The polymorphisms of extracellular matrix-remodeling genes are associated with pelvic organ prolapse

Introduction and hypothesis Extracellular matrix (ECM) synthesis and metabolism abnormalities may influence the pelvic supporting system and lead to the occurrence and development of pelvic organ prolapse (POP). Genetic polymorphisms of such related genes have been increasingly studied. This study aims to explore the association between the single-nucleotide polymorphisms (SNPs) of genes encoding ECM processing enzymes (a disintegrin and metalloproteinase with thrombospondin motifs [ADAMTSs]), ECM degrading enzymes (matrix metalloproteinases [MMPs]) and their tissue inhibitors of metalloproteinase (TIMPs), and POP. Methods We conducted an association study including 48 women with POP at stages III and IV and 48 women without prolapse in Chinese groups. SNPs were identified using the target region sequencing technique. We performed Fisher’s exact tests to assess the association between SNPs and POP in the unadjusted model and logistic regression analysis in the adjusted model, adjusting for delivery and pregnancy. Results There was a significant association between TIMP2 SNP rs2277698 (odds ratio [OR], 0.37; 95% confidence interval [CI], 0.16–0.82; P = 0.015), ADAMTS13 SNP rs149586801 (OR, 0.18; 95% CI, 0.05–0.69; P = 0.012), and ADAMTS1 SNPs rs370850 and rs422803 (OR, 3.71; 95% CI, 1.35–10.15; P = 0.011 for both), rs402007, rs428785, rs434857, and rs445784 (OR, 2.18; 95% CI, 1.05–4.56; P = 0.038 for the four), and POP in the adjusted model. Conclusion TIMP2, ADAMTS13, and ADAMTS1 might be candidate genes for POP. Our results provide preliminarily new evidence for future investigation of these genes in the pathophysiology of POP.

DNA fluctuations reveal the size and dynamics of topological domains

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real-time and at the single molecule level. Our approach is based on quantifying the extension fluctuations -in addition to the mean extension- of supercoiled DNA in magnetic tweezers. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our approach to enable quantification of the dynamics and reaction pathways of DNA processing enzymes and motor proteins, in the context of physiologically relevant forces and supercoiling densities.

The Synthesis of Azasugars Using an I2-mediated Carbamate Annulation

<p>The biological activity of azasugars has largely been attributed to their ability to mimic the oxocarbenium ion-like transition state formed during reactions with carbohydrate-processing enzymes and, for this reason, functional and stereochemical modifications of the azasugar scaffold have led to the development of specific and potent glycosidase inhibitors. Given the potential of azasugars as glycosidase inhibitors, we were interested in developing efficient methodology for their synthesis. This thesis highlights synthetic methodology developed to produce amino-imino-hexitols as azasugar scaffolds. Key in the synthesis of the amino-imino-hexitols was the application of a stereoselective Strecker reaction, without the need for chiral Lewis acids or catalysts, and an extension of an I2-mediated carbamate annulation to cyclise functionalised and protected alkenylamines. Sixteen amino-imino-hexitols were synthesized, including ten previously undisclosed substrates with the D-galacto, D-talo, and L-altro configurations. The novel amino-imino-hexitols were then tested for their ability to act as glycosidase inhibitors and substrates of the D-talo configuration showed promising inhibitory effects. Mechanistic considerations of the I2-mediated carbamate annulation are discussed and although the exact annulation mechanism has yet to be determined, experimental studies have revealed that an aziridine is not an intermediate in the reaction. Factors influencing the diastereoselectivity of the carbamate annulation are also explored. Furthermore, an in depth analysis of the high cis-selectivity of the carbamate annulation is investigated using density functional theory to calculate the transition states of iodocyclisations en route to the formation of carbamates. Taken as a whole, the applicability of the carbamate annulation to a variety of alkenylamines and an understanding of the factors controlling the diastereoselectivity of the reaction should make this methodology a valuable addition to the synthetic chemist’s toolbox.</p>

The Synthesis of Azasugars Using an I2-mediated Carbamate Annulation

<p>The biological activity of azasugars has largely been attributed to their ability to mimic the oxocarbenium ion-like transition state formed during reactions with carbohydrate-processing enzymes and, for this reason, functional and stereochemical modifications of the azasugar scaffold have led to the development of specific and potent glycosidase inhibitors. Given the potential of azasugars as glycosidase inhibitors, we were interested in developing efficient methodology for their synthesis. This thesis highlights synthetic methodology developed to produce amino-imino-hexitols as azasugar scaffolds. Key in the synthesis of the amino-imino-hexitols was the application of a stereoselective Strecker reaction, without the need for chiral Lewis acids or catalysts, and an extension of an I2-mediated carbamate annulation to cyclise functionalised and protected alkenylamines. Sixteen amino-imino-hexitols were synthesized, including ten previously undisclosed substrates with the D-galacto, D-talo, and L-altro configurations. The novel amino-imino-hexitols were then tested for their ability to act as glycosidase inhibitors and substrates of the D-talo configuration showed promising inhibitory effects. Mechanistic considerations of the I2-mediated carbamate annulation are discussed and although the exact annulation mechanism has yet to be determined, experimental studies have revealed that an aziridine is not an intermediate in the reaction. Factors influencing the diastereoselectivity of the carbamate annulation are also explored. Furthermore, an in depth analysis of the high cis-selectivity of the carbamate annulation is investigated using density functional theory to calculate the transition states of iodocyclisations en route to the formation of carbamates. Taken as a whole, the applicability of the carbamate annulation to a variety of alkenylamines and an understanding of the factors controlling the diastereoselectivity of the reaction should make this methodology a valuable addition to the synthetic chemist’s toolbox.</p>

A simple and general approach to control the activity of DNA processing enzymes

DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays, and showed comparable performance to commercial hot-start enzymes.

Small RNAs Asserting Big Roles in Mycobacteria

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50-350 nts in length and smaller RNAs (sncRNA) &lt;50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists and locked nucleic acid sequence specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs summarized.

Hybrid Multivalent Jack Bean α-Mannosidase Inhibitors: The First Example of Gold Nanoparticles Decorated with Deoxynojirimycin Inhitopes

Among carbohydrate-processing enzymes, Jack bean α-mannosidase (JBα-man) is the glycosidase with the best responsiveness to the multivalent presentation of iminosugar inhitopes. We report, in this work, the preparation of water dispersible gold nanoparticles simultaneously coated with the iminosugar deoxynojirimycin (DNJ) inhitope and simple monosaccharides (β-d-gluco- or α-d-mannosides). The display of DNJ at the gold surface has been modulated (i) by using an amphiphilic linker longer than the aliphatic chain used for the monosaccharides and (ii) by presenting the inhitope, not only in monomeric form, but also in a trimeric fashion through combination of a dendron approach with glyconanotechnology. The latter strategy resulted in a strong enhancement of the inhibitory activity towards JBα-man, with a Ki in the nanomolar range (Ki = 84 nM), i.e., more than three orders of magnitude higher than the monovalent reference compound.

Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.

Aldh2 dependent formaldehyde metabolism fuels purine demands in melanocyte stem cells

ABSTRACTAldehyde-processing enzymes are viewed as essential clearing agents that rapidly deactivate harmful aldehydes. In the bone marrow, two specific enzymes, aldehyde dehydrogenase (ALDH) 2 and alcohol dehydrogenase (ADH) 5, were previously reported to protect hematopoietic stem cells from endogenous formaldehyde accumulation. Unexpectedly, we found that melanocyte stem cells (McSCs) in zebrafish depend on formate, an Aldh2-generated reaction product, to drive regeneration. Activated McSCs require Aldh2 (but not Adh5) to generate differentiated progeny, and by using scRNA-sequencing analysis, we identified a de novo purine biosynthesis program that is uniquely present in activated McSCs. Consistent with formate serving as one-carbon units for nucleotide biosynthesis, we found that purine supplementation (but not pyrimidine supplementation) was able to restore melanocyte regeneration in the absence of Aldh2. This work shows that Aldh2 enzymes generate reaction products that are needed to meet metabolic demands in regeneration.

Programmed Cell Death in Developing Brachypodium distachyon Grain

The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species such as barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of the wild model species Brachypodium distachyon. We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified in Brachypodium the orthologs of protease genes known to contribute to grain PCD and surveyed their expression. We found that, similar to cereals, PCD in the Brachypodium nucellus occurs in a centrifugal pattern following anthesis. However, compared to cereals, the rate of post-mortem clearance in the Brachypodium nucellus is slower. However, compared to wheat and barley, mesocarp PCD in Brachypodium proceeds more rapidly in lateral cells. Remarkably, Brachypodium mesocarp PCD is not coordinated with endosperm development. Phylogenetic analysis suggests that barley and wheat possess more vacuolar processing enzymes that drive nucellar PCD compared to Brachypodium and rice. Our expression analysis highlighted putative grain-specific PCD proteases in Brachypodium. Combined with existing knowledge on grain PCD, our study suggests that the rate of nucellar PCD moderates grain size and that the pattern of mesocarp PCD influences grain shape.