bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Pili and Fimbriae
Authors: Ramirez Nicholas A , Ton‐That Hung 
Published: March 2020

Abstract

Bacterial proteinaceous filaments termed pili or fimbriae are nonflagellar, hair‐like structures protruding from the cell surface that are critical for bacterial virulence and fitness. Present in both Gram‐negative and Gram‐positive bacteria, pili are involved in many processes such as conjugation, adherence, twitching motility, biofilm formation and immunomodulation. Considerably diverse and complex, Gram‐negative pili are formed by noncovalent polymerisation of various pilin subunits; many of these pili require chaperones and usher proteins for their assembly. In contrast, fewer pilus systems have been described for the Gram‐positive counterparts; notably well studied are the heterotrimeric or ‐dimeric pili that are covalently assembled by a transpeptidase enzyme called sortase. Furthermore, type IV pili have been identified in several Gram‐positive bacteria, especially in clostridia.

Key Concepts

Noncovalent pilus polymerisation is a general mechanism of pilus assembly in Gram‐negative bacteria, including the chaperone/usher assembly pathway and type IV pilus pathway, which generates noncovalent pilus polymers.

Sortase‐mediated pilus assembly is a general mechanism of pilus assembly in Gram‐positive bacteria that involves a transpeptidase enzyme named sortase, which cleaves pilin precursors at sorting signals between threonine and glycine residues and utilises the side‐chain amino groups of pilin motif sequences to generate covalent links between pilin subunits.

The sorting signal consists of an LPXTG motif followed by a hydrophobic domain and a positively charged tail.

The pilin motif is an 11 amino acid sequence of WxxxVxVYPKN located near the
N
‐terminus of major pilin subunits, in which the electron‐donating lysine residue forms an isopeptide bond with the threonine residue generated from the cleavage of the LPXTG motif of adjacent pilin subunits.

Tissue tropism is referred to as the ability of a pathogen to adhere specifically to some particular epithelial cells.

Phase variation involves switching of surface antigens such as pili that allows a pathogen to evade the host immune system.

Immunomodulation is a process of changing the host's immune system by certain molecules known as immunomodulators including pili that can activate or suppress immune cells.

Dental plaque is one of the most complex bacterial biofilms that is formed by sequential colonisation of initial colonisers such as
Actinomyces
spp. and oral streptococci and late colonisers; this process involves
Actinomyces
fimbriae.

Twitching motility mediated by pili allows translocation between mucosal surfaces, colonisation of host tissues and establishment of biofilms by a pathogen.
Ultramicrobacteria
Authors: Duda Vitaly I , Suzina Natalia E , Boronin Alexander M 
Published: March 2020

Abstract

Ultramicrobacteria (UMB) are characterised by the following properties:

UMB are species of prokaryotic organisms belonging to the domain Bacteria.

UMB cells possess extremely small size; their volume is ≤0.1 μm
3
irrespective of growth conditions and development cycle.

UMB feature a very small size of genome (mainly from 3.2 to 0.58 Mb).

An obligate capability of self‐reproduction.

UMB feature a combination of such determining characters as ultrasmall size of proliferating cells, small size of genome and capability of self‐reproduction. As a synonym for UMB, some authors use the term ‘nanobacteria’ (NB).
Several dozens of UMB species have been isolated from various habitats, such as aquatic and soil environments, sediments, silts, Greenland ice, permafrost, human intestines and insects; and are cultured under laboratory conditions on various nutritive media. The term ‘nan(n)obacteria’ is also used to designate ultrasmall bacterium‐like particles occurring in rocks, sands, soils, in deep subsurface, meteorite and clinical samples. UMB include species of free‐living and parasitic (predatory) bacteria. Their cells divide by constriction, septation or budding. Unique processes UMB perform are dehalorespiration and epibiont obligate and facultative parasitism. UMB have been found among organisms of six large phylogenetic branches of prokaryotes.

Key Concepts

Formation of a minimal self‐reproducing microbial cell is the prerogative of the prokaryotes.

Ultrasmall size of cells enables parasitism (predation) of UMB on ‘large‐cell’ species of prokaryotes.

UMB are important model objects for studies of genome evolution in prokaryotes.

UMB studies are of vital importance for solving issues of the origin and evolution of primeval living objects.

UMB research opens new trends in biotechnology.

Use of UMB representatives, mycoplasms, played a crucial role in pioneering works by J. C. Venter and collaborators for experimentally creating a new living being (cells with chemically synthesised genome) and a new bacterial species.

Description of new UMB cell structures expands the diversity pattern of the ultrastructural and molecular organisation of the prokaryotic cell.

Gram‐negative, Gram‐positive or archaeal type of cell organisation is not the prohibitive factors for UMB or ultramicroarchaea to form.
TheSLAC1Anion Channel
Authors: Hõrak Hanna 
Published: March 2020

AbstractThe balance between CO2uptake for photosynthesis and water loss through transpiration determines plant growth and productivity. Guard cells form stomatal pores in plant epidermis that adjust this balance via volume changes that control stomatal aperture. Guard cell volume is regulated by fluxes of ions and water across the membrane via various ion channels. The slow anion channel 1 (SLAC1) is essential for efficient stomatal regulation, as it is the major mediator of the efflux of anions from guard cells during stomatal closure. The activation of SLAC1 requires phosphorylation and is the end point of signalling pathways initiated by abiotic and biotic triggers that cause stomata to close, such as the phytohormone abscisic acid, elevated CO2levels, darkness, low air humidity, ozone; and pathogen and damage‐associated molecular patterns and hormones. SLAC1 is conserved in evolution, but SLACs in different plant groups have different mechanisms of regulation.Key ConceptsSLAC1 is the major guard cell slow‐type anion channel that needs to be activated by phosphorylation in theN‐ andC‐terminal regions for stomatal closure in response to endogenous and environmental stimuli.The plant hormone abscisic acid (ABA) triggers SLAC1 activation through a signalling pathway that involves ABA receptors and PP2C phosphatases, which regulate the Ca2+‐independent kinase OST1 and several Ca2+‐dependent protein kinases that phosphorylate SLAC1. The same pathway is involved in SLAC1 activation in response to darkness, CO2, ozone and low air humidity.Elevated CO2activates SLAC1 via bicarbonate, which directly enhances ion channel activity. The Raf‐type kinase HT1 and mitogen‐activated protein kinases MPK12 and MPK4 regulate SLAC1 activation in response to CO2, but not ABA, contributing to a CO2‐specific branch of SLAC1 activation.Pathogen‐associated molecules trigger the activation of SLAC1 and its homologue SLAH3 that contributes to guard cell anion currents. SLAH3 is the key anion channel in stomatal response to fungal chitin, whereas SLAC1, SLAH3 and OST1 contribute to bacterial flagellin‐induced stomatal closure.SLAC1 and OST1 are conserved in early land plants, such as mosses, lycophytes and ferns, but their role in these plants needs further study. The regulation of SLAC1 anion channel differs among plant groups – for example, the monocot SLACs, unlike Arabidopsis SLAC1, require external nitrate for activation.
Endoderm Formation in Vertebrates
Authors: Wardle Fiona C 
Published: March 2020

AbstractDuring vertebrate embryogenesis, endoderm, the inner‐most germ layer, will form the gut and associated organs, including liver and pancreas. Studies in the zebrafish,Xenopusand mouse have shown that the signalling pathways and transcription factors that regulate endodermal cell fate in the early embryo are largely conserved in vertebrates. Evidence from these model systems indicates Nodal signalling induces endoderm, in combination with the activity of transcription factors from the Mix, Gata, Sox and T‐box families. Other signalling pathways, such as Fgf, Bmp and Wnt, ensure the correct balance of mesoderm and endoderm is formed during gastrulation.Key ConceptsEndoderm formation is initiated during mid‐blastula stages in zebrafish andXenopus.High levels of Nodal signalling induce endoderm formation.A conserved set of transcription factors, of the Sox, Mix, Gata and T‐box families, act in a network with Nodal to establish endodermal fate during gastrulation.The role of these factors and pathways downstream of Nodal signalling in early endoderm formation is mostly conserved; however, there are some species‐specific differences.Other signalling pathways, notably the Fgf, Bmp and Wnt pathways, regulate the amount of endoderm that forms versus other germ layers.
Plant Endophytes
Authors: Jørgensen Hans J Lyngs , Collinge David B , Rojas Edward C , Latz Meike A C , Manzotti Andrea , Ntana Fani , Jensen Birgit 
Published: March 2020

Abstract

Endophytes are defined as microorganisms colonising the interior of plants without causing disease. They comprise mainly fungi and bacteria, and their lifestyle range from merely receiving shelter and nutrients from the host to interactions benefitting both themselves and the host plant. In recent years, there has been an increased interest in understanding the communities of organisms inside plants; how they influence the host and how they can be utilised to benefit plants and humans. Therefore, the transmission and recruitment of endophytes, as well as methods to study the composition of endophytic communities, are important issues for successful exploitation. Beneficial effects include protection against biotic stress caused by pests and pathogens as well as against abiotic stress, for instance, drought, salinity and temperature. Furthermore, endophytes can promote growth by production of plant hormones and nutrient acquisition and some endophytes can be used for bioremediation and production of pharmaceuticals and nutraceuticals.

Key Concepts

Endophytes are organisms living inside plants without causing disease.

Most endophytes are commensalistic, but some are mutualistic.

Most endophytes are bacteria and fungi.

Endophyte communities can be studied by culture‐dependent and culture‐independent methods.

Recruitment of endophytes can be from environment or from mother plants.

Endophytes can protect plants from biotic and abiotic stress.

Endophytes can help in nutrient acquisition for the plant and cause growth promotion.

Endophytes can help in bioremediation and participate in the production of specialised metabolites with industrial application.
Cover crop impact on irrigated cotton yield and net return in the southern Great Plains
Authors: DeLaune P.B. , Mubvumba P. , Fan Y. , Bevers S. 
Published: March 2020

AbstractCover crops have the potential to increase ecosystem services of cropping systems, although mixed results have been found throughout the U.S. Great Plains. Crop performance and economic returns are often used by producers to gauge the feasibility of adoption. In addition, soil moisture use by cover crops is a concern in semiarid environments. The objective of this research was to determine the impact of cover crops on cotton (Gossypium hirsutum L.) yield and economic return compared with conventional practices in pivot irrigated systems of the southern Great Plains. A 6‐yr study was conducted at the Texas A&M AgriLife Chillicothe Research Station evaluating the following treatments: (i) conventional till (CT); (ii) no‐till (NT); (iii) NT with winter wheat (Triticum aestivum L.) cover crop (NT‐W); and (iv) NT with a multi‐species cover crop mixture (NT‐M). Cotton yields, expenses, and returns were determined over a 6‐yr period (2013–2018). No significant treatment effect was determined for crop yield. Compared to NT, lint yields were increased 9.5% by NT‐M and 9.4% by NT‐W. Cover crop treatments significantly increased total costs compared to NT. However, net returns were 12% greater for NT‐W and 8% greater for NT‐M compared to NT. Over the 6‐yr study, NT‐M did not provide an agronomic or economic advantage over NT‐W. Under irrigated conditions in the southern Great Plains, cover crops were implemented without negatively affecting lint yield or net returns in continuous cotton systems at seeding rates of 34 kg ha–1.
Modeling the impacts of climate, soil, and cultivar on optimal irrigation amount of winter wheat in the North China Plain
Authors: Zheng Junqing , Wang Jing , Ren Wei , Tang Jianzhao , He Di , Huang Mingxia , Bai Huiqing , Wu Bingjie 
Published: March 2020

AbstractImproving winter wheat (Triticum aestivum L.) productivity and water use efficiency (WUE) in the North China Plain (NCP) is critical to maintain grain security and ease the water shortage in this region. This study was conducted to examine the optimal irrigation amount (OI) for winter wheat across the NCP and analyze its responses to the climate, soil, and cultivar. We applied a novel approach with the Agricultural Production Systems sIMulator (APSIM) during 1961–2010 to estimate the OI by considering the trade‐off between yield and WUE. Our results suggested that the optimum irrigation amount determined by climate (OIc) ranged from 3–342 mm for simulation experiments considering climate impacts alone. When soil conditions were additionally considered, the optimal irrigation amount (OIcs) showed an average decrease of 45 mm across 19 sites in the northern NCP but an average increase of 42 mm across 29 sites in the southern NCP. When all three factors were included, the estimated optimal irrigation amount (OIcsc) fell within the range of 3–286 mm across the NCP, lower than OIc and OIcs. Climate, soil, and cultivar explained 54, 27, and 19% of the spatial variation in the optimal irrigation amount, respectively. Further analysis indicated relatively higher optimal irrigation amounts for late‐maturing cultivars, but their inter‐annual variations and decadal changing rates were lower relative to the early‐ and medium‐maturing cultivars. Our study demonstrated the incorporation of the genotypes and environmental factors, and recommended the optimal irrigation amount of 3–286 mm for winter wheat in the NCP.
Synthesis of Highly Enantioenriched Bis‐spirooxindole Pyrrolizidine/Pyrrolidines through Asymmetric [3+2] Cycloaddition Reaction
Authors: Shahrestani Naeimeh , Tovfighmadar Kolsoum , Eskandari Mehdi , Jadidi Khosrow , Notash Behrouz , Mirzaei Peiman 
Published: March 2020

AbstractSynthesis of highly enantioenriched bis‐spirooxindole pyrrolizidine scaffold was established using 1,3‐dipolar cycloaddition of isatin‐derived azomethine ylides by (E)‐2‐oxoindolin‐3‐ylidene acetyl sultam with four contiguous and two quaternary stereogenic centers in generally high yields (up to 96%) and diastereoselectivities (up to 99 : 1). In addition, highly enantioenriched bis‐spirooxindole pyrrolidines were generated in high yields and highly regio‐ and ‐diastereoselectivities (up to 99 : 1) by utilizing this chiral auxiliary controlled method. The obtained cycloadducts underwent retro‐Mannich ring‐opening cyclization and produced new diastereoisomers of bis‐spirooxindole pyrrolizidine/pyrrolidines skeleton that could not be accessed by direct 1,3‐dipolar cycloaddition.
Noncovalent Chalcogen‐Bonding Catalysis Using ppm‐Level Catalyst Loading to Achieve Cyanosilylation of Ketones
Authors: Bao Lintao , Kong Xiangjin , Wang Yao 
Published: March 2020

AbstractAs noncovalent chalcogen‐bonding interaction is comparatively weak, it remains a true challenge to implement chalcogen‐bonding catalysis in an efficient manner. We herein show that a chalcogen‐bonding catalysis approach to cyanosilylation of a broad range of ketones can be achieved even using as low as parts per million (ppm) level catalyst loading while the reactions were completed within several minutes at room temperature. Considering the nature of weak noncovalent forces, this chalcogen‐bonding catalysis approach is remarkable as it can give up to 106/h turnover frequency numbers.
Raman Optical Activity (ROA) as a New Tool to Elucidate the Helical Structure of Poly(phenylacetylene)s
Authors: Palomo Luis , Rodríguez Rafael , Medina Samara , Quiñoá Emilio , Casado Juan , Freire Félix , Ramírez Francisco J. 
Published: March 2020

AbstractPoly(phenylacetylene)s are a family of helical polymers constituted by conjugated double bonds. Raman spectra of these polymers show a structural fingerprint of the polyene backbone which, in combination with its helical orientation, makes them good candidates to be studied by Raman optical activity (ROA). Four different well‐known poly(phenylacetylene)s adopting different scaffolds and ten different helical senses have been prepared. Raman and ROA spectra were recorded and allowed to establish ROA‐spectrum/helical‐sense relationships: a left/right‐handed orientation of the polyene backbone (Mhelix/Phelix) produces a triplet of positive/negative ROA bands. Raman and ROA spectra of each polymer exhibited the same profile, and the sign of the ROA spectrum was opposite to the lowest‐energy electronic circular dichroism (ECD) band, indicating a resonance effect. Resonance ROA appears then as an indicator of the helical sense of poly(phenylacetylene)s, especially for those with an extra Cotton band in the ECD spectrum, where a wrong helical sense is assigned based on ECD, while ROA alerts of this misassignment.
Enantioselective Twofold C−H Annulation of Formamides and Alkynes without Built‐in Chelating Groups
Authors: Chen Hao , Wang Yin‐Xia , Luan Yu‐Xin , Ye Mengchun 
Published: March 2020

AbstractTwofold C−H annulation of readily available formamides and alkynes without built‐in chelating groups was achieved. Ni−Al bimetallic catalysis enabled by a bulky BINOL‐derived chiral secondary phosphine oxide (SPO) ligand proved to be critical for high reactivity and high selectivity. This reaction uses readily available formamides as starting materials and provides a concise synthetic pathway to a broad range of chiral ferrocenes in 40–98 % yield and 93–99 % ee.
Mechanistische Studien zu Cobalta(III/IV/II)‐Elektrokatalyse: Oxidativ‐induzierte reduktive Eliminierung zur zweifachen C‐H‐Aktivierung
Authors: Meyer Tjark H. , Oliveira João C. A. , Ghorai Debasish , Ackermann Lutz 
Published: March 2020

AbstractDie Kombination aus Cobalt‐katalysierter C‐H‐Aktivierung und Elektrosynthese ermöglicht zahlreiche neue Möglichkeiten in der ressourcenschonenden molekularen Synthese, allerdings bleibt ihr Wirkungsmechanismus bisher nur wenig verstanden. Innerhalb dieser Studie haben wir die Identifikation und vollständige Charakterisierung von elektrochemisch synthetisierten, hoch‐valenten Cobalt(III/IV)‐Komplexen vorgenommen, die als Schlüsselintermediate in elektrochemischen Cobalt‐katalysierten C‐H‐Oxygenierungen identifiziert werden konnten. Detaillierte mechanistische Studien lieferten Hinweise auf eine oxidativ‐induzierte reduktive Eliminierung ausgehend von hoch‐reaktiven Cobalt(IV)‐Intermediaten. Diese Beobachtung ermöglichte den Zugang zu bisher unbekannter Cobalt‐elektrokatalysierter zweifacher C‐H/C‐H‐Aktivierung.
Synthesis and characterization of renewable polyesters based on vanillic acid
Authors: Zhang Silong , Cheng Zhengzai , Zeng Sheng , Li Guangyao , Xiong Jing , Ding Ling , Gauthier Mario 
Published: March 2020

AbstractVanillic acid, potentially derived from biosourced feedstocks, was used as starting material in the synthesis of novel polyesters. A diester obtained by esterification and etherification of vanillic acid served as first monomer, in combination with resorcinol bis(2‐hydroxyethyl) ether, hydroquinone bis(2‐hydroxyethyl) ether, or aliphatic diols with different carbon chain lengths as second monomers, and antimony trioxide as catalyst to synthesize a series of polyesters by melt polymerization. The materials obtained had polystyrene‐equivalent M
n = 10,000–19,500 g/mol and M
w = 19,300–39,500 g/mol. Thermal analysis yielded melting temperatures of 76–114°C and onset decomposition temperatures T5% = 321–360°C. Dynamic mechanical and tensile testing confirmed that polyesters derived from vanillic acid have properties superior to poly(ethylene terephthalate) (PET). Aqueous degradation experiments with bulk polyester samples at different pH over 16 weeks led to intrinsic viscosity decreases of 9–23% under neutral conditions (pH 7), 10–26% under acidic conditions (pH 3), and 7–19% under alkaline conditions (pH 12). The results obtained show that the good thermal stability and degradability of vanillic acid‐based polyesters, and the tunability of the properties of these materials through selection of the diol monomer used in their synthesis, make them excellent biosourced replacements for commercial polyesters such as PET.
Extraction of high‐quality, high‐molecular‐weight DNA depends heavily on cell homogenization methods in green microalgae
Authors: Stark Jordan R. , Cardon Zoe G. , Peredo Elena L. 
Published: March 2020

PremiseNew sequencing technologies have facilitated genomic studies in green microalgae; however, extracting high‐quality DNA is often a bottleneck for long‐read sequencing.Methods and ResultsHere, we present a low‐cost, highly transferrable method for the extraction of high‐molecular‐weight (HMW), high‐purity DNA from microalgae. We first determined the effect of sample preparation on DNA quality using three homogenization methods: manual grinding using a mini‐pestle, automatic grinding using a vortex adapter, and grinding in liquid nitrogen. We demonstrated the versatility of grinding in liquid nitrogen followed by a modified cetyltrimethylammonium bromide (CTAB) extraction across a suite of aquatic‐ and desert‐evolved algal taxa. Finally, we tested the protocol's robustness by doubling the input material to increase yield, producing per sample up to 20 μg of high‐purity DNA longer than 21.2 kbp.ConclusionsAll homogenization methods produced DNA within acceptable parameters for purity, but only liquid nitrogen grinding resulted in HMW DNA. The optimization of cell lysis while minimizing DNA shearing is therefore crucial for the isolation of DNA for long‐read genomic sequencing because template DNA length strongly affects read output and length.
N‐Arylation of Diketopyrrolopyrroles with Aryl Triflates
Authors: Gutkowski Krzysztof , Skonieczny Kamil , Bugaj Marta , Jacquemin Denis , Gryko Daniel T. 
Published: March 2020

AbstractA new methodology for the doubleN‐arylation of diketopyrrolopyrroles with aryl triflates has been developed. It is now possible to prepare diketopyrrolopyrroles bearingN‐substituents derived from naphthalene, anthracene and coumarin in two steps from commercially available phenols. This represents the first time arenes lacking strong electron‐withdrawing groups were inserted onto lactamic nitrogen atoms via arylation. The ability to incorporate heretofore unprecedented substituents translates to increased modulation of the resulting photophysical properties such as switching‐on/off solvatofluorochromism. TD‐DFT calculations have been performed to explore the nature of the relevant excited states. This new synthetic method made it possible to elucidate the influence of such substituents on the absorption and emission properties of tetraaryl substituted diketopyrrolopyrroles.