bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Primosome
Authors: Tanaka Taku , Masai Hisao 
Published: October 2019

AbstractDNA (deoxyribonucleic acid) replication requires operation of molecular machinery which efficiently elongates nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA (DNA polymerases) but also those providing primer RNAs (ribonucleic acid) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins, DNA helicase and primase are sequentially assembled on the template DNA to generate a primosome. Once assembled, it, in conjunction with DNA polymerases, facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein including DnaA or PriA, which recognises the site of assembly. Primosome is assembled also in replication restart process at stalled or processed replication forks, triggered by PriA. Primosome constitutes an essential component for active replication fork machinery. Recent advances in this field provide structural basis regarding how these factors function during the assembly of a primosome on viral origins as well as during the restart from the stalled DNA replication forks. These new knowledges provide important insight into how replication forks are protected from various genotoxic agents in eukaryotes.Key ConceptsReplication fork is the site of DNA replication where DNA synthesis occurs, and primosome is its integral component.Primosome is capable of duplex DNA unwinding and primer RNA synthesis at the replication fork.In bacteria, replication is normally initiated at a single locus,oriC, on the genome.Bacterial DNA replication is initiated by an initiator, DnaA, which generates aoriC‐primosome.The stalled DNA replication fork needs to be swiftly detected and rescued to prevent its collapse and to ensure the completion of genome replication.Another primosome mediated by PriA serves for reassembly of replication fork at a stalled fork in bacteria.Bacterial genomes can be replicated by an alternative mode that involves RNA‐DNA hybrids.Primosomes in eukaryotes may be more complex, but essential components would be conserved.
D
esulfocucumaceae fam. nov.
Authors: Watanabe Miho , Fukui Manabu , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.cu.cu.ma.ce'ae. N.L. masc. n.
Desulfocucumis
type genus of the family; suff.
‐aceae
ending to denote a family; N.L. fem. pl. n.
Desulfocucumaceae
the family of
Desulfocucumis
.

Desulfotomaculota (Firmicutes_B) / Desulfotomaculia / Desulfotomaculales / Desulfocucumaceae / Desulfocucumaceae fam. nov.

Cells are curved rods to vibrios. Gram‐stain‐negative. Spherical spores occur at the cell terminals. Motile with peritrichous flagella. Strictly anaerobic, having a respiratory type of metabolism. Mesophilic and neutrophilic. NaCl is not required for growth. Chemolithoautotroph or chemoorganotroph using organic acids, yeast extract, and alcohols. Substrate oxidation is complete. Sulfate, thiosulfate, and elemental sulfur are used as electron acceptors and are reduced to sulfide. Grows fermentatively on organic acids. Desulfoviridin is absent. Branched‐chain fatty acids are the major cellular fatty acids. Major menaquinone is MK‐7. The family currently accommodates a single genus
Desulfocucumis
. The type species of the genus
Desulfocucumis
was isolated from marsh soil.

DNA G + C content (mol%)
: 46.6

Type genus
:
Desulfocucumis
Watanabe, Kojima and Fukui 2017, 2681
VP
.
D
esulfobacter
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.bac'ter. L. pref.
de
from L. neut. n.
sulfur
; N.L. masc. n.
bacter
rod or staff; N.L. masc. n.
Desulfobacter
, a rod‐shaped sulfate‐reducing bacterium.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulfobacteraceae / Desulfobacter

Oval‐to‐rod‐shaped or slightly curved‐to‐vibrio‐shaped cells, 0.5–2.5 × 1.5–8 µm. Occur singly or in pairs. Spore formation is not observed. Gram‐stain‐negative. Cells are nonmotile or motile by a single polar flagellum. Strict anaerobe with a respiratory type of metabolism. Chemoorganoheterotrophs or chemolithoautotrophs. Acetate is the preferred electron donor and carbon source, and it is completely oxidized to CO
2
. Some species also use ethanol, and a few species use H
2
/CO
2
or pyruvate. H
2
‐utilizing
Desulfobacter hydrogenophilus
grows autotrophically with CO
2
as the sole carbon source. Sulfate and, usually, sulfite and thiosulfate serve as terminal electron acceptors and are reduced to H
2
S. Sulfur and nitrate are not used as terminal electron acceptors. Fermentative growth has not been observed. Desulfoviridin is absent, but desulforubidin is present in some species. The major type of menaquinone is MK‐7. Growth occurs in defined media containing sulfide as a reductant. Most species require vitamins. Many members of this genus can fix N
2
. The addition of ≥7 g NaCl and ≥1 g MgCl
2
·6H
2
O per liter medium is usually stimulatory or required for growth. The optimal temperature range for growth is 28–34°C. Thermophilic species have not been described. Neutrophilic. The optimal pH range for growth is 6.5–7.4. Carbon monoxide dehydrogenase activity is absent. Acetyl‐CoA oxidation in most species and CO
2
fixation with H
2
as electron donor in
D. hydrogenophilus
is accomplished via a modified tricarboxylic acid cycle cycle.
Desulfobacter
species are most common in anoxic brackish or marine sediments, but some species may be found in anoxic freshwater sediments or in activated sludge.

DNA G + C content (mol%)
: 44.0–49.0 (
T
m
, LC, genome).

Type species
:
Desulfobacter postgatei
Widdel 1981, 382
VP
(Effective publication: Widdel 1980, 373).
D
esulfatiferula
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fa.ti.fe'ru.la. L. pref.
de
, from; N.L. n.
sulfas ‐atis
, sulfate; L. fem. n.
ferula
, a staff, a small rod; N.L. fem. n.
Desulfatiferula
, a rod‐shaped sulfate‐reducer.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulforegulaceae / Desulfatiferula

Curved rods, 0.45–0.6 µm × 0.8–5.0 µm. Occur singly or in pairs. Spore formation is not observed. Gram‐stain‐negative. Motile. Strictly anaerobic, having a respiratory and sometimes fermentative type of metabolism. Chemoorganoheterotrophs, using short and long straight‐chain fatty acids and alkenes as carbon sources and electron donors. Long straight‐chain organic electron donors with even number of carbon atons are incompletely oxidized to acetate. One species can grow chemolithoautotrophically on H
2
+ CO
2
without acetate. Sulfate serves as terminal electron acceptor for all species and is reduced to H
2
S. Fermentative growth on pyruvate might occur. Mesophilic. Neutrophilic. Optimal growth temperature 30–32°C. Media containing a reductant are necessary for growth. Vitamins are required for growth of one species. The genus
Desulfatiferula
contains two described species.
Desulfatiferula
species occur in anoxic sediments of freshwater, brackish, and marine habitats.

DNA G + C content (mol%)
: 45.5–50.2 (LC).

Type species
:
Desulfatiferula olefinivorans
Cravo‐Laureau, Labat, Joulian, Matheron and Hirschler‐Rea 2007, 2701
VP
.
D
esulfopila
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.pi'la. L. prep.
de
, from; L. neut. n.
sulfur
, sulfur; N.L. pref.
desulfo
‐, desulfuricating (prefix used to characterize a dissimilatory sulfate‐reducing procaryote); L. fem. n.
pila
, pillar; N.L. fem. n.
Desulfopila
, a sulfate‐reducing pillar.

Desulfobacterota / Desulfobulbia / Desulfobulbales / Desulfocapsaceae / Desulfopila

Rod‐shaped cells, 0.3–1.2 µm × 1.0–3.8 µm. Occur singly or in pairs. Spore formation is not observed. Stain Gram‐negative. Motility might occur depending on the species. Strictly anaerobic, having a respiratory and a fermentative metabolism. Chemoorganoheterotrophs, using simple organic compounds like lactate, pyruvate, fumarate, and alcohols as carbon sources and electron donors. Electron donors are incompletely oxidized to acetate.
Desulfopila inferna
can grow chemolithoautotrophically with H
2
and CO
2
via the anaerobic C
1
‐pathway (carbon monoxide dehydrogenase or Wood–Ljungdahl pathway). Formate is used with or without acetate, depending on the species. Sulfate and sulfite serve as terminal electron acceptors and are reduced to H
2
S.
Desulfopila aestuarii
can also use thiosulfate and fumarate as electron acceptors. Mesophilic. Optimal temperature for growth, 28–35°C. Neutrophilic. The optimal pH for growth is 7.2–7.6. Best growth in marine medium, the optimal concentration of NaCl for growth is between 10 and 30 g/l. Media containing a reductant and vitamins are necessary for cultivation. The genus currently accommodates two species.
Desulfopila
spp. occur in anoxic marine sediments.

DNA G + C content (mol%)
: 49.6–50.3 (genome, LC).

Type species
:
Desulfopila aestuarii
Suzuki, Ueki, Amaishi and Ueki 2007, 524
VP
.
Biomimetic Nanosilica–Collagen Scaffolds for In Situ Bone Regeneration: Toward a Cell‐Free, One‐Step Surgery
Authors: Wang Shao‐Jie , Jiang Dong , Zhang Zheng‐Zheng , Chen You‐Rong , Yang Zheng‐Dong , Zhang Ji‐Ying , Shi Jinjun , Wang Xing , Yu Jia‐Kuo 
Published: October 2019

AbstractCurrent approaches to fabrication of nSC composites for bone tissue engineering (BTE) have limited capacity to achieve uniform surface functionalization while replicating the complex architecture and bioactivity of native bone, compromising application of these nanocomposites for in situ bone regeneration. A robust biosilicification strategy is reported to impart a uniform and stable osteoinductive surface to porous collagen scaffolds. The resultant nSC composites possess a native‐bone‐like porous structure and a nanosilica coating. The osteoinductivity of the nSC scaffolds is strongly dependent on the surface roughness and silicon content in the silica coating. Notably, without the use of exogenous cells and growth factors (GFs), the nSC scaffolds induce successful repair of a critical‐sized calvarium defect in a rabbit model. It is revealed that topographic and chemical cues presented by nSC scaffolds could synergistically activate multiple signaling pathways related to mesenchymal stem cell recruitment and bone regeneration. Thus, this facile surface biosilicification approach could be valuable by enabling production of BTE scaffolds with large sizes, complex porous structures, and varied osteoinductivity. The nanosilica‐functionalized scaffolds can be implanted via a cell/GF‐free, one‐step surgery for in situ bone regeneration, thus demonstrating high potential for clinical translation in treatment of massive bone defects.
(Thio)etherification of Quinoxalinones under Visible‐Light Photoredox Catalysis
Authors: Zhou Jiadi , Zhou Peng , Zhao Tingting , Ren Quanlei , Li Jianjun 
Published: October 2019

AbstractAn efficient visible‐light‐induced (thio)etherification of quinoxalin‐2(1H)‐ones with divergent aliphatic alcohols and thiols (primary, secondary, and tertiary) at room temperature in air has been developed. This protocol was highlighted by its mild conditions, readily available starting materials, operational simplicity, and wide functional group tolerance.magnified image
Localized High‐Concentration Electrolytes Boost Potassium Storage in High‐Loading Graphite
Authors: Qin Lei , Xiao Neng , Zheng Jingfeng , Lei Yu , Zhai Dengyun , Wu Yiying 
Published: October 2019

AbstractReversible intercalation of potassium‐ion (K+) into graphite makes it a promising anode material for rechargeable potassium‐ion batteries (PIBs). However, the current graphite anodes in PIBs often suffer from poor cyclic stability with low coulombic efficiency. A stable solid electrolyte interphase (SEI) is necessary for stabilizing the large interlayer expansion during K+ insertion. Herein, a localized high‐concentration electrolyte (LHCE) is designed by adding a highly fluorinated ether into the concentrated potassium bis(fluorosulfonyl)imide/dimethoxyethane, which forms a durable SEI on the graphite surface and enables highly reversible K+ intercalation/deintercalation without solvent cointercalation. Furthermore, this LHCE shows a high ionic conductivity (13.6 mS cm−1) and excellent oxidation stability up to 5.3 V (vs K+/K), which enables compatibility with high‐voltage cathodes. The kinetics study reveals that K+ intercalation/deintercalation does not follow the same pathway. The potassiated graphite exhibits excellent depotassiation rate capability, while the formation of a low stage intercalation compound is the rate‐limiting step during potassiation.
Unusual Through‐Space Interactions between Oxygen Atoms that Mediate Inverse Morphochromism of an AIE Luminogen
Authors: Viglianti Lucia , Xie Ni , Sung Herman H. Y. , Voityuk Alexander A. , Leung Nelson L. C. , Tu Yujie , Baldoli Clara , Williams Ian D. , Kwok Ryan T. K. , Lam Jacky W. Y. , Licandro Emanuela , Blancafort Lluís , Tang Ben Zhong 
Published: October 2019

AbstractWe have studied the photophysics of tetrafurylethene, an aggregation‐induced emission luminogen with exceptionally short intramolecular O−O distances of 2.80 Å and a significant red‐shifted morphochromism (27 nm) when going from the aggregate to the crystal. The short O−O distances, which are substantially smaller than the sum of the van der Waals radii (3.04 Å), are due to the fact that the oxygen atoms act as an electronic bridge connecting the furan rings on opposite ends of the central double bond, giving rise to a circular delocalization of the π‐electron density across the rings. In the excited state the O−O distance is further reduced to 2.70 Å; the increased O−O interaction causes a narrowing of the HOMO–LUMO gap, resulting in the red morphochromism of the emission. Our results show the structural origin of the red‐shifted emission lies in close O−O contacts, paving the way for understanding the clusteroluminescence of oxygen‐rich non‐conjugated systems that emit visible light.
Inorganic–Organic Hybrid Polyoxoniobates: Polyoxoniobate Metal Complex Cage and Cage Framework
Authors: Zhu Zeng‐Kui , Lin Ya‐Yun , Yu Hao , Li Xin‐Xiong , Zheng Shou‐Tian 
Published: October 2019

AbstractThe combination of polyoxoniobates (PONbs) with 3d metal ions, azoles, and organoamines is a general synthetic procedure for making unprecedented PONb metal complex cage materials, including discrete molecular cages and extended cage frameworks. By this method, the first two PONb metal complex cages K4@{[Cu29(OH)7(H2O)2(en)8(trz)21][Nb24O67(OH)2(H2O)3]4} and [Cu(en)2]@{[Cu2(en)2(trz)2]6(Nb68O188)} have been made. The former exhibits a huge tetrahedral cage with more than 120 metal centers, which is the largest inorganic–organic hybrid PONb known to date. The later shows a large cubic cage, which can act as building blocks for cage‐based extended assembly to form a 3D cage framework {[Cu(en)2]@{[Cu2(trz)2(en)2]6[H10Nb68O188]}}. These materials exhibit visible‐light‐driven photocatalytic H2 evolution activity and high vapor adsorption capacity. The results hold promise for developing both novel cage materials and largely unexplored inorganic–organic hybrid PONb chemistry.
Hydrotrifluoromethylthiolation of Unactivated Alkenes and Alkynes with Trifluoromethanesulfonic Anhydride through Deoxygenative Reduction and Photoredox Radical Processes
Authors: Ouyang Yao , Xu Xiu‐Hua , Qing Feng‐Ling 
Published: October 2019

AbstractAn ongoing challenge in trifluoromethylthiolation reactions is the use of less expensive and easily available trifluoromethylthio sources. Herein, we disclose an unprecedented usage of trifluoromethanesulfonic anhydride (Tf2O) as a radical trifluoromethylthiolating reagent. Hydrotrifluoromethylthiolation of unactivated alkenes and alkynes with Tf2O in the presence of PMePh2 and H2O under visible‐light photoredox catalysis gave the addition products. The trifluoromethylthio radical (.SCF3) was first formed from Tf2O through a photoredox radical processes and deoxygenative reduction of PMePh2, and H2O serves as the H‐atom donor for the hydrotrifluoromethylthiolation reaction. This reaction provides a new strategy for radical trifluoromethylthiolation.
Das quasi‐binäre Acetonitriltriid Sr3[C2N]2
Authors: Clark William P. , Köhn Andreas , Niewa Rainer 
Published: October 2019

AbstractDas erste quasi‐binäre Acetonitriltriid Sr3[C2N]2 wurde durch Reaktion von Sr‐Metall, Graphit und elementarem N2, erzeugt durch Zersetzung von Sr(N3)2, in einer verschlossenen Ni‐Ampulle mithilfe einer Alkalimetallschmelze in Form von nahezu farblosen Kristallen erhalten. Die Kristallstruktur der Verbindung wurde mittels Einkristall‐Röntgenbeugung bestimmt, die Identität des [C2N]3−‐Anions durch Raman‐Spektroskopie bestätigt und mit quantenchemischen Methoden weiter untersucht. Die berechneten interatomaren Abstände innerhalb des [C2N]3−‐Anions stimmen bemerkenswert gut mit den experimentellen Daten überein.
Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine N‐Oxide Complexes
Authors: Puttreddy Rakesh , Rautiainen J. Mikko , Mäkelä Toni , Rissanen Kari 
Published: October 2019

AbstractA study of the strong N−X⋅⋅⋅−O−N+ (X=I, Br) halogen bonding interactions reports 2×27 donor×acceptor complexes of N‐halosaccharins and pyridine N‐oxides (PyNO). DFT calculations were used to investigate the X⋅⋅⋅O halogen bond (XB) interaction energies in 54 complexes. A simplified computationally fast electrostatic model was developed for predicting the X⋅⋅⋅O XBs. The XB interaction energies vary from −47.5 to −120.3 kJ mol−1; the strongest N−I⋅⋅⋅−O−N+ XBs approaching those of 3‐center‐4‐electron [N−I−N]+ halogen‐bonded systems (ca. 160 kJ mol−1). 1H NMR association constants (KXB) determined in CDCl3 and [D6]acetone vary from 2.0×100 to >108 m−1 and correlate well with the calculated donor×acceptor complexation enthalpies found between −38.4 and −77.5 kJ mol−1. In X‐ray crystal structures, the N‐iodosaccharin‐PyNO complexes manifest short interaction ratios (RXB) between 0.65–0.67 for the N−I⋅⋅⋅−O−N+ halogen bond.
A Carbene‐Extended ATRA Reaction
Authors: Wu Guojiao , Börger Jennifer , Jacobi von Wangelin Axel 
Published: October 2019

AbstractAtom‐transfer radical addition (ATRA) reactions have gained a strong foothold in organic synthesis by virtue of their operational simplicity, synthetic versatility, and perfect atom economy. A rich chemical space can be accessed through clever combinations of the simple starting materials. Many variations of this general motif have been reported. However, the vast majority involve the addition of an organic halide across a C=C double bond, resulting in the formation of 1,2‐bifunctional products. This report introduces a significant expansion of this general reactivity concept to give 1,3‐bifunctional adducts through the combination of 1,1‐ATRA to a carbenoid and 1,2‐ATRA to an alkyne. Both processes operate under mild conditions (RT, 5 h) with the same commercial catalyst (CoBr2, dppbz).
Photoinduced Deoxygenative Borylations of Aliphatic Alcohols
Authors: Wu Jingjing , Bär Robin M. , Guo Lin , Noble Adam , Aggarwal Varinder K. 
Published: October 2019

AbstractA photochemical method for converting aliphatic alcohols into boronic esters is described. Preactivation of the alcohol as a 2‐iodophenyl‐thionocarbonate enables a novel Barton–McCombie‐type radical deoxygenation that proceeds efficiently with visible light irradiation and without the requirement for a photocatalyst, a radical initiator, or tin or silicon hydrides. The resultant alkyl radical is intercepted by bis(catecholato)diboron, furnishing boronic esters from a diverse range of structurally complex alcohols.
A Chiral Polycyclic Aromatic Hydrocarbon Monkey Saddle
Authors: Kirschbaum Tobias , Rominger Frank , Mastalerz Michael 
Published: October 2019

AbstractA contorted polycyclic aromatic hydrocarbon (PAH) in the shape of a monkey saddle has been synthesized in three steps from a readily available truxene precursor. The monkey saddle PAH is consisting of three five‐, seven six‐, and three eight‐membered rings and has been unambiguously characterized by single‐crystal X‐ray diffraction. Owing to the three biaryl axes the monkey saddle PAH is inherently chiral. The inversion of the two enantiomeric structures into each other preferably occurs through a twisting of peripheral rings rather than by a fully planar intermediate, as has been calculated by DFT methods. Enantiomers were separated by chiral HPLC and inversion barriers determined by variable temperature circular dichroism spectroscopy, supporting the twisting mechanism.
Rheumatoid Arthritis Morning Stiffness Is Associated With Synovial Fibrin and Neutrophils
Authors: Orange Dana E. , Blachere Nathalie E. , DiCarlo Edward F. , Mirza Serene , Pannellini Tania , Jiang Caroline S. , Frank Mayu O. , Parveen Salina , Figgie Mark P. , Gravallese Ellen M. , Bykerk Vivian P. , Orbai Ana‐Maria , Mackie Sarah L. , Goodman Susan M. 
Published: October 2019

ObjectiveMorning stiffness is a hallmark symptom of rheumatoid arthritis (RA), but its etiology is poorly understood. This study was undertaken to determine whether any histologic features of synovium are associated with this symptom.MethodsData on patient‐reported morning stiffness duration and severity, and Disease Activity Score in 28 joints (DAS28) were collected from 176 patients with RA undergoing arthroplasty. Synovium was scored for 10 histopathologic features: synovial lining hyperplasia, lymphocytes, plasma cells, Russell bodies, binucleate plasma cells, fibrin, synovial giant cells, detritus, neutrophils, and mucin. Fibrinolysis of clots seeded with various cell types was measured in turbidimetric lysis assays.ResultsStiffness severity and morning stiffness duration were both significantly associated with DAS28 (P = 0.0001 and P = 0.001, respectively). None of the synovial features examined were associated with patient‐reported stiffness severity. The presence of neutrophils and fibrin in RA synovial tissue were significantly associated (P < 0.0001) with patient‐reported morning stiffness of ≥1 hour, such that 73% of patients with both synovial fibrin and neutrophils reported morning stiffness of ≥1 hour. Further, neutrophils and fibrin deposits colocalized along the synovial lining. In in vitro analyses, fibrin clots seeded with necrotic neutrophils were more resistant to fibrinolysis than those seeded with living neutrophils or no cells (P = 0.008). DNase I treatment of necrotic neutrophils abrogated the delay in fibrinolysis.ConclusionIn RA, prolonged morning stiffness may be related to impaired fibrinolysis of neutrophil‐enmeshed fibrin deposits along the synovial membrane. Our findings also suggest that morning stiffness severity and duration may reflect distinct pathophysiologic phenomena.