification H3K4me3, a mark critical for co-transcriptional splicing.

Vimentin is involved in regulation of mitochondrial motility and membrane potential by Rac1.

In this study we show that binding of mitochondria to vimentin intermediate filaments (VIF) is regulated by GTPase Rac1. The activation of Rac1 leads to a redoubling of mitochondrial motility in murine fibroblasts. Using double-mutants Rac1(G12V, F37L) and Rac1(G12V, Y40H) that are capable to activate different effectors of Rac1, we show that mitochondrial movements are regulated through PAK1 kinase.

A new variant of KMT2A(MLL)-FLNA fusion transcript in acute myeloid leukemia with ins(X;11)(q28;q23q23).

The KMT2A gene (previously known as MLL) located at 11q23 is often involved in recurrent chromosomal translocations that lead to the development of acute leukemia, particularly in infants. Acute leukemias with KMT2A rearrangements have different prognoses, which depend on the partner gene involved in the translocation. The detection of all possible types of KMT2A gene rearrangements is of key importance for the identification of biological subgroups, which may differ in clinical outcome.

Mitochondrial membrane potential is regulated by vimentin intermediate filaments.

This study demonstrates that the association of mitochondria with vimentin intermediate filaments (VIFs) measurably increases their membrane potential. This increase is detected by quantitatively comparing the fluorescence intensity of mitochondria stained with the membrane potential-sensitive dye tetramethylrhodamine-ethyl ester (TMRE) in murine vimentin-null fibroblasts with that in the same cells expressing human vimentin (∼35% rise). When vimentin expression is silenced by small hairpin RNA (shRNA) to reduce vimentin by 90%, the fluorescence intensity of mitochondria decreases by 20%.

Phosphonium-iodonium ylides with heteroatomic groups in the synthesis of annelated P-containing heterocycles.

The preparation and chemistry of novel sulfonyl- and phosphoryl-derived λ(3)-iodanes are reported. These compounds with three different heteroatoms attached to a negatively charged C atom represent potentially useful reagents that combine in one molecule the synthetic advantages of a phosphonium ylide and an iodonium salt. Specifically, they can react with a number of acetylenes, leading to hitherto unknown sulfonyl- and phosphoryl-substituted phosphinolines, phosphininothiophenes, and a novel type of annelated P-containing heterocycle--phosphininopyrazole.

Hetaryl-substituted phosphonium-iodonium ylides in synthesis of heterocycles.

A series of hitherto unknown hetaryl-substituted (in phosphonium part) phosphonium-iodonium ylides were synthesized. The reaction of these mixed phosphonium-iodonium ylides with acetylenes opens a way to new furyl annelated phosphinolines or unusually substituted phosphininofurans.

Kindling-induced asymmetric accumulation of hippocampal 7S SNARE complexes correlates with enhanced glutamate release.

Purpose: To correlate kindling-associated alterations of the neurotransmitter secretory machinery, glutamate release in the trisynaptic hippocampal excitatory pathway, and the behavioral evolution of kindling-induced epileptogenesis.

Method: Neurotransmitter release requires the fusion of vesicle and plasma membranes; it is initiated by formation of a stable, ternary complex (7SC) of SNARE [soluble N-ethylmaleimide sensitive factor (NSF) attachment protein receptor] proteins. Quantitative Western blotting was used to monitor levels of 7SC and SNARE regulators [NSF, SV2 (synaptic vesicle protein 2)] in hippocampal synaptosomes from amygdala-kindled animals.

Photochemical synthesis of phosphinolines from phosphonium-iodonium ylides.

We describe three different series of experiments which were undertaken to test our hypothesis that during irradiation of phosphonium-iodonium ylides (1a, 1b) an electrophilic carbene is generated. By opposing the assumed intermediate to monosubstituted alkynes, we observed in the case of electron-rich substituents at the triple bond a domination of a 1,3-dipolar cycloaddition of the intermediate with the triple bond to yield furans. In the case of electron poorer substituents, the formation of phosphinolines prevails.

Heterocycles from phosphonium-iodonium ylides. Photochemical synthesis of lambda(5)-phosphinolines.

A photochemical reaction of mixed phosphonium-iodonium ylides with acetylenes yielding lambda(5)-phosphinolines, a rare class of phosphorus heterocycles hardly accessible by other methods, was found. The yields of lambda(5)-phosphinolines vary from 35% to 80%. The structures of two phosphinolines were established by single-crystal X-ray diffraction.

Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.

N-Ethylmaleimide-sensitive factor (NSF) is a homo-hexameric member of the AAA(+) (ATPases associated with various cellular activities plus) family. It plays an essential role in most intracellular membrane trafficking through its binding to and disassembly of soluble NSF attachment protein (SNAP) receptor (SNARE) complexes. Each NSF protomer contains an N-terminal domain (NSF-N) and two AAA domains, a catalytic NSF-D1 and a structural NSF-D2.

A dynamic reciprocal RBR-PRC2 regulatory circuit controls Arabidopsis gametophyte development.

Unlike animals that produce gametes upon differentiation of meiotic products, plants develop haploid male and female gametophytes that differentiate gametes such as sperm, egg and central cells, and accessory cells [1, 2]. Both gametophytes participate in double fertilization and give rise to the next sporophytic generation. Little is known about the function of cell-cycle genes in differentiation and development of gametophytes and in reproduction [1, 2].

Levetiracetam prevents kindling-induced asymmetric accumulation of hippocampal 7S SNARE complexes.

Purpose: Understanding the molecular mechanisms underlying epilepsy is crucial to designing novel therapeutic regimens. This report focuses on alterations in the secretory machinery responsible for neurotransmitter (NT) release. Soluble N-ethylmaleimide sensitive factor (NSF) attachment protein receptor (SNARE) complexes mediate the fusion of synaptic vesicle and active zone membranes, thus mediating NT secretion.

Asymmetric accumulation of hippocampal 7S SNARE complexes occurs regardless of kindling paradigm.

Modifications of neurotransmission may contribute to the synchronization of neuronal networks that are a hallmark of epileptic seizures. In this study we examine the synaptosomal proteins involved in neurotransmitter release to determine if alterations in their interactions correlate with the chronic epileptic state. Using quantitative western blotting, we measured the levels of 7S SNARE complexes and SNARE effectors in the effected hippocampi from animals that were electrically kindled through stimulation from one of three different foci.

Type I PDZ ligands are sufficient to promote rapid recycling of G Protein-coupled receptors independent of binding to N-ethylmaleimide-sensitive factor.

Molecular sorting of G protein-coupled receptors (GPCRs) between divergent recycling and lysosomal pathways determines the functional consequences of agonist-induced endocytosis. The carboxyl-terminal cytoplasmic domain of the beta2 adrenergic receptor (beta2AR) mediates both PDZ binding to Na+/H+ exchanger regulatory factor/ezrin/radixin/moesin-binding phosphoprotein of 50 kDa (NHERF/EBP50) family proteins and non-PDZ binding to the N-ethylmaleimide-sensitive factor (NSF). We have investigated whether PDZ interaction(s) are actually sufficient to promote rapid recycling of endocytosed receptors and, if so, whether PDZ-mediated sorting is restricted to the beta2AR tail or to sequences that bind NHERF/EBP50.

Multiple binding proteins suggest diverse functions for the N-ethylmaleimide sensitive factor.

The hexameric ATPase, N-ethylmaleimide sensitive factor (NSF), is essential to vesicular transport and membrane fusion because it affects the conformations and associations of the soluble NSF attachment protein receptor (SNARE) proteins. NSF binds SNAREs through adaptors called soluble NSF attachment proteins (alpha- or beta-SNAP) and disassembles SNARE complexes to recycle the monomers. NSF contains three domains, two nucleotide-binding domains (NSF-D1 and -D2) and an amino terminal domain (NSF-N) that is required for SNAP-SNARE complex binding.

Preparation and chemistry of phosphoranyl-derived iodanes.

The preparation and chemistry of novel phosphoranyl-derived lambda(3)-iodanes is reported. The phosphoranyl-derived phenyliodonium sulfonates were prepared in good yields by the reaction of stabilized phosphonium ylides [1-triphenylphosphoranylidene-2-propanone, methyl(triphenylphosphoranylidene)acetate, (triphenylphosphoranylidene)acetaldehyde, and (triphenylphosphoranylidene)acetonitrile] with the pyridinium complex of iodobenzene ditriflate or with [hydroxy(tosyloxy)iodo]benzene under mild conditions. These compounds represent a potentially useful class of reagents that combine in one molecule synthetic advantages of a phosphonium ylide and an iodonium salt.