bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloning and sequence analysis of the rpsL and rpsG genes of Mycobacterium smegmatis and characterization of mutations causing resistance to streptomycin
Authors: Kenney T J , Churchward G
Published: November 2016

The Mycobacterium smegmatis rpsL and rpsG genes, encoding the ribosomal proteins S12 and S7, were cloned, and their DNA sequence was determined. The third nucleotide of the S12 termination codon overlapped the first nucleotide of the S7 translation initiation codon. A collection of 28 spontaneous streptomycin-resistant mutants of M. smegmatis were isolated. All had single-base-pair substitutions in the rpsL gene which were changed to a streptomycin-sensitive phenotype by complementation with a low-copy-number plasmid carrying the wild-type M. smegmatis rpsL gene. A total of eight different mutations were found in two specific regions of the rpsL gene. Fifty-seven percent (16 of 28) altered the Lys codon at position 43. Forty-six percent of the mutations (13 of 28) were due to a transition changing an AAG Lys codon to an AGG Arg codon, with eight changes at codon 43 and five at codon 88.
Interactions between a Bacillus subtilis anti-sigma factor (RsbW) and its antagonist (RsbV)
Authors: Dufour A , Haldenwang W G
Published: November 2016

The activity of sigma B, a secondary sigma factor of Bacillus subtilis, is primarily controlled by an anti-sigma factor protein (RsbW) that binds to sigma B and blocks its ability to form an RNA polymerase holoenzyme (E-sigma B). Inhibition of sigma B by RsbW is counteracted by RsbV, a protein that is essential for the activation of sigma B-dependent transcription. When crude B. subtilis extracts were fractionated by gel filtration chromatography or electrophoresis through nondenaturing polyacrylamide gels, a complex composed of RsbW and RsbV that is distinct from the previously observed RsbW-sigma B complex was detected. In analogous experiments, RsbX, an additional regulator of sigma B-dependent transcription that is thought to act independently of RsbV-RsbW, was not found to associate with any of the other sigB operon products. Two forms of RsbV were visualized when crude cell extracts of B. subtilis were subjected to isoelectric focusing (IEF), with the more negatively charged RsbV species absent from extracts prepared from RsbW- strains. In vitro, RsbV became phosphorylated when incubated with ATP and RsbW but not with ATP alone. The phosphorylated RsbV species comigrated during IEF with the RsbW-dependent form of RsbV found in crude cell extracts. These results suggest that the modified RsbV, present in crude cell extracts, is phosphorylated. When gel filtration fractions containing RsbV-RsbW complexes or RsbV alone were subjected to IEF, only the unmodified form of RsbV was found associated with RsbW. The presumed phosphorylated variant of RsbV was present only in fractions that did not contain RsbW. The data support a model whereby RsbV binds directly to RsbW and blocks its ability to form the RsbW-sigma B complex. This activity of RsbV appears to be inhibited by RsbW-dependent phosphorylation.
Pseudomonas aeruginosa AlgG is a polymer level alginate C5-mannuronan epimerase
Authors: Franklin M J , Chitnis C E , Gacesa P , Sonesson A , White D C , Ohman D E
Published: November 2016

Alginate is a viscous extracellular polymer produced by mucoid strains of Pseudomonas aeruginosa that cause chronic pulmonary infections in patients with cystic fibrosis. Alginate is polymerized from GDP-mannuronate to a linear polymer of beta-1-4-linked residues of D-mannuronate and its C5-epimer, L-guluronate. We previously identified a gene called algG in the alginate biosynthetic operon that is required for incorporation of L-guluronate residues into alginate. In this study, we tested the hypothesis that the product of algG is a C5-epimerase that directly converts D-mannuronate to L-guluronate. The DNA sequence of algG was determined, and an open reading frame encoding a protein (AlgG) of approximately 60 kDa was identified. The inferred amino terminus of AlgG protein contained a putative signal sequence of 35 amino acids. Expression of algG in Escherichia coli demonstrated both 60-kDa pre-AlgG and 55-kDa mature AlgG proteins, the latter of which was localized to the periplasm. An N-terminal analysis of AlgG showed that the signal sequence was removed in the mature form. Pulse-chase experiments in both E. coli and P. aeruginosa provided evidence for conversion of the 60- to the 55-kDa size in vivo. Expression of algG from a plasmid inan algG (i.e., polymannuronate-producing) mutant of P. aeruginosa restored production of an alginate containing L-guluronate residues. The observation that AlgG is apparently processed and exported from the cytoplasm suggested that it may act as a polymer-level mannuronan C5-epimerase. An in vitro assay for mannuronan C5 epimerization was developed wherein extracts of E. coli expressing high levels of AlgG were incubated with polymannuronate. Epimerization of D-mannuronate to L-guluronate residues in the polymer was detected enzymatically, using a L-guluronate-specific alginate lyase of Klebsiella aerogenes. Epimerization was also detected in the in vitro reaction between recombinant AlgG and poly-D-mannuronate, using high-performance anion-exchange chromatography. The epimerization reaction was detected only when acetyl groups were removed from the poly-D-mannuronate substrate, suggesting that AlgG epimerization activity in vivo may be sensitive to acetylation of the D-mannuronan residues. These results demonstrate that AlgG has polymer-level mannuronan C5-epimerase activity.
Mutations which alter the kinetics of calcium transport alter the regulation of competence in Streptococcus pneumoniae
Authors: Trombe M C , Rieux V , Baille F
Published: November 2016

In Streptococcus pneumoniae, Ca2+ induces a stress response which is regulated by a proteic activator known as competence factor (CF). This stress response is expressed as the induction of competence for DNA uptake and genetic transformation in exponentially growing cultures and by autolysis in late exponential phase. DNA transport during competence can be described as a homeostatic response that prevents autolysis of the cultures. Electrogenic and cooperative calcium transport with a Hill number (nH) of 2 appears to mediate this Ca2+ response. Mutant strains altered in their kinetics for Ca2+ transport, with nHs of 1 and 4, were isolated and characterized in order to address the role of the kinetics of Ca2+ transport in the Ca2+ response. The reduced cooperativity of Ca2+ uptake in mutant strain Cp2200 was associated with an absolute requirement for added CF to develop competence and with resistance to autolysis. The enhanced cooperativity of Ca2+ uptake in mutant strain Cp3300 was associated with facilitated competence and hypersensitivity to autolysis. Moreover, the mutation carried by strain Cp3300 increases the CF response of previously described competence-defective mutants. The pleiotropic mutants Cp2200 and Cp3300 allowed us to demonstrate that cooperativity of transport determines the Ca2+ response in S. pneumoniae.
Rhizobium meliloti contains a novel second homolog of the cell division gene ftsZ
Authors: Margolin W , Long S R
Published: November 2016

We have identified a second homolog of the cell division gene, ftsZ, in the endosymbiont Rhizobium meliloti. The ftsZ2 gene was cloned by screening a genomic lambda library with a probe derived from PCR amplification of a highly conserved domain. It encodes a 36-kDa protein which shares a high level of sequence similarity with the FtsZ proteins of Escherichia coli and Bacillus subtilis and FtsZ1 (Z1) of R. meliloti but lacks the carboxy-terminal region conserved in other FtsZ proteins. The identity of the ftsZ2 gene product was confirmed both by in vitro transcription-translation in an R. meliloti S-30 extract and by overproduction in R. meliloti cells. As with Z1, the overproduction of FtsZ2 in E. coli inhibited cell division and induced filamentation, although to a lesser extent than with Z1. However, the expression of ftsZ2 in E. coli under certain conditions caused some cells to coil dramatically, a phenotype not observed during Z1 overproduction. Although several Tn3-GUS (glucuronidase) insertions in a plasmid-borne ftsZ2 gene failed to cross into the chromosome, one interruption in the chromosomal ftsZ2 gene was isolated, suggesting that ftsZ2 is nonessential for viability. The two ftsZ genes were genetically mapped to the R. meliloti main chromosome, approximately 100 kb apart.
Locations of genetic markers on the physical map of the chromosome of Neisseria gonorrhoeae FA1090
Authors: Dempsey J A , Cannon J G
Published: November 2016

To increase the utility of the previously constructed physical map of the chromosome of Neisseria gonorrhoeae FA1090, 28 additional genetic markers were localized on the map. Cloned gonococcal genes were used to probe Southern blots of restriction enzyme-digested DNA separated on pulsed-field gels, thus identifying the fragment in each of several digests to which the probe hybridized and the map location of each gene. The addition of the new markers brings the total number of mapped loci for this strain to 68; the locations of all of those markers on the updated map are shown.
Autoradiographic study of hyphal growth during aerial mycelium development in Streptomyces antibioticus
Authors: Miguelez E M , García M , Hardisson C , Manzanal M B
Published: November 2016

The pattern of growth of aerial mycelium in Streptomyces species was investigated by autoradiography. Colonies of Streptomyces antibiotics were labeled with N-acetyl-D-[1-3H] glucosamine to localize the sites of hyphal growth during the development of aerial mycelium. Autoradiographs obtained with sections of the colonies revealed that hyphal growth occurs not only at the top of the colony but also in the inner zones of the aerial mycelium.
Fibrillarin-like proteins occur in the domain Archaea
Authors: Amiri K A
Published: November 2016

Fibrillarin is found in the nucleolus of Eucarya and associated with small nucleolar RNAs. It is involved in the processing of precursor rRNA. Two genes, encoding fibrillarin-like proteins from Methanococcus voltae and Methanococcus vannielii, have been isolated. The genes were named flpA (fibrillarin-like protein).
Reconstruction of glucose uptake and phosphorylation in a glucose-negative mutant of Escherichia coli by using Zymomonas mobilis genes encoding the glucose facilitator protein and glucokinase
Authors: Snoep J L , Arfman N , Yomano L P , Fliege R K , Conway T , Ingram L O
Published: November 2016

Expression of the Zymomonas mobilis glf (glucose facilitator protein) and glk (glucokinase) genes in Escherichia coli ZSC113 (glucose negative) provided a new functional pathway for glucose uptake and phosphorylation. Both genes were essential for the restoration of growth in glucose minimal medium and for acid production on glucose-MacConkey agar plates.
A ColE1-encoded gene directs entry exclusion of the plasmid
Authors: Yamada Y , Yamada M , Nakazawa A
Published: November 2016

To detect entry exclusion of the ColE1 plasmid, we established an assay system that was not influenced by incompatibility of extant plasmids in the recipient cells or by the viability of the cells due to the killing action of colicin E1 protein. The assay revealed that exc1 and exc2, assigned as genes directing entry exclusion, had no exclusion activity. Instead, mbeD, which had been characterized as a gene for plasmid mobilization, directed the exclusion activity. MbeD was overexpressed and identified as a 35S-labeled protein, which was recovered in both the soluble and membrane fractions, particularly in the inner membrane fraction. An amphipathic helical structure was predicted in the N-terminal region of MbeD as well as in the corresponding homologous proteins of ColA and ColK. These proteins may bind to the inner membrane via the N-terminal amphipathic helix and function in entry exclusion.
Cloning and characterization of a polyketide synthase gene from Streptomyces fradiae Tü2717, which carries the genes for biosynthesis of the angucycline antibiotic urdamycin A and a gene probably involved in its oxygenation
Authors: Decker H , Haag S
Published: November 2016

A DNA fragment was cloned as cosmid purd8, which encodes a polyketide synthase involved in the production of the angucycline antibiotic urdamycin from Streptomyces fradiae Tü2717. Deletion of the polyketide synthase genes from the chromosome abolished urdamycin production. In addition, purd8 conferred urdamycin resistance on introduction into Streptomyces lividans TK24. Sequence analysis of 5.7 kb of purd8 revealed six open reading frames transcribed in the same direction. The deduced amino acid sequences of the six open reading frames strongly resemble proteins from known type II polyketide synthase gene clusters: a ketoacyl synthase, a chain length factor, an acyl carrier protein, a ketoreductase, a cyclase, and an oxygenase. Heterologous expression of the urdamycin genes encoding a ketoacyl synthase and a chain length factor in Streptomyces glaucescens tetracenomycin C-nonproducing mutants impaired in either the TcmK ketoacyl synthase or TcmL chain length factor resulted in the production of tetracenomycin C. Heterologous expression of a putative oxygenase gene from the urdamycin gene cluster in S. glaucescens GLA.O caused production of the hybrid antibiotic 6-hydroxy tetracenomycin C.
Glucose kinase-dependent catabolite repression in Staphylococcus xylosus
Authors: Wagner E , Marcandier S , Egeter O , Deutscher J , Götz F , Brückner R
Published: November 2016

By transposon Tn917 mutagenesis, 16 mutants of Staphylococcus xylosus were isolated that showed higher levels of beta-galactosidase activity in the presence of glucose than the wild-type strain. The transposons were found to reside in three adjacent locations in the genome of S. xylosus. The nucleotide sequence of the chromosomal fragment affected by the Tn917 insertions yielded an open reading frame encoding a protein with a size of 328 amino acids with a high level of similarity to glucose kinase from Streptomyces coelicolor. Weaker similarity was also found to bacterial fructokinases and xylose repressors of gram-positive bacteria. The gene was designated glkA. Immediately downstream of glkA, two open reading frames were present whose deduced gene products showed no obvious similarity to known proteins. Measurements of catabolic enzyme activities in the mutant strains grown in the presence or absence of sugars established the pleiotropic nature of the mutations. Besides beta-galactosidase activity, which had been used to detect the mutants, six other tested enzymes were partially relieved from repression by glucose. Reduction of fructose-mediated catabolite repression was observed for some of the enzyme activities. Glucose transport and ATP-dependent phosphorylation of HPr, the phosphocarrier of the phosphoenolpyruvate:carbohydrate phosphotransferase system involved in catabolite repression in gram-positive bacteria, were not affected. The cloned glkA gene fully restored catabolite repression in the mutant strains in trans. Loss of GlkA function is thus responsible for the partial relief from catabolite repression. Glucose kinase activity in the mutants reached about 75% of the wild-type level, indicating the presence of another enzyme in S. xylosus. However, the cloned gene complemented an Escherichia coli strain in glucose kinase. Therefore, the glkA gene encodes a glucose kinase that participates in catabolite repression in S. xylosus.
Purification and characterization of a benzylviologen-linked, tungsten-containing aldehyde oxidoreductase from Desulfovibrio gigas
Authors: Hensgens C M , Hagen W R , Hansen T A
Published: November 2016

Desulfovibrio gigas NCIMB 9332 cells grown in ethanol-containing medium with 0.1 microM tungstate contained a benzylviologen-linked aldehyde oxidoreductase. The enzyme was purified to electrophoretic homogeneity and found to be a homodimer with a subunit M(r) of 62,000. It contained 0.68 +/- 0.08 W, 4.8 Fe, and 3.2 +/- 0.2 labile S per subunit. After acid iodine oxidation of the purified enzyme, a fluorescence spectrum typical for form A of molybdopterin was obtained. Acetaldehyde, propionaldehyde, and benzaldehyde were excellent substrates, with apparent Km values of 12.5, 10.8, and 20 microM, respectively. The natural electron acceptor is not yet known; benzylviologen was used as an artificial electron acceptor (apparent Km, 0.55 mM). The enzyme was activated by potassium ions and strongly inhibited by cyanide, arsenite, and iodoacetate. In the as-isolated enzyme, electron paramagnetic resonance studies readily detected W(V) as a complex signal with g values in the range of 1.84 to 1.97. The dithionite-reduced enzyme exhibited a broad signal at low temperature with g = 2.04 and 1.92; this is indicative of a [4Fe-4S]1+ cluster interacting with a second paramagnet, possibly the S = 1 system of W(IV). Until now W-containing aldehyde oxidoreductases had only been found in two Clostridium strains and two hyperthermophilic archaea. The D. gigas enzyme is the first example of such an enzyme in a gram-negative bacterium.
A new Escherichia coli cell division gene, ftsK
Authors: Begg K J , Dewar S J , Donachie W D
Published: November 2016

A mutation in a newly discovered Escherichia coli cell division gene, ftsK, causes a temperature-sensitive late-stage block in division but does not affect chromosome replication or segregation. This defect is specifically suppressed by deletion of dacA, coding for the peptidoglycan DD-carboxypeptidase, PBP 5. FtsK is a large polypeptide (147 kDa) consisting of an N-terminal domain with several predicted membrane-spanning regions, a proline-glutamine-rich domain, and a C-terminal domain with a nucleotide-binding consensus sequence. FtsK has extensive sequence identity with a family of proteins from a wide variety of prokaryotes and plasmids. The plasmid proteins are required for intercellular DNA transfer, and one of the bacterial proteins (the SpoIIIE protein of Bacillus subtilis) has also been implicated in intracellular chromosomal DNA transfer.
In vitro sulfotransferase activity of NodH, a nodulation protein of Rhizobium meliloti required for host-specific nodulation
Authors: Ehrhardt D W , Atkinson E M , Faull K F , Freedberg D I , Sutherlin D P , Armstrong R , Long S R
Published: November 2016

Early stages of nodulation involve the exchange of signals between the bacterium and the host plant. Bacterial nodulation (nod) genes are required for Rhizobium spp. to synthesize lipooligosaccharide morphogens, termed Nod factors. The common nod genes encode enzymes that synthesize the factor core structure, which is modified by host-specific gene products. Here we show direct in vitro evidence that Rhizobium meliloti NodH, a host-specific nodulation gene, catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to the terminal 6-O position of Nod factors, and we show substrate requirements for the reaction. Our results indicate that polymerization of the chitooligosaccharide backbone likely precedes sulfation and that sulfation is not absolutely dependent on the presence or the particular structure of the N-acyl modification. NodH sulfation provides a tool for the enzymatic in vitro synthesis of novel Nod factors, or putative Nod factors intermediates, with high specific activity.
Identification of Molds by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Sanguinetti Maurizio , Posteraro Brunella
Published: November 2016

Although to a lesser extent than diagnostic bacteriology, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has recently revolutionized the diagnostic mycology workflow. With regard to filamentous fungi (or molds), the precise recognition of pathogenic species is important for rapid diagnosis and appropriate treatment, especially for invasive diseases. This review summarizes the current experience with MALDI-TOF MS-based identification of common and uncommon mold species of
Aspergillus
,
Fusarium
, Mucorales, dimorphic fungi, and dermatophytes. This experience clearly shows that MALDI-TOF MS holds promise as a fast and accurate identification tool, particularly with common species or typical strains of filamentous fungi.
Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses
Authors: Hackenbrack Nicole , Rogers Matthew B. , Ashley Robert E. , Keel M. Kevin , Kubiski Steven V. , Bryan John A. , Ghedin Elodie , Holmes Edward C. , Hafenstein Susan L. , Allison Andrew B.
Published: November 2016

Since the first description of adenoviruses in bats in 2006, a number of micro- and megabat species in Europe, Africa, and Asia have been shown to carry a wide diversity of adenoviruses. Here, we report on the evolutionary, biological, and structural characterization of a novel bat adenovirus (BtAdV) recovered from a Rafinesque's big-eared bat (
Corynorhinus
rafinesquii
) in Kentucky, USA, which is the first adenovirus isolated from North American bats. This virus (BtAdV 250-A) exhibits a close phylogenetic relationship with
Canine mastadenovirus A
(CAdV A), as previously observed with other BtAdVs. To further investigate the relationships between BtAdVs and CAdVs, we conducted mass spectrometric analysis and single-particle cryo-electron microscopy reconstructions of the BtAdV 250-A capsid and also analyzed the
in vitro
host ranges of both viruses. Our results demonstrate that BtAdV 250-A represents a new mastadenovirus species that, in contrast to CAdV, has a unique capsid morphology that contains more prominent extensions of protein IX and can replicate efficiently in a phylogenetically diverse range of species. These findings, in addition to the recognition that both the genetic diversity of BtAdVs and the number of different bat species from disparate geographic regions infected with BtAdVs appears to be extensive, tentatively suggest that bats may have served as a potential reservoir for the cross-species transfer of adenoviruses to other hosts, as theorized for CAdV.

IMPORTANCE
Although many adenoviruses are host specific and likely codiverged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic diversity of adenoviruses in bats and their close phylogenetic relationship to
Canine mastadenovirus
A
(CAdV A) has raised important questions about how CAdV A, and possibly other mammalian adenoviruses, may have emerged. Although most adenoviruses tend to cause limited disease in their natural hosts, CAdV A is unusual in that it may cause high morbidity and sometimes fatal infections in immunocompetent hosts and is thus an important pathogen of carnivores. Here, we performed a comparative evolutionary and structural study of representative bat and canine adenoviruses to better understand the relationship between these two viral groups.
Phosphorylation of the Bovine Papillomavirus E2 Protein on Tyrosine Regulates Its Transcription and Replication Functions
Authors: Culleton Sara P. , Kanginakudru Sriramana , DeSmet Marsha , Gilson Timra , Xie Fang , Wu Shwu-Yuan , Chiang Cheng-Ming , Qi Guihong , Wang Mu , Androphy Elliot J.
Published: November 2016

Papillomaviruses are small, double-stranded DNA viruses that encode the E2 protein, which controls transcription, replication, and genome maintenance in infected cells. Posttranslational modifications (PTMs) affecting E2 function and stability have been demonstrated for multiple types of papillomaviruses. Here we describe the first phosphorylation event involving a conserved tyrosine (Y) in the bovine papillomavirus 1 (BPV-1) E2 protein at amino acid 102. While its phosphodeficient phenylalanine (F) mutant activated both transcription and replication in luciferase reporter assays, a mutant that may act as a phosphomimetic, with a Y102-to-glutamate (E) mutation, lost both activities. The E2 Y102F protein interacted with cellular E2-binding factors and the viral helicase E1; however, in contrast, the Y102E mutant associated with only a subset and was unable to bind to E1. While the Y102F mutant fully supported transient viral DNA replication, BPV genomes encoding this mutation as well as Y102E were not maintained as stable episomes in murine C127 cells. These data imply that phosphorylation at Y102 disrupts the helical fold of the N-terminal region of E2 and its interaction with key cellular and viral proteins. We hypothesize that the resulting inhibition of viral transcription and replication in basal epithelial cells prevents the development of a lytic infection.

IMPORTANCE
Papillomaviruses (PVs) are small, double-stranded DNA viruses that are responsible for cervical, oropharyngeal, and various genitourinary cancers. Although vaccines against the major oncogenic human PVs are available, there is no effective treatment for existing infections. One approach to better understand the viral replicative cycle, and potential therapies to target it, is to examine the posttranslational modification of viral proteins and its effect on function. Here we have discovered that the bovine papillomavirus 1 (BPV-1) transcription and replication regulator E2 is phosphorylated at residue Y102. While a phosphodeficient mutant at this site was fully functional, a phosphomimetic mutant displayed impaired transcription and replication activity as well as a lack of an association with certain E2-binding proteins. This study highlights the influence of posttranslational modifications on viral protein function and provides additional insight into the complex interplay between papillomaviruses and their hosts.
Molecular Architecture of the Cleavage-Dependent Mannose Patch on a Soluble HIV-1 Envelope Glycoprotein Trimer
Authors: Behrens Anna-Janina , Harvey David J. , Milne Emilia , Cupo Albert , Kumar Abhinav , Zitzmann Nicole , Struwe Weston B. , Moore John P. , Crispin Max
Published: November 2016

The formation of a correctly folded and natively glycosylated HIV-1 viral spike is dependent on protease cleavage of the gp160 precursor protein in the Golgi apparatus. Cleavage induces a compact structure which not only renders the spike capable of fusion but also limits further maturation of its extensive glycosylation. The redirection of the glycosylation pathway to preserve underprocessed oligomannose-type glycans is an important feature in immunogen design, as glycans contribute to or influence the epitopes of numerous broadly neutralizing antibodies. Here we present a quantitative site-specific analysis of a recombinant, trimeric mimic of the native HIV-1 viral spike (BG505 SOSIP.664) compared to the corresponding uncleaved pseudotrimer and the matched gp120 monomer. We present a detailed molecular map of a trimer-associated glycan remodeling that forms a localized subdomain of the native mannose patch. The formation of native trimers is a critical design feature in shaping the glycan epitopes presented on recombinant vaccine candidates.

IMPORTANCE
The envelope spike of human immunodeficiency virus type 1 (HIV-1) is a target for antibody-based neutralization. For some patients infected with HIV-1, highly potent antibodies have been isolated that can neutralize a wide range of circulating viruses. It is a goal of HIV-1 vaccine research to elicit these antibodies by immunization with recombinant mimics of the viral spike. These antibodies have evolved to recognize the dense array of glycans that coat the surface of the viral molecule. We show how the structure of these glycans is shaped by steric constraints imposed upon them by the native folding of the viral spike. This information is important in guiding the development of vaccine candidates.
‘There was no great ceremony’: patient narratives and the diagnostic encounter in the context of Parkinson's
Authors: Peek Jane
Published: November 2016

This paper draws on stories of diagnosis that emerged from a broader narrative study exploring the lived experience of Parkinson's (n.37). Despite the life-changing nature of their diagnosis, participants' narratives highlighted considerable shortcomings in the way in which their diagnostic encounter was handled, echoing the findings of previous research in which it has been noted that ‘the human significance’ of diagnosis was passed over. Building on the literature, this paper provides empirical material that reveals the sensitivities involved at the moment of diagnosis. By examining both the structure and content of participants' narratives, this article discusses the diagnostic encounter in relation to three key concepts that connected many participants' stories: a ‘bareness’ or lack of ‘ceremony’, a sense of emotional and physical ‘abandonment’ and the impact on a person's illness story when faced with a ‘hierarchy’ of illness. This paper aims to raise awareness of contemporary issues related to the diagnosis of Parkinson's, and invites reflection on how diagnosis might be undertaken in a way that truly acknowledges its human significance.
Modulatory role of Co-enzyme Q10 on methionine and choline deficient diet-induced non-alcoholic steatohepatitis (NASH) in albino rats
Authors: Saleh Dalia O. , Ahmed Rania F. , Amin Mohamed M.
Published: November 2016

The present study aimed to evaluate the hepato-protective and neuro-protective activity of Co-enzyme Q10 (CoQ10) on non-alcoholic steatohepatitis (NASH) in albino rats induced by methionine and choline-deficient (MCD) diet. Rats were fed an MCD diet for 8 weeks to induce non-alcoholic steatohepatitis. CoQ10 (10 mg/(kg·day)−1) was orally administered for 2 consecutive weeks. Twenty-four hours after the last dose of the drug, the behavioral test, namely the activity cage test, was performed and the activity counts were recorded. Serum alanine transaminase, aspartate aminotransferase, alkaline phosphatase, gamma-glutamyl transferase, total/direct bilirubin, and albumin were valued to assess liver function. Moreover, hepatic cytokines interleukin-6 as well as its modulator nuclear factor kappa-light-chain-enhancer of activated B cells were determined. In addition, brain biomarkers, viz ammonia, nitric oxide, and brain-derived neurotrophic factor (BDNF), were measured as they are reliable indices to assess brain damage. Histopathological and immunohistochemical examination of brain proliferating cell nuclear antigen in brain and liver tissues were also evaluated. Results revealed that MCD-induced NASH showed impairment in the liver functions with an increase in the liver inflammatory markers. Moreover, NASH resulted in pronounced brain dysfunction as evidenced by hyper-locomotor activity, a decrease in the BDNF level, as well as an increase in the brain nitric oxide and ammonia contents. Oral treatment of MCD-diet−fed rats with CoQ10 for 14 days showed a marked improvement in all the assigned parameters. Finally, it can be concluded that CoQ10 has a hepatoprotective and neuroprotective role in MCD-diet−induced NASH in rats.
Design and manufacture of propellers for small unmanned aerial vehicles
Authors: Rutkay Brian , Laliberté Jeremy
Published: November 2016

The objective of this research was to develop a process for the design and manufacture of mission- and aircraft-specific propellers for small unmanned aerial vehicles. This objective was met by creating a computer program to design a propeller that meets user-defined aircraft performance requirements within the limitations of the electric motor, user-selected materials, and manufacturing methods. A comprehensive review of prior UAV propeller design and additive manufacturing for small propellers is also presented in this paper. The use of additive manufacturing (3D printing) in making flightworthy propellers was explored through material testing, manufacturing trials, and by testing the propellers under simulated flight conditions in a wind tunnel. It was found that the propeller performance generated nearly the predicted design thrust but the efficiency and power consumption could not be accurately measured with the present test setup. While flight testing was not completed at this time, ground and wind tunnel testing were sufficient to demonstrate the feasibility of producing flightworthy propellers using additive manufacturing.
Effects on the optical properties and conductivity of Ag–N co-doped ZnO
Authors: Xu Zhenchao , Hou Qingyu , Qu Lingfeng
Published: November 2016

Nowadays, the studies of the effects on the optical bandgap, absorption spectrum, and electrical properties of Ag–N co-doped ZnO have been extensively investigated. However, Ag and N atoms in doped systems are randomly doped, and the asymmetric structure of ZnO is yet to be explored. In this paper, the geometric structure, stability, density of states, absorption spectra and conductivity of pure and Ag–N co-doped Zn[Formula: see text]Ag[Formula: see text]O[Formula: see text]N[Formula: see text]([Formula: see text]=0.03125, 0.0417 and 0.0625) in different orientations are calculated by using plane-wave ultrasoft pseudopotential on the basis of density functional theory with GGA[Formula: see text]U method. Results show that the volume, equivalent total energy and formation energy of the doped system increase as the concentration of Ag–N co-doped Zn[Formula: see text]Ag[Formula: see text]O[Formula: see text]N[Formula: see text] increases at the same doping mode. The doped systems also become unstable, and difficulty in doping. At the same concentration of Ag–N co-doped Zn[Formula: see text]Ag[Formula: see text]O[Formula: see text]N[Formula: see text], the systems with Ag–N along the [Formula: see text]-axis orientation is unstable, and doping is difficult. The optical bandgap of Ag–N co-doped systems is narrower than that of the pure ZnO. At the same doping mode, the optical bandgap of the systems with Ag–N perpendicular to the [Formula: see text]-axis orientation becomes narrow as the concentration of Ag–N co-doped Zn[Formula: see text]Ag[Formula: see text]O[Formula: see text]N[Formula: see text] increases. The absorption spectra of the doped systems exhibit a red shift, and this red shift becomes increasingly significant as the concentration of Ag–N co-doped Zn[Formula: see text]Ag[Formula: see text]O[Formula: see text]N[Formula: see text] increases. Under the same condition, the relative hole concentrations of the doped systems increases, the hole effective mass in valence band maximum decreases, the hole mobility decreases, the ionization energy decreases, Bohr radius increases, the conductance increases and the conductivity become better. Our results may be used as a basis for the designing and preparation of new optical and electrical materials for Ag–N co-doped ZnO applied in low temperature end of temperature difference battery.
The dynamics of a very large intra-plate continental basaltic volcanic province, the Newer Volcanics Province, SE Australia, and implications for other provinces
Authors: Cas R. A. F. , van Otterloo J. , Blaikie T. N. , van den Hove J.
Published: November 2016

The Newer Volcanics Province of SE Australia is a very large continental basaltic province, with an area of >23 000 km
2
, a dense rock equivalent volume of <900 km
3
and >400 monogenetic volcanoes; it has been active since
c.
8 Ma. Lava fields, shields, scoria cones are common, and there are >40 maars and volcanic complexes. Maars occur dominantly in the south where magmas erupted through Tertiary sedimentary aquifers, whereas in the north, over Palaeozoic crust, there are few. Complex interactions of the magma volatile content, magma ascent rates, conduit characteristics and the availability and depth of aquifers caused diverse eruption styles. Volcanoes commonly occur close to major crustal faults, which acted as magma conduits. There is no simple age pattern of volcanism across the province. Volcanism was probably triggered by transtensional decompression in the crust where fault sets intersect, affecting hot, hydrated mantle that had welled up through edge-driven convection where the base of the lithosphere thins abruptly at the edge of the continent. Rock compositions range from picritic to basaltic andesitic. Some volcanoes are polymagmatic. Regional geophysical datasets have clarified the regional characteristics of the province, whereas detailed ground magnetic and gravity surveys resulted in new insights into the subsurface structure of maar-diatremes.
The Precambrian–Phanerozoic and Ediacaran–Cambrian boundaries: a historical approach to a dilemma
Authors: Geyer Gerd , Landing Ed
Published: November 2016

The Cambrian was originally defined as a rock interval with a trilobite-dominated fauna that overlay a presumed biologically barren Precambrian epoch. Work to formally define the Cambrian base arose after the discovery of Precambrian macrofossils in South Australia. The Working Group on the Precambrian–Cambrian Boundary (set up in 1972) promoted an emphasis on an extended pre-trilobitic interval with mineralized skeletal elements (small shelly fossils or early skeletal fossils). The study of early skeletal fossils made the Ulakhan-Sulugur (Siberia) and Meishucun (South China) sections candidates for the basal Cambrian Global Stratotype Section and Point (GSSP), but difficulties in correlation and the taxonomy of early skeletal fossils did not allow the selection of a reliably correlative horizon. Bilaterian ichnofaunas below the first diverse early skeletal fossils suggested the definition of a Cambrian base GSSP below the early skeletal fossils. Work on the thick, stratigraphically continuous and fairly unifacial sections in the Burin Peninsula, southeastern Newfoundland led in 1992 to an ichnofossil-defined GSSP at Fortune Head. Despite arguments for a revision and redefinition of the lower boundary of the Cambrian System, the best definition of the basal Cambrian GSSP is at Fortune Head and does not rely on the
Treptichnus/Trichophycus pedum
(abbreviated below as
T. pedum
) first appearance datum, but rather on the base of the
T. pedum
Assemblage Zone at the highest occurrence of Ediacaran taxa and in the lower range of
T. pedum
.
X-ray microtomography as a tool for investigating the petrological context of Precambrian cellular remains
Authors: Hickman-Lewis Keyron , Garwood Russell J. , Withers Philip J. , Wacey David
Published: November 2016

A wide spectrum of tomographic techniques now exists for studying palaeontological specimens, but the suitability of these methods for assessing Earth's oldest prokaryotic life has not been comprehensively investigated. We evaluated the ability of X-ray computed tomography – specifically X-ray microtomography – to reveal the morphology and petrological context of Precambrian microfossils, pseudofossils and biosedimentary structures, all of which are important in the origin and early evolution of life of Earth. The materials tested came from the Pilbara Craton of Western Australia (the 3.49 Ga Dresser Formation, the 3.46 Ga Apex chert and the 3.43 Ga Strelley Pool Formation) and the 1.88 Ga Gunflint Formation of Ontario, Canada. These units chart key developments in palaeobiology. The oldest formations contain profoundly controversial microfossil-like objects and microbially-induced sedimentary structures, whereas definitive prokaryotes are found in the youngest formations. We demonstrate that the imaging of individual microfossils and pseudofossils currently lies at the limits of the capabilities of laboratory-based X-ray microtomography and requires beneficial taphonomy. However, microtomography does provide a good overview of their petrological context at flexible spatial scales, although the quality of the data obtained from mesoscopic microbially-induced sedimentary structures and stromatolites depends largely on their style of preservation.

Supplementary material:
A zipped Drishti volume for all CT scans, a 0.7z split zip file of one Drishti volume and a HDMI supplementary movie showing digital visualizations for all of the scans are available at
https://doi.org/10.5281/zenodo.58161
Martin Brasier's contribution to the palaeobiology of the Ediacaran–Cambrian transition
Authors: Liu Alexander G. , Menon Latha R. , Shields Graham A. , Callow Richard H. T. , McIlroy Duncan
Published: November 2016

Martin Brasier's work spanned almost the entire geological column, but the origin of animals and the nature of the Cambrian explosion were areas of particular interest to him. Martin adopted a holistic approach to the study of these topics that considered the interplay between multiple geological and biological phenomena and he sought to interpret the fossil record within the broad context of geological, biogeochemical and ecological changes in the Earth system. Here we summarize Martin's main contributions to this area of research and assess the impact of his findings on the development of this field.
The Effects of Guizhi Fuling Capsule Drug Serum on Uterine Leiomyoma Cells and Its Mechanism
Authors: Shen Qi , Ye Weijing , Hu Xiaoli , Zhao Chuchu , Zhou Lulu , Zhu Xueqiong
Published: November 2016

Aims. To observe the effects of Guizhi Fuling Capsule (GZFLC) drug serum on uterine leiomyoma cells and explore its mechanism. Main Methods. Sixty Sprague Dawley rats were randomly divided into two groups (normal saline lavage group and GZFLC lavage group), then, respectively, blank serum and GZFLC drug serum were collected, and finally human uterine leiomyoma cells were treated. Human leiomyoma tissues were collected from 20 patients who underwent uterine leiomyomas operations, and leiomyoma cells were primary cultured. The leiomyoma cells were treated by GZFLC drug serum in different concentrations (10%, 20%, and 30%) and variable treatment time (12 h, 24 h, 36 h, 48 h, and 72 h). Cell proliferation was observed using CCK8 assay. Flow cytometry and Annexin V/PI were used to assay the effects of GZFLC drug serum on cell apoptosis. Western blot analysis was used to assay the effects of GZFLC drug serum on TSC2, FOXO, and 14‐3‐3γ expression in uterine leiomyoma cells. Key Findings. In the concentrations of 10%～30%, GZFLC drug serum could inhibit proliferation of leiomyoma cells in dose‐dependent manner; at the time of 36 h, cell inhibition rate was at the peak; GZFLC drug serum could induce apoptosis of leiomyoma also in a dose‐dependent manner, and apoptosis rate quickly achieved maximum at 12 h time points, and then second apoptosis peak appeared at 36 h. Compared to nontreatment group, TSC2, FOXO, and 14‐3‐3γ expressions in drug serum group were significantly changed after 12 h treatment. Significance. GZFLC drug serum can efficiently inhibit the proliferation and induce apoptosis of leiomyoma cells, which is related to the 14‐3‐3γ pathway.
Phase II Trial of Angiotensin-(1-7) for the Treatment of Patients with Metastatic Sarcoma
Authors: Savage Paul D. , Lovato James , Brosnihan K. Bridget , Miller Antonius A. , Petty W. Jeffrey
Published: November 2016

Background. Angiotensin-(1-7) [Ang-(1-7)] is an endogenous antiangiogenic hormone with anticancer activity. In a phase I study of Ang-(1-7), two of three patients with metastatic sarcoma experienced disease stabilization. This phase II study examined clinical and biomarker outcomes for patients with metastatic sarcoma. Methods. Ang-(1-7) was administered by subcutaneous injection at a dose of 20 mg daily. If excessive toxicities occurred in the first cohort, a dose deescalation cohort was allowed. Blood samples were obtained to measure changes in biomarkers. Results. Treatment was well-tolerated and the dose deescalation cohort was not required. Plasma PlGF concentrations following treatment were not statistically significantly changed. A significant increase in plasma Ang-(1-7) was observed at 4 hours after injection. The median progression-free survival was 2.7 months (95% CI; 1.4 to 4.1 months), and the median overall survival was 10.2 months (95% CI; 5.3 to 18.3 months). Two patients with vascular sarcomas demonstrated prolonged disease stabilization of 10 months (hemangiopericytoma) and 19 months (epithelioid hemangioendothelioma). Conclusions. Ang-(1-7) at a dose of 20 mg daily was well-tolerated. This prospective phase II study failed to confirm the PlGF biomarker effect identified in the prior phase I study. Prolonged disease stabilization in hemangiopericytoma and epithelioid hemangioendothelioma may warrant further investigation.
Miniopen Transforaminal Lumbar Interbody Fusion with Unilateral Fixation: A Comparison between Ipsilateral and Contralateral Reherniation
Authors: Li Zheng , Liu Fubing , Liu Shuhao , Chen Zixian , Jiang Chun , Feng Zhenzhou , Jiang Xiaoxing
Published: November 2016

The aim of this study was to evaluate the risk factors between ipsilateral and contralateral reherniation and to compare the effectiveness of miniopen transforaminal lumbar interbody fusion (TLIF) with unilateral fixation for each group. From November 2007 to December 2014, clinical and radiographic data of each group (ipsilateral or contralateral reherniation) were collected and compared. Functional assessment (Visual Analog Scale (VAS) score and Japanese Orthopaedic Association (JOA)) and radiographic evaluation (fusion status, disc height, lumbar lordosis (LL), and functional spine unit (FSU) angle) were applied to compare surgical effect for each group preoperatively and at final followup. MacNab questionnaire was applied to further evaluate the satisfactory rate after the discectomy and fusion. No difference except pain-free interval was found between ipsilateral and contralateral groups. There was a significant difference in operative time between two groups. No differences were found in clinical and radiographic data for assessment of surgical effect between two groups. The satisfactory rate was decreasing in both groups with time passing after discectomy. Difference in pain-free interval may be a distinction for ipsilateral and contralateral reherniation. Miniopen TLIF with unilateral pedicle screw fixation can be a recommendable way for single level reherniation regardless of ipsilateral or contralateral reherniation.
Efficacy of Danlou Tablet in Patients with Non‐ST Elevation Acute Coronary Syndrome Undergoing Percutaneous Coronary Intervention: Results from a Multicentre, Placebo‐Controlled, Randomized Trial
Authors: Wang Lei , Zhao Xujie , Mao Shuai , Liu Shaonan , Guo Xinfeng , Guo Liheng , Du Tinghai , Yang Haiyu , Zhao Fuhai , Wu Keng , Cong Hongliang , Wu Yang , Yang Phillip C. , Chen Keji , Zhang Minzhou
Published: November 2016

This study seeks to investigate potential cardioprotection of Danlou Tablets in patients undergoing PCI with non‐ST elevation acute coronary syndrome (NSTE‐ACS). 219 patients with NSTE‐ACS were randomised to Danlou Tablet pretreatment (n = 109) or placebo (n = 110). No patients received statins prior to PCI and all patients were given atorvastatin (10 mg/day) after procedure. The main endpoint was the composite incidence of major adverse cardiac events (MACEs) within 30 days after PCI. The proportion of patients with elevated levels of cTn I>5 × 99% of upper reference limit was significantly lower in the Danlou Tablet group at 8 h (22.0% versus 34.5%, p = 0.04) and 24 h (23.9% versus 38.2%, p = 0.02) after PCI. The 30‐day MACEs occurred in 22.0% of the Danlou Tablet group and 33.6% in the placebo group (p = 0.06). The incidence of MACE at 90‐day follow‐up was significantly decreased in the Danlou Tablet group compared to the placebo group (23.9% versus 37.3%, p = 0.03). The difference between the groups at 90 days was the incidence of nonfatal myocardial infarction (22% versus 34.5%, p = 0.04). These findings might support that treatment with Danlou Tablet could reduce the incidence of periprocedural myocardial infarction in patients with ACS undergoing PCI.