bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant Polycomb‐Group Proteins: Epigenetic Regulators of Development
Authors: Perera Pumi , Goodrich Justin 
Published: September 2016

Abstract

Although all cells in a multicellular organism contain the same set of genes, the spatiotemporal expression of these genes needs to be dynamically regulated for proper development (i.e. morphogenesis and life cycle transitions) to take place. Epigenetic mechanisms (i.e. heritable but reversible changes to chromatin) are important to maintain such gene expression patterns. Polycomb‐group proteins are evolutionarily conserved epigenetic regulators that function – via epigenetic marks such as histone modifications and alterations to chromatin structure – to maintain the repression of developmentally important genes so that these genes are expressed appropriately. Although they maintain specific patterns of gene repression, Polycomb‐group proteins are ubiquitously expressed. How their activity is regulated is a largely unexplored area but recent research in both metazoans and plants suggests myriad methods of regulation, including control of mRNA (messenger ribonucleic acid) and protein abundance and stability, post‐translational modifications and interactions with proteins and noncoding
RNAs
.

Key Concepts

Chromatin comprises of DNA folded up to form higher order structures, the basic unit of which is a nucleosome, which consists of DNA wrapped around histone proteins.

Epigenetic changes can regulate transcription and include alterations to DNA packaging and covalent modifications of histones or DNA.

Epigenetic changes are important for development because they can cause gene expression patterns that are heritable through cell divisions but more easily reversible than changes to DNA sequence.

Polycomb‐group proteins are conserved epigenetic regulators that maintain the repression of developmentally important genes in plants and animals.

Polycomb‐group proteins form various complexes that can modify chromatin (by adding epigenetic marks such as H3K27me3 and H2Aub to histones and altering chromatin structure and accessibility).

Polycomb‐group proteins are expressed ubiquitously and therefore need to be finely regulated to allow for specific and dynamic repression of their target genes.

Polycomb‐group protein levels or activity may be regulated by post‐translational modifications and controlled degradation.

Polycomb‐group proteins associate with other proteins or long noncoding RNAs that may regulate their activity or recruitment to specific targets.

Polycomb‐group repression can be reversed by antagonistic transcriptional activators and removers of Polycomb‐group epigenetic marks, some of which are part of the evolutionarily conserved trithorax‐group of proteins.
Genetics of Early Miscarriages
Authors: Vaiman Daniel 
Published: September 2016

Abstract

Early miscarriage or early pregnancy loss (EPL) is defined by an embryonic foetal loss occurring before 13 weeks of gestation. In this article, we focus on the genetics of this complex human disease from studies of human patients, sometimes including foetal losses occurring before 20 weeks. Most of the mouse studies on EPL are based on gene invalidation experiments having much wider and pleiotropic effects than a mere defect of implantation or placental development, and therefore they will not be analyzed here. In addition, many good reviews are already available on gene polymorphisms relevant to early miscarriage and are only briefly summarised here. We develop more in‐depth aspects connected to microRNA and copy number variations with EPL, issues that have been much less reviewed in the past.

Key Concepts

Early pregnancy loss is a complex multifactorial disease, leading to embryo loss in an estimated >70% of the fertilisation events in humans.

Besides chromosome anomalies, detected by cytogenetics or CGH arrays (array‐based comparative genomic hybridisation), gene variants are associated with an increased risk of pregnancy loss. These genes may be regulators of immune response including cytokines, modulators of the coagulation cascade, equilibrators of the oxidative stress or, rarely, genes involved in chromosome segregation at meiosis or mitosis. Other genes may be found by genome‐wide association studies.

Recent novel studies are developing on the impact of epigenetic regulators (essentially microRNAs) on miscarriages. These can be relevant markers to categorise gene expression deregulation in pregnancy losses.
The Nuclear Envelope Protein Emerin and Its Interacting Proteins
Authors: Collins Carol M , Nee Kimbre A , Holaska James M 
Published: September 2016

Abstract

Emerin is a highly conserved and ubiquitously expressed inner nuclear membrane protein of the nuclear envelope. Mutations in the gene encoding emerin cause X‐linked Emery–Dreifuss muscular dystrophy (EDMD), a tissue‐specific, progressive disease that selectively affects skeletal muscle, the cardiac conduction system and tendons. Emerin regulates a number of nuclear functions through interactions with many different binding partners. These emerin‐regulated cellular functions include regulating genomic architecture, maintaining nuclear structure and regulating gene transcription in response to mechanical and chemical signals. Emerin regulation of these activities is important for controlling the coordinated temporal expression of myogenic differentiation genes during skeletal muscle regeneration. This article focuses on the mechanisms by which emerin regulates chromatin architecture and gene transcription and how these mechanisms may function in the development of EDMD.

Key Concepts

Proteins of the nuclear lamina are important for chromatin architecture and regulation of gene transcription.

Emerin is a nuclear lamina protein that plays key roles in regulating chromatin organisation and gene expression.

Emerin regulates the coordinated temporal expression of myogenic differentiation genes.

Emerin is required for proper myogenic differentiation.

Loss of emerin causes Emery–Dreifuss muscular dystrophy.
Reverse Signalling
Authors: Ross Emily F , Ali Maria F , Woo Laura A , Chadwick Sean R , Lee Eunji , Sangston Ryan M , Sood Chhavi , Zhang Qi , Zhang Xiaomu , Deppmann Christopher D 
Published: September 2016

Abstract

Cellular signal transduction is defined as the conversion of an extracellular signal to a response within a cell. Commonly referred to as forward signalling, this extracellular signal often comes in the form of a soluble ligand that binds to a membrane‐spanning receptor. However, many ligands or their precursors are also transmembrane or membrane associated. It is now appreciated that these ligands may also act as receptors in a process referred to as reverse signalling. There is a growing body of evidence that reverse signalling occurs for several classes of ligands including: ephrins, semaphorins, interleukins, tumour necrosis factor family members and Notch‐associated ligands. This type of signalling has been linked to immune responses, axon guidance, cell proliferation and differentiation. Here we review reverse signalling of ligands categorised by how they associate with the membrane: transmembrane type 1 (TM1), transmembrane type 2 (TM2), or GPI‐linked. Within this structure we will emphasize the physiological and pathological roles of reverse signaling.

Key Concepts

Ligand classes that possess the ability to reverse signal include, but are not limited to, members of the tumour necrosis factor superfamily (TNFSF), ephrin family, semaphorin family, interleukin family and Notch‐associated ligands.

These ligands can be categorized into the following subgroups: transmembrane type 1 (TM1), transmembrane type 2 (TM2), and GPI‐linked.

Ligands can reverse signal by directly recruiting adaptor or effector proteins, acting in concert with coreceptors or by liberation of the intracellular domain to influence transcription.

Reverse signalling has been shown to be involved in processes including axon guidance, tissue development and immune responses.

Ectopic regulation of reverse signalling is associated with a range of pathologies including cancer, developmental defects and osteoporosis.
Micellar Nanoreactors
Authors: Scarso Alessandro 
Published: September 2016

Abstract
All chemical disciplines, primarily homogeneous catalysis, are experiencing a great revolution owing to the emerging and increasingly stringent requirements represented by green chemistry principles. Replacement of traditional organic solvents with water is nowadays a viable solution where the use surfactants for the formation of nanometric micelles in water as a place to carry out reactions plays a key role. The use of micelles in catalysis is a simple and economic approach to circumvent solubilization problems in water. Moreover, the confinement of the catalyst in several cases enables simple catalyst recycling together with facile product isolation by means of extraction with an apolar solvent in limited amounts. Micelles operate as nanometric reactors where substrates and catalysts are confined and this proves to favor catalytic activity and, more importantly, selectivity at all levels for a wide range of chemical transformations, also in the stereoselective manner, in most cases with better performance compared to traditional organic solvents. In this contribution, after a brief introduction on surfactants, their aggregation properties in water, and micelle formation, a wide selection of catalytic reactions in micellar conditions is discussed with the aim of making this approach to homogeneous catalysis more familiar for students and colleagues in the academia as well as in chemical companies.
Ionic Liquids: Applications by Computational Design
Authors: Karunanithi Arunprakash T. , Farahipour Reza , Dilmurat Kamila 
Published: September 2016

Abstract
Ionic liquids (ILs) are molten salts that exist as liquids at relatively low temperatures and have unique properties. The most exciting aspect of ILs is the opportunity to fine‐tune their physicochemical and thermodynamic properties based on careful selection of cations and anions. There are no limits to the number of possible IL combinations as there are a large number of cation and anion variants that can be combined together to form binary and ternary ionic liquids. To effectively identify task‐specific ILs, we propose a computer‐aided ionic liquid design (CAILD) approach with an aim to screen thousands of IL combinations to identify optimal candidates for a given application. We present a novel approach that uses the concept of group contribution modeling to predict surface charge density of ionic liquid structures generated by DFT calculations, which is further combined with COSMO‐SAC model to enable thermodynamic property predictions of systems involving ionic liquids without any need for experimental data. This allows us to consider more diverse set of ionic liquids for design purposes. In this chapter, we summarize these methodological advancements and present two proof‐of‐concept case studies.
Toxicity Assessment of Molecular Rhenium(VII) Epoxidation Catalysts
Authors: Cokoja Mirza , Markiewicz Marta , Stolte Stefan , Kühn Fritz E. 
Published: September 2016

AbstractMethyltrioxorhenium(VII) (MTO) is a highly efficient epoxidation catalyst with a broad substrate scope. Evaluation of its hazard potential shows that it is able to cause short‐term (eco)toxicological effects with indications for genotoxicity. However, under catalytic conditions, MTO (and its catalytically active derivatives) decomposes slowly to perrhenates, displaying low toxicity. In aqueous solutions, particularly in the presence of bases, this decomposition is rather quick. Accordingly, MTO is not long‐time stable in an aqueous environment, yielding far less toxic decomposition products. Perrhenate‐containing ionic liquids are also of low toxicity (at least with respect to the rhenium‐containing anion); their epoxidation activity, however, is ‐ so far—no match for MTO. The latter molecule, however, due to its limited stability in aqueous environments and the low toxicity of its decomposition products, combined with its high catalytic activity and selectivity may be regarded as a useful catalyst for practical applications under controlled and safe reaction conditions.
Solvent Systems for Sustainable Chemistry
Authors: Kerton Francesca M. 
Published: September 2016

Abstract
Reduced use of volatile organic compounds as solvents in chemical processes is highly desirable from a sustainability point of view. This is because many conventional organic solvents have high vapor pressures, which can lead to hazards including low flash points, high flammability, toxicity, and atmospheric pollution. In order to make decisions regarding solvent use in a chemical process, it is important to evaluate the options available both from a chemical point of view and also with regards to the environment and safety. The typical physicochemical properties and parameters that need to be considered are briefly described. An overview of the environmental, health, and safety criteria used to assess all solvent systems (traditional and environmentally friendly) is provided. The concept of life‐cycle assessment when applied to solvents in either a quantitative or a qualitative way is introduced. Guidance provided by industrial users of solvents, especially the pharmaceutical industry, is highlighted. A range of sustainable solvent systems are described in this chapter. These include: water, supercritical carbon dioxide, carbon dioxide‐expanded liquids, solvents of switchable polarity and volatility, room temperature ionic liquids and deep eutectic solvents, bio‐derived solvents (e.g., 2‐methyltetrahydrofuran and glycerol), and solvent‐free systems. Their advantages, disadvantages, and properties are discussed, and examples of chemistries performed in them are given. Biphasic systems based on sustainable solvents and aimed at allowing their more efficient use and potential catalyst recycling are described. These include water/bio‐derived solvent, supercritical carbon dioxide/water, and supercritical carbon dioxide/ionic liquid systems.
Sustainable Synthesis of Fine Chemicals from Aliphatic Nitro Compounds
Authors: Ballini Roberto , Palmieri Alessandro 
Published: September 2016

AbstractThe demands of modern society for new functional chemical entities have driven the development of novel methods that are revolutionizing the way we think, plan, and optimize chemical processes. Chemical industries, in general, use a large volume of organic solvents and catalysts in their manufacturing processes. However, the toxic and volatile nature of many organic solvents have posed serious threats to the environment. Hence, industries are finding it very difficult to meet the standards set by pollution regulatory boards while using traditional methods. Thus, redesign of chemical processes for reducing or avoiding hazardous organic solvents and toxic catalysts is highly desirable. In 1998, Anastas and Warner teamed up to write the best‐selling and most cited book in the field of Green Chemistry, “Green Chemistry: Theory and Practice”, which explicated the 12 principles of Green Chemistry. The application of many of these principles could be strongly favored by the right choice of the starting material in a synthetic process, in particular those such as nitroalkanes that show high chemical versatility. This article deals with this issue and highlights some representative examples on the application of nitroalkanes as key starting molecules for the sustainable synthesis of fine chemicals via (i) one‐pot synthetic processes, (ii) reactions in aqueous medium, and (iii) solvent‐free reactions (SolFR).
Sustainable Surfactants Based on Amino Acids
Authors: Pérez Lourdes , Infante M. Rosa , Pinazo Aurora 
Published: September 2016

AbstractSurfactants are chemical products consumed in large quantities every day on a worldwide scale. In recent years, environmental concerns and regulatory pressure have emerged as the driving forces to partly replace petrochemical‐based surfactants with those based on naturally occurring renewable sources. The hope that such surfactants would be biodegradable and biocompatible has provided strong incentive for the research of less irritant and less toxic consumer‐friendly surfactants. Biodegradability, low toxicity, and antimicrobial activity are properties common to surfactants derived from amino acids. In this chapter we offer an overview of the synthesis methods and properties published in the literature concerning four families of amino acid based surfactants: single chain, amino acid based surfactants, diacyl‐glycerolipid conjugates, gemini surfactants from amino acids, and polydispersed lipopeptides from a mixture of amino acids. Whenever present in the source material, specific applications are described.
Dimethylcarbonate for the Catalytic Upgrading of Amines and Bio‐Based Derivatives
Authors: Selva Maurizio , Perosa Alvise , Guidi Sandro , Cattelan Lisa 
Published: September 2016

Abstract

An archetype of a green and sustainable strategy for the catalytic upgrading of both anilines and bio‐based derivatives including glycerol acetals,
p
‐coumaryl‐like alcohols, and lactones can be devised by the use of dimethyl carbonate (DMC). In the presence of different heterogeneous catalysts such as alkaline carbonates and alkali metal‐exchanged faujasites, DMC allows quantitative mono‐N‐methylation and O‐methylation processes with excellent selectivity up to 99% and no by‐products except for methanol (recyclable to the synthesis of DMC) and CO
2
. Also, selective transesterifications of DMC with glycerol acetals and lactones can be achieved under thermal or catalytic conditions. The mechanism of such reactions has been formulated based on the steric requisites and the amphoteric nature of faujasites, the combined effect of the temperature and base catalysts, and the ambident electrophilic reactivity of DMC. Overall, methylations and methoxycarbonylations mediated by DMC are not only more selective but far safer than conventional procedures involving noxious phosgene and methyl halides or dimethyl sulfate.
Water Treatment by Electrocoagulation
Authors: Kuokkanen Ville V. 
Published: September 2016

Abstract

Electrocoagulation (EC) is an emerging technology that is applied in water and wastewater treatment, which combines the functions and advantages of conventional chemical coagulation (CC), flotation, and electrochemistry. Although EC has been known for over a century, it is currently under a strongly renewed global research, and has also gained industrial interest. This is mainly due to its cost‐, material‐, and eco‐efficiency. Furthermore, environmental regulations regarding wastewater discharge are becoming increasingly stringent. Therefore, it has become a necessity to develop more effective alternative and automatic treatment methods for water purification and/or enhance the operation of the existing, more classical methods. As a result, the range of feasible EC applications is expanding. Innovations in this field have also been made recently. At its simplest, an EC system may consist of two plate electrodes, an anode and a cathode, and a direct current power source. In short, EC is based on coagulation brought about by aluminum or iron derived (in situ) from electrochemical dissolution of the anode metal, which is used as the so‐called sacrificial anode. Simultaneously with the anodic reaction, hydrogen gas bubbles are generated at the cathode surface, promoting electroflotation (EF). Furthermore, in an EC system, a variety of minor side reactions may take place. EC also neutralizes solution pH, mainly due to cathodic OH
−
ion generation. This is converse to CC. Since CC may naturally be seen as the main competitor to EC, comparison between the two technologies is inevitable. EC has multiple advantages over CC. Firstly, these include economic aspects: EC is energy‐efficient, and its running costs as well as investment costs in establishing EC systems are low due to their small size and simplicity. Second, since no chemicals are needed in EC, secondary pollution is avoided, which makes EC “a green technology”. Third, EC is also readily automated and hybridizable with other methods, and produces low amounts of sludge of a better quality than CC sludge. The most obvious disadvantage of EC is the need to periodically replace the electrodes, along with the need for sufficient water conductivity. Electrode passivation may also occur.
Role of Mixed Metal Oxides in Heterogeneous Catalysis
Authors: Burange Anand S. , Gawande Manoj B. 
Published: September 2016

Abstract
In this article, we include numerous types of mixed metal oxides (MMOs) including their properties and catalytic applications for several types of reactions, focusing on their active sites (acidic and basic). Owing to the acid–base and redox properties of MMOs, they establish a largest family of catalysts in heterogeneous catalysis. Generally, in most of the examples, MMOs have superior properties in terms of acidic or basic sites and surface area than single oxide. In addition, some examples of mixed metal ratio are also discussed on specific catalytic applications.
Tandem Chemoselective 1,2‐/1,4‐Migration of the Thio Group in Keto Thioesters: An Efficient Approach to Substituted Butenolides
Authors: Mal Kanchan , Naskar Sandip , Sen Shovan Kumar , Natarajan Ramalingam , Das Indrajit 
Published: September 2016

AbstractWe report herein an efficient and mechanistically unique tandem chemoselective 1,2‐/1,4‐migration of the thio group in keto thioesters that provides substituted butenolides in moderate to excellent yields. Thus, α‐keto thioesters in the presence of stabilized phosphonate carbanions undergo tandem 1,2‐sulfur migration; whereas 1,4‐migration of the thio group has been achieved with the same thioesters after the treatment with Wittig reagents followed by BF3⋅OEt2‐catalyzed tandem reaction. The crossover experiments and the isolation of intermediates reveal a stepwise mechanism for both of these transformations.magnified image
Single‐Biocatalyst Synthesis of Enantiopure d‐Arylalanines Exploiting an Engineered d‐Amino Acid Dehydrogenase
Authors: Parmeggiani Fabio , Ahmed Syed T. , Thompson Matthew P. , Weise Nicholas J. , Galman James L. , Gahloth Deepankar , Dunstan Mark S. , Leys David , Turner Nicholas J. 
Published: September 2016

AbstractA practical and efficient biocatalytic synthesis of aromatic d‐amino acids has been developed, based on the reductive amination of the corresponding α‐keto acids via a recombinant whole cell system composed of an engineered dehydrogenase and cofactor recycling apparatus. The reaction was shown to give excellent enantioselectivity (≥98%) and good yields at the preparative scale across a broad range of substrates. Additionally, the structure of the variant enzyme was solved to allow rationalisation of the observed reaction rates. The engineered whole cell catalyst was also used to mediate the production of d‐phenylalanine derivatives from racemic mixtures and cheaper l‐amino acids by combining it with an enantiocomplementary deaminase.magnified image