bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of the Aspergillus nidulans glucosylceramide pathway reveals that LCB Δ8‐desaturation and C9‐methylation are relevant to filamentous growth, lipid raft localization and Psd1 defensin activity
Authors: Fernandes C. M. , de Castro P. A. , Singh A. , Fonseca F. L. , Pereira M. D. , Vila T. V. M. , Atella G. C. , Rozental S. , Savoldi M. , Del Poeta M. , Goldman G. H. , Kurtenbach E. 
Published: August 2016

SummaryC8‐desaturated and C9‐methylated glucosylceramide (GlcCer) is a fungal‐specific sphingolipid that plays an important role in the growth and virulence of many species. In this work, we investigated the contribution of Aspergillus nidulans sphingolipid Δ8‐desaturase (SdeA), sphingolipid C9‐methyltransferases (SmtA/SmtB) and glucosylceramide synthase (GcsA) to fungal phenotypes, sensitivity to Psd1 defensin and Galleria mellonella virulence. We showed that ΔsdeA accumulated C8‐saturated and unmethylated GlcCer, while gcsA deletion impaired GlcCer synthesis. Although increased levels of unmethylated GlcCer were observed in smtA and smtB mutants, ΔsmtA and wild‐type cells showed a similar 9,Me‐GlcCer content, reduced by 50% in the smtB disruptant. The compromised 9,Me‐GlcCer production in the ΔsmtB strain was not accompanied by reduced filamentation or defects in cell polarity. When combined with the smtA deletion, smtB repression significantly increased unmethylated GlcCer levels and compromised filamentous growth. Furthermore, sdeA and gcsA mutants displayed growth defects and raft mislocalization, which were accompanied by reduced neutral lipids levels and attenuated G. mellonella virulence in the ΔgcsA strain. Finally, ΔsdeA and ΔgcsA showed increased resistance to Psd1, suggesting that GlcCer synthesis and fungal sphingoid base structure specificities are relevant not only to differentiation but also to proper recognition by this antifungal defensin.
Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis
Authors: Xiong Fangjie , Zhang Rui , Meng Zhigang , Deng Kexuan , Que Yumei , Zhuo Fengping , Feng Li , Guo Sundui , Datla Raju , Ren Maozhi 
Published: August 2016

Summary

The components of the target of rapamycin (TOR) signaling pathway have been well characterized in heterotrophic organisms from yeast to humans. However, because of rapamycin insensitivity, embryonic lethality in tor null mutants and a lack of reliable ways of detecting TOR protein kinase in higher plants, the key players upstream and downstream of TOR remain largely unknown in plants.

Using engineered rapamycin‐sensitive Binding Protein 12‐2 (BP12‐2) plants, the present study showed that combined treatment with rapamycin and active‐site TOR inhibitors (asTORis) results in synergistic inhibition of TOR activity and plant growth in Arabidopsis.

Based on this system, we revealed that TOR signaling plays a crucial role in modulating the transition from heterotrophic to photoautotrophic growth in Arabidopsis. Ribosomal protein S6 kinase 2 (S6K2) was identified as a direct downstream target of TOR, and the growth of TOR‐suppressed plants could be rescued by up‐regulating S6K2. Systems, genetic, and biochemical analyses revealed that Brassinosteriod Insensitive 2 (BIN2) acts as a novel downstream effector of S6K2, and the phosphorylation of BIN2 depends on TOR‐S6K2 signaling in Arabidopsis.

By combining pharmacological with genetic and biochemical approaches, we determined that the TOR‐S6K2‐BIN2 signaling pathway plays important roles in regulating the photoautotrophic growth of Arabidopsis.
Demands and challenges for patients with sickle‐cell disease requiring hematopoietic stem cell transplantation in Saudi Arabia
Authors: Alsultan Abdulrahman , Jastaniah Wasil , Al Afghani Sameera , Al Bagshi Muneer H. , Nasserullah Zaki , Al‐Suliman Ahmed M. , Alabdulaali Mohammed K. 
Published: August 2016

AbstractAllogeneic HSCT is the only curative treatment for SCD. In this study, we estimated the number of Saudi patients with SCD who are candidates for HSCT. We used the presence of overt stroke, recurrent ACS, and frequent severe pain crisis as indications for HSCT. We calculated the frequencies of these complications among a Saudi SCD cohort of 376 patients with SCD, 250 from SW and 126 from Eastern (E) provinces. We found that 59 (23.6%) of SW patients were transplant candidates compared to 22 (17.4%) from E province. It is estimated that about 61 000 patients with SCD live in Saudi Arabia. Thus, the projected number of Saudi patients with SCD who are candidates for HSCT is 10 536 patients. Of those, 2148 are children. The burden of SCD on HSCT centers in Saudi Arabia is substantial and is difficult currently to meet the demand. We recommend recruiting/training more transplant physicians and nurses, expand current capacity of centers if feasible, and open new transplant centers to make HSCT a practical therapeutic option for patients with severe SCD in Saudi Arabia.
Vitamin C supplementation to optimize growth, health and stress resistance in aquatic animals
Authors: Dawood Mahmoud A.O. , Koshio Shunsuke 
Published: August 2016

AbstractVitamins are organic compounds that can be synthesized from other essential nutrients; however, they are required in trace amounts from an exogenous source for normal growth, reproduction and health. Vitamin C (ascorbic acid, AA) is an essential micronutrient for normal growth and physiological function of most aquatic animals. In terrestrial animal nutrition, vitamin C has recently spurred scientific interest because of the increasing knowledge on vitamin C involvement in gene expression, cell cycle and reproduction in mammals; in addition, recent advances in molecular biology techniques allow the more effective estimation of the effect of vitamin C on metabolism and physiology. In contrast, this information is scarce in aquatic animal nutrition, as studies have essentially focused on the estimation of minimum vitamin C requirement for maximum growth and immune response as well as for the formulation of least‐cost diet. This scarcity of information is also due to the lack of well‐established indicators of vitamin C status in aquatic organisms. The present review summarizes and discusses information about vitamin C sources, bioavailability, deficiency and requirement in aquatic animals to plan further studies. In the future, vitamin C nutrition studies in aquaculture should also include immune responses, histopathology of the gills, liver, gonad development, gamete quality and quantity, fecundity, larvae survival and gene expression. Dietary vitamin C requirements should be estimated at every life‐history stage of cultured species. All this information will allow a better understanding of the essentiality of vitamin C in aquatic animal growth, development, reproduction and health.
The other face of Eurolegalism: The multifaceted convergence of national enforcement styles
Authors: Bastings Lincey , Mastenbroek Ellen , Versluis Esther 
Published: August 2016

AbstractThis article analyzes the implications of European integration for national regulatory enforcement. More specifically, it tests the Eurolegalism thesis, which holds that the tendency of using more detailed, prescriptive European Union (EU) regulation combined with more public and private enforcement leads to a convergence in national enforcement styles. It does so by developing and applying a fine‐grained conceptualization of enforcement style. This conceptualization forms the basis of a focused comparison of enforcement of the highly detailed and strict EU Packaging Waste Directive in the Netherlands and Germany – two countries known for their opposed enforcement styles. Our analysis shows that although convergence toward a more insistent enforcement style seems to have taken place, the two countries have arrived at this position in markedly different ways. By identifying differences in style underneath the surface of convergence, the article qualifies the Eurolegalism argument, thus, advancing the literature on EU enforcement styles and deepening our understanding of the subtle and divergent ways in which common international regulatory inputs may affect domestic enforcement.
Establishing robustness of a spatial dataset in a tolerance‐based vector model
Authors: Belussi Alberto , Migliorini Sara , Negri Mauro , Pelagatti Giuseppe 
Published: August 2016

AbstractSpatial data are usually described through a vector model in which geometries are represented by a set of coordinates embedded into an Euclidean space. The use of a finite representation, instead of the real numbers theoretically required, causes many robustness problems which are well known in the literature. Such problems are made even worse in a distributed context, where data is exchanged between different systems and several perturbations can be introduced in the data representation.In order to discuss the robustness of a spatial dataset, two implementation models have to be distinguished: the identity and the tolerance model. The robustness of a dataset in the identity model has been widely discussed in the literature and some algorithms of the Snap Rounding (SR) family can be successfully applied in such contexts. Conversely, this problem has been less explored in the tolerance model. The aim of this article is to propose an algorithm inspired by those of the SR family for establishing or restoring the robustness of a vector dataset in the tolerance model. The main ideas are to introduce an additional operation which spreads instead of snapping geometries, in order to preserve the original relation between them, and to use a tolerance region for such an operation instead of a single snapping location. Finally, some experiments on real‐world datasets are presented, confirming how the proposed algorithm can establish the robustness of a dataset.
Clinical Variants of the Native Class D β-Lactamase of Acinetobacter baumannii Pose an Emerging Threat through Increased Hydrolytic Activity against Carbapenems
Authors: Schroder Emma C. , Klamer Zachary L. , Saral Aysegul , Sugg Kyle A. , June Cynthia M. , Wymore Troy , Szarecka Agnieszka , Leonard David A. 
Published: August 2016

ABSTRACT

The threat posed by the chromosomally encoded class D β-lactamase of
Acinetobacter baumannii
(OXA-51/66) has been unclear, in part because of its relatively low affinity and turnover rate for carbapenems. Several hundred clinical variants of OXA-51/66 have been reported, many with substitutions of active-site residues. We determined the kinetic properties of OXA-66 and five clinical variants with respect to a wide variety of β-lactam substrates. The five variants displayed enhanced activity against carbapenems and in some cases against penicillins, late-generation cephalosporins, and the monobactam aztreonam. Molecular dynamics simulations show that in OXA-66, P130 inhibits the side-chain rotation of I129 and thereby prevents doripenem binding because of steric clash. A single amino acid substitution at this position (P130Q) in the variant OXA-109 greatly enhances the mobility of both I129 and a key active-site tryptophan (W222), thereby facilitating carbapenem binding. This expansion of substrate specificity represents a very worrisome development for the efficacy of β-lactams against this troublesome pathogen.
Mutational Consequences of Ciprofloxacin in Escherichia coli
Authors: Song Lisa Yun , Goff Marisa , Davidian Christina , Mao Zhiyuan , London Marisa , Lam Karen , Yung Madeline , Miller Jeffrey H. 
Published: August 2016

ABSTRACT

We examined the mutagenic specificity of the widely used antibiotic ciprofloxacin (CPR), which displays weak to moderate mutagenic activity in several bacteria and generates short in-frame deletions in
rpoB
in
Staphylococcus aureus
. To determine the spectrum of mutations in a system where any gene knockout would result in a recovered mutant, including frameshifts and both short and long deletions, we examined CPR-induced mutations in the thymidylate synthase-encoding
thyA
gene. Here, any mutation resulting in loss of thymidylate synthase activity generates trimethoprim (Trm) resistance. We found that deletions and insertions in all three reading frames predominated in the spectrum. They tend to be short deletions and cluster in two regions, one being a GC-rich region with potential extensive secondary structures. We also exploited the well-characterized
rpoB
-Rif
r
system in
Escherichia coli
to determine that cells grown in the presence of sublethal doses of CPR not only induced short in-frame deletions in
rpoB
, but also generated base substitution mutations resulting from induction of the SOS system. Some of the specific point mutations prominent in the spectrum of a strain that overproduces the
dinB
-encoded Pol IV were also present after growth in CPR. However, these mutations disappeared in CPR-treated
dinB
mutants, whereas the deletions remained. Moreover, CPR-induced deletions also occurred in a strain lacking all three SOS-induced polymerases. We discuss the implications of these findings for the consequences of overuse of CPR and other antibiotics.
Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization
Authors: Blanchette Krystle A. , Shenoy Anukul T. , Milner Jeffrey , Gilley Ryan P. , McClure Erin , Hinojosa Cecilia A. , Kumar Nikhil , Daugherty Sean C. , Tallon Luke J. , Ott Sandra , King Samantha J. , Ferreira Daniela M. , Gordon Stephen B. , Tettelin Hervé , Orihuela Carlos J. 
Published: August 2016

ABSTRACT

Streptococcus pneumoniae
is an opportunistic pathogen that colonizes the nasopharynx. Herein we show that carbon availability is distinct between the nasopharynx and bloodstream of adult humans: glucose is absent from the nasopharynx, whereas galactose is abundant. We demonstrate that pneumococcal neuraminidase A (NanA), which cleaves terminal sialic acid residues from host glycoproteins, exposed galactose on the surface of septal epithelial cells, thereby increasing its availability during colonization. We observed that
S. pneumoniae
mutants deficient in NanA and β-galactosidase A (BgaA) failed to form biofilms
in vivo
despite normal biofilm-forming abilities
in vitro
. Subsequently, we observed that glucose, sucrose, and fructose were inhibitory for biofilm formation, whereas galactose, lactose, and low concentrations of sialic acid were permissive. Together these findings suggested that the genes involved in biofilm formation were under some form of carbon catabolite repression (CCR), a regulatory network in which genes involved in the uptake and metabolism of less-preferred sugars are silenced during growth with preferred sugars. Supporting this notion, we observed that a mutant deficient in pyruvate oxidase, which converts pyruvate to acetyl-phosphate under non-CCR-inducing growth conditions, was unable to form biofilms. Subsequent comparative transcriptome sequencing (RNA-seq) analyses of planktonic and biofilm-grown pneumococci showed that metabolic pathways involving the conversion of pyruvate to acetyl-phosphate and subsequently leading to fatty acid biosynthesis were consistently upregulated during diverse biofilm growth conditions. We conclude that carbon availability in the nasopharynx impacts pneumococcal biofilm formation
in vivo
. Additionally, biofilm formation involves metabolic pathways not previously appreciated to play an important role.
Intestinal Enteroids Model Guanylate Cyclase C-Dependent Secretion Induced by Heat-Stable Enterotoxins
Authors: Pattison Amanda M. , Blomain Erik S. , Merlino Dante J. , Wang Fang , Crissey Mary Ann S. , Kraft Crystal L. , Rappaport Jeff A. , Snook Adam E. , Lynch John P. , Waldman Scott A. 
Published: August 2016

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) causes ∼20% of the acute infectious diarrhea (AID) episodes worldwide, often by producing heat-stable enterotoxins (STs), which are peptides structurally homologous to paracrine hormones of the intestinal guanylate cyclase C (GUCY2C) receptor. While molecular mechanisms mediating ST-induced intestinal secretion have been defined, advancements in therapeutics have been hampered for decades by the paucity of disease models that integrate molecular and functional endpoints amenable to high-throughput screening. Here, we reveal that mouse and human intestinal enteroids in three-dimensional
ex vivo
cultures express the components of the GUCY2C secretory signaling axis. ST and its structural analog, linaclotide, an FDA-approved oral secretagog, induced fluid accumulation quantified simultaneously in scores of enteroid lumens, recapitulating ETEC-induced intestinal secretion. Enteroid secretion depended on canonical molecular signaling events responsible for ETEC-induced diarrhea, including cyclic GMP (cGMP) produced by GUCY2C, activation of cGMP-dependent protein kinase (PKG), and opening of the cystic fibrosis transmembrane conductance regulator (CFTR). Importantly, pharmacological inhibition of CFTR abrogated enteroid fluid secretion, providing proof of concept for the utility of this model to screen antidiarrheal agents. Intestinal enteroids offer a unique model, integrating the GUCY2C signaling axis and luminal fluid secretion, to explore the pathophysiology of, and develop platforms for, high-throughput drug screening to identify novel compounds to prevent and treat ETEC diarrheal disease.
Identification and Characterization of a Putative Manganese Export Protein in Vibrio cholerae
Authors: Fisher Carolyn R. , Wyckoff Elizabeth E. , Peng Eric D. , Payne Shelley M. 
Published: August 2016

ABSTRACT

Manganese plays an important role in the cellular physiology and metabolism of bacterial species, including the human pathogen
Vibrio cholerae
. The intracellular level of manganese ions is controlled through coordinated regulation of the import and export of this element. We have identified a putative manganese exporter (VC0022), named
mneA
(
m
a
n
ganese
e
xporter
A
), which is highly conserved among
Vibrio
spp. An
mneA
mutant exhibited sensitivity to manganese but not to other cations. Under high-manganese conditions, the
mneA
mutant showed an almost 50-fold increase in intracellular manganese levels and reduced intracellular iron relative to those of its wild-type parent, suggesting that the mutant's manganese sensitivity is due to the accumulation of toxic levels of manganese and reduced iron. Expression of
mneA
suppressed the manganese-sensitive phenotype of an
Escherichia coli
strain carrying a mutation in the nonhomologous manganese export gene,
mntP
, further supporting a manganese export function for
V. cholerae
MneA. The level of
mneA
mRNA was induced approximately 2.5-fold after addition of manganese to the medium, indicating regulation of this gene by manganese. This study offers the first insights into understanding manganese homeostasis in this important pathogen.

IMPORTANCE
Bacterial cells control intracellular metal concentrations by coordinating acquisition in metal-limited environments with export in metal-excess environments. We identified a putative manganese export protein, MneA, in
Vibrio cholerae
. An
mneA
mutant was sensitive to manganese, and this effect was specific to manganese. The
mneA
mutant accumulated high levels of intracellular manganese with a concomitant decrease in intracellular iron levels when grown in manganese-supplemented medium. Expression of
mneA
in
trans
suppressed the manganese sensitivity of an
E. coli mntP
mutant. This study is the first to investigate manganese export in
V. cholerae
.
Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals
Authors: Arakaki Atsushi , Kikuchi Daiki , Tanaka Masayoshi , Yamagishi Ayana , Yoda Takuto , Matsunaga Tadashi 
Published: August 2016

ABSTRACT
The magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-length linear, long-length linear, cell membrane, and intracellular dispersing), which were related to the protein functions. Mms6, which regulates magnetite crystal growth, localized along magnetosome chain structures under magnetite-forming (microaerobic) conditions but was dispersed in the cell under nonforming (aerobic) conditions. Correlative fluorescence and electron microscopy analyses revealed that Mms6 preferentially localized to magnetosomes enclosing magnetite crystals. We suggest that a highly organized spatial regulation mechanism controls magnetosome protein localization during magnetosome formation in magnetotactic bacteria.

IMPORTANCE
Magnetotactic bacteria synthesize magnetite (Fe
3
O
4
) nanocrystals in a prokaryotic organelle called the magnetosome. This organelle is formed using various magnetosome proteins in multiple steps, including vesicle formation, magnetosome alignment, and magnetite crystal formation, to provide compartmentalized nanospaces for the regulation of iron concentrations and redox conditions, enabling the synthesis of a morphologically controlled magnetite crystal. Thus, to rationalize the complex organelle development, the localization of magnetosome proteins is considered to be highly regulated; however, the mechanisms remain largely unknown. Here, we performed comparative localization analysis of magnetosome proteins that revealed the presence of a spatial regulation mechanism within the linear structure of magnetosomes. This discovery provides evidence of a highly regulated protein localization mechanism for this bacterial organelle development.
Biogenic overgrowth on detrital pyrite in ca. 3.2 Ga Archean paleosols
Authors: Nabhan Sami , Wiedenbeck Michael , Milke Ralf , Heubeck Christoph 
Published: August 2016

Abstract
Regionally traceable paleosols in the lower Moodies Group of the Barberton greenstone belt (ca. 3.22 Ga, northeastern South Africa and Swaziland) contain locally abundant silicified nodules, originally composed of pedogenic carbonates and sulfates, interbedded with heavy-mineral laminae dominated by pyrite. Pyrite grains show rounded detrital cores and secondary idiomorphic rims with trace element concentrations and δ34S ratios clearly different from those of the cores. While cores have low Co and Ni concentrations and high Co/Ni ratios, rims show as much as 5.5 wt% of these elements and low Co/Ni ratios, reflecting the weathering of nearby ultramafic rocks. In-situ sulfur isotope analyses of pyrite cores show δ34SVCDT (Vienna Canyon Diablo troilite) values between +5‰ and −5‰, while the rims show δ34SVCDT values between −20‰ and −24.5‰, suggesting biogenic fractionation of sulfur. The close spatial association and microtextural evidence for nearly contemporaneous formation of the pedogenic sulfate nodules and the secondary pyrite rims suggests microbial processing of sulfur in the paleosols, which provided reduced and 34S-depleted sulfur for the growth of authigenic pyrite. This indicates that vadose-zone soil-forming processes in the Archean involved not only physical and chemical modification of moist, unconsolidated sediment in a terrestrial environment but also already included its microbiological modification.