bluuebunny/crossref_metadata_2025_split huggingface dataset:
A safety vs efficiency trade‐off identified in the hydraulic pathway of grass leaves is decoupled from photosynthesis, stomatal conductance and precipitation
Authors: Ocheltree Troy W. , Nippert Jesse B. , Prasad P. V. Vara 
Published: December 2015

Summary

A common theme in plant physiological research is the trade‐off between stress tolerance and growth; an example of this trade‐off at the tissue level is the safety vs efficiency hypothesis, which suggests that plants with the greatest resistance to hydraulic failure should have low maximum hydraulic conductance.

Here, we quantified the leaf‐level drought tolerance of nine C4 grasses as the leaf water potential at which plants lost 50% (P50 × RR) of maximum leaf hydraulic conductance (Ksat), and compared this trait with other leaf‐level and whole‐plant functions.

We found a clear trade‐off between Ksat and P50 × RR when Ksat was normalized by leaf area and mass (P = 0.05 and 0.01, respectively). However, no trade‐off existed between P50 × RR and gas‐exchange rates; rather, there was a positive relationship between P50 × RR and photosynthesis (P = 0.08). P50 × RR was not correlated with species distributions based on precipitation (P = 0.70), but was correlated with temperature during the wettest quarter of the year (P < 0.01).

These results suggest a trade‐off between safety and efficiency in the hydraulic system of grass leaves, which can be decoupled from other leaf‐level functions. The unique physiology of C4 plants and adaptations to pulse‐driven systems may provide mechanisms that could decouple hydraulic conductance from other plant functions.
Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants
Authors: Polturak Guy , Breitel Dario , Grossman Noam , Sarrion‐Perdigones Alejandro , Weithorn Efrat , Pliner Margarita , Orzaez Diego , Granell Antonio , Rogachev Ilana , Aharoni Asaph 
Published: December 2015

Summary

Betalains are tyrosine‐derived red‐violet and yellow pigments, found in plants only of the Caryophyllales order. Although much progress has been made in recent years in the understanding of the betalain biosynthetic process, many questions remain open with regards to several of the proposed steps in the pathway. Most conspicuous by its absence is the characterization of the first committed step in the pathway, namely the 3‐hydroxylation of tyrosine to form l‐3,4‐dihydroxyphenylalanine (l‐DOPA).

We used transcriptome analysis of the betalain‐producing plants red beet (Beta vulgaris) and four o'clocks (Mirabilis jalapa) to identify a novel, betalain‐related cytochrome P450‐type gene, CYP76AD6, and carried out gene silencing and recombinant expression assays in Nicotiana benthamiana and yeast cells to examine its functionality.

l‐DOPA formation in red beet was found to be redundantly catalyzed by CYP76AD6 together with a known betalain‐related enzyme, CYP76AD1, which was previously thought to only catalyze a succeeding step in the pathway. While CYP76AD1 catalyzes both l‐DOPA formation and its subsequent conversion to cyclo‐DOPA, CYP76AD6 uniquely exhibits only tyrosine hydroxylase activity.

The new findings enabled us to metabolically engineer entirely red‐pigmented tobacco plants through heterologous expression of three genes taking part in the fully decoded betalain biosynthetic pathway.
A first report of leptospirosis after liver transplantation
Authors: Song A.T.W. , Abas L. , Andrade L.C. , Andraus W. , D'Albuquerque L.A.C. , Abdala E. 
Published: December 2015

AbstractLeptospirosis has been rarely reported in solid organ transplant recipients. We report the first case to our knowledge of leptospirosis in a liver transplant recipient who developed jaundice and renal insufficiency. We describe his favorable clinical progression and discuss the possible mechanisms involved in the more benign disease course. We also review the previously published cases of leptospirosis in solid organ transplant recipients. Although this disease does not appear to present any particularities in this context, we highlight the importance of clinical suspicion in this setting, particularly after liver transplantation.
Imipenem Treatment Induces Expression of Important Genes and Phenotypes in a Resistant Acinetobacter baumannii Isolate
Authors: Dhabaan Ghulam Nasser , AbuBakar Sazaly , Cerqueira Gustavo Maia , Al-Haroni Mohammed , Pang Sui Ping , Hassan Hamimah 
Published: December 2015

ABSTRACT

Acinetobacter baumannii
has emerged as a notorious multidrug-resistant pathogen, and development of novel control measures is of the utmost importance. Understanding the factors that play a role in drug resistance may contribute to the identification of novel therapeutic targets. Pili are essential for
A. baumannii
adherence to and biofilm formation on abiotic surfaces as well as virulence. In the present study, we found that biofilm formation was significantly induced in an imipenem-resistant (Imp
r
) strain treated with a subinhibitory concentration of antibiotic compared to that in an untreated control and an imipenem-susceptible (Imp
s
) isolate. Using microarray and quantitative PCR analyses, we observed that several genes responsible for the synthesis of type IV pili were significantly upregulated in the Imp
r
but not in the Imp
s
isolate. Notably, this finding is corroborated by an increase in the motility of the Imp
r
strain. Our results suggest that the ability to overproduce colonization factors in response to imipenem treatment confers biological advantage to
A. baumannii
and may contribute to clinical success.
The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components
Authors: Raj Shriya , Krishnan Karthik , Askew David S. , Helynck Olivier , Suzanne Peggy , Lesnard Aurélien , Rault Sylvain , Zeidler Ute , d'Enfert Christophe , Latgé Jean-Paul , Munier-Lehmann Hélène , Saveanu Cosmin 
Published: December 2015

ABSTRACT

In a search for new antifungal compounds, we screened a library of 4,454 chemicals for toxicity against the human fungal pathogen
Aspergillus fumigatus
. We identified sr7575, a molecule that inhibits growth of the evolutionary distant fungi
A. fumigatus
,
Cryptococcus neoformans
,
Candida albicans
, and
Saccharomyces cerevisiae
but lacks acute toxicity for mammalian cells. To gain insight into the mode of inhibition, sr7575 was screened against 4,885
S. cerevisiae
mutants from the systematic collection of haploid deletion strains and 977 barcoded haploid DAmP (decreased abundance by mRNA perturbation) strains in which the function of essential genes was perturbed by the introduction of a drug resistance cassette downstream of the coding sequence region. Comparisons with previously published chemogenomic screens revealed that the set of mutants conferring sensitivity to sr7575 was strikingly narrow, affecting components of the endoplasmic reticulum-associated protein degradation (ERAD) stress response and the ER membrane protein complex (EMC). ERAD-deficient mutants were hypersensitive to sr7575 in both
S. cerevisiae
and
A. fumigatus
, indicating a conserved mechanism of growth inhibition between yeast and filamentous fungi. Although the unfolded protein response (UPR) is linked to ERAD regulation, sr7575 did not trigger the UPR in
A. fumigatus
and UPR mutants showed no enhanced sensitivity to the compound. The data from this chemogenomic analysis demonstrate that sr7575 exerts its antifungal activity by disrupting ER protein quality control in a manner that requires ERAD intervention but bypasses the need for the canonical UPR. ER protein quality control is thus a specific vulnerability of fungal organisms that might be exploited for antifungal drug development.
Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumannii
Authors: Blackwell Grace A. , Nigro Steven J. , Hall Ruth M. 
Published: December 2015

ABSTRACT

A320, isolated in the Netherlands in 1982 and also known as RUH134, is the earliest available multiply antibiotic-resistant (MAR)
Acinetobacter baumannii
isolate belonging to global clone 2 (GC2) and is the reference strain for this clone. The draft genome sequence of A320 was used to investigate the original location and configuration of the IS
26
-bounded AbGRI2 resistance island found in current GC2 isolates. PCR mapping and sequencing were used to order contigs composing the resistance islands. A320 contains two IS
26
-bounded resistance islands, AbGRI2-0a and AbGRI2-0b, of 7.8 kb and 25.4 kb, respectively. Together they contain
bla
TEM
,
aacC1
,
aadA1
,
sul1
,
catA1
, and
aphA1b
genes, which confer resistance to antibiotics used clinically in the 1970s, as well as an incomplete mercury resistance module. Tracking the continuity of the chromosome and the target site duplications revealed that the two resistance islands were originally together as AbGRI2-0, an island of 32.4 kb, and were subsequently separated via an IS
26
-mediated intramolecular inversion that reversed the orientation of 1.54 Mb of the chromosome and duplicated an IS
26
. A320 contains an ancestral form of AbGRI2, and the original insertion site of the AbGRI2 island was identified. Many of the AbGRI2 versions present in the completed GC2 genomes can be derived from it via the variant AbGRI2-1. IS
26
-mediated inversions have also played a part in forming AbGRI2-0, and, upon reversal, large regions of AbGRI2-0 are identical to parts of AbaR0, the ancestral version of the AbaR islands present in GC1 isolates. This indicates a common source.
Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate
Authors: Rahman Maliha , Nguyen Scott V. , McCullor Kimberly A. , King Catherine J. , Jorgensen James H. , McShan W. Michael 
Published: December 2015

ABSTRACT

Streptococcus anginosus
is an opportunistic human pathogen that causes abscesses of the brain, liver, and other organs. Here, we announce the complete genome sequence of a clinically isolated strain of
S. anginosus
J4211. The genome sequence contains two prophages and multiple mobile genetic elements.
Complete Genome Sequence of the Porcine Epidemic Diarrhea Virus Variant CH/HNYF/2014
Authors: Li Renfeng , Tian Xiangqin , Qiao Songlin , Guo Junqing , Xie Weitao , Zhang Gaiping 
Published: December 2015

ABSTRACT

Sow's milk is a potential route for the vertical transmission of porcine epidemic diarrhea virus (PEDV) from sow to suckling piglet. We report here the complete genome sequence of PEDV strain CH/HNYF/2014, which was isolated from milk samples
.
This information provides further understanding of the transmission mechanisms and genetic diversity of PEDV.
Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25
Authors: Lindsey Rebecca L. , Knipe Kristen , Rowe Lori , Garcia-Toledo Lisley , Loparev Vladimir , Juieng Phalasy , Trees Eija , Strockbine Nancy , Stripling Devon , Gerner-Smidt Peter 
Published: December 2015

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) is an important foodborne pathogen. Here, we report complete whole-genome sequences for two STEC strains of serotypes O119:H4 and O165:H25 isolated from clinical cases in the United States.
A Coming of Age Story: Chlamydia in the Post-Genetic Era
Authors: Hooppaw Anna J. , Fisher Derek J. 
Published: December 2015

ABSTRACT

Chlamydia
spp. are ubiquitous, obligate, intracellular Gram-negative bacterial pathogens that undergo a unique biphasic developmental cycle transitioning between the infectious, extracellular elementary body and the replicative, intracellular reticulate body. The primary
Chlamydia
species associated with human disease are
C. trachomatis
, which is the leading cause of both reportable bacterial sexually transmitted infections and preventable blindness, and
C. pneumoniae
, which infects the respiratory tract and is associated with cardiovascular disease. Collectively, these pathogens are a significant source of morbidity and pose a substantial financial burden on the global economy. Past efforts to elucidate virulence mechanisms of these unique and important pathogens were largely hindered by an absence of genetic methods. Watershed studies in 2011 and 2012 demonstrated that forward and reverse genetic approaches were feasible with
Chlamydia
and that shuttle vectors could be selected and maintained within the bacterium. While these breakthroughs have led to a steady expansion of the chlamydial genetic tool kit, there are still roads left to be traveled. This minireview provides a synopsis of the currently available genetic methods for
Chlamydia
along with a comparison to the methods used in other obligate intracellular bacteria. Limitations and advantages of these techniques will be discussed with an eye toward the methods still needed, and how the current state of the art for genetics in obligate intracellular bacteria could direct future technological advances for
Chlamydia
.
Acinetobacter baumannii Is Dependent on the Type II Secretion System and Its Substrate LipA for Lipid Utilization and
In Vivo
Fitness
Authors: Johnson Tanya L. , Waack Ursula , Smith Sara , Mobley Harry , Sandkvist Maria 
Published: December 2015

ABSTRACT

Gram-negative bacteria express a number of sophisticated secretion systems to transport virulence factors across the cell envelope, including the type II secretion (T2S) system. Genes for the T2S components GspC through GspN and PilD are conserved among isolates of
Acinetobacter baumannii
, an increasingly common nosocomial pathogen that is developing multidrug resistance at an alarming rate. In contrast to most species, however, the T2S genes are dispersed throughout the genome rather than linked into one or two operons. Despite this unique genetic organization, we show here that the
A. baumannii
T2S system is functional. Deletion of
gspD
or
gspE
in
A. baumannii
ATCC 17978 results in loss of secretion of LipA, a lipase that breaks down long-chain fatty acids. Due to a lack of extracellular lipase, the
gspD
mutant, the
gspE
mutant, and a
lipA
deletion strain are incapable of growth on long-chain fatty acids as a sole source of carbon, while their growth characteristics are indistinguishable from those of the wild-type strain in nutrient-rich broth. Genetic inactivation of the T2S system and its substrate, LipA, also has a negative impact on
in vivo
fitness in a neutropenic murine model for bacteremia. Both the
gspD
and
lipA
mutants are outcompeted by the wild-type strain as judged by their reduced numbers in spleen and liver following intravenous coinoculation. Collectively, our findings suggest that the T2S system plays a hitherto-unrecognized role in
in vivo
survival of
A. baumannii
by transporting a lipase that may contribute to fatty acid metabolism.

IMPORTANCE
Infections by multidrug-resistant
Acinetobacter baumannii
are a growing health concern worldwide, underscoring the need for a better understanding of the molecular mechanisms by which this pathogen causes disease. In this study, we demonstrated that
A. baumannii
expresses a functional type II secretion (T2S) system that is responsible for secretion of LipA, an extracellular lipase required for utilization of exogenously added lipids. The T2S system and the secreted lipase support
in vivo
colonization and thus contribute to the pathogenic potential of
A. baumannii
.
Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome
Authors: Carpenter Megan R. , Rozovsky Sharon , Boyd E. Fidelma 
Published: December 2015

ABSTRACTPathogenicity islands (PAIs) are mobile integrated genetic elements (MIGEs) that contain a diverse range of virulence factors and are essential in the evolution of pathogenic bacteria. PAIs are widespread among bacteria and integrate into the host genome, commonly at a tRNA locus, via integrase-mediated site-specific recombination. The excision of PAIs is the first step in the horizontal transfer of these elements and is not well understood. In this study, we examined the role of recombination directionality factors (RDFs) and their relationship with integrases in the excision of two PAIs essential forVibrio choleraehost colonization:Vibriopathogenicity island 1 (VPI-1) and VPI-2. VPI-1 does not contain an RDF, which allowed us to answer the question of whether RDFs are an absolute requirement for excision. We found that an RDF was required for efficient excision of VPI-2 but not VPI-1 and that RDFs can induce excision of both islands. Expression data revealed that the RDFs act as transcriptional repressors to both VPI-1- and VPI-2-encoded integrases. We demonstrated that the RDFsVibrioexcision factor A (VefA) and VefB bind at the attachment sites (overlapping theintpromoter region) of VPI-1 and VPI-2, thus supporting this mode of integrase repression. In addition,V. choleraeRDFs are promiscuous due to their dual functions of promoting excision of both VPI-1 and VPI-2 and acting as negative transcriptional regulators of the integrases. This is the first demonstration of cross talk between PAIs mediated via RDFs which reveals the complex interactions that occur between separately acquired MIGEs.IMPORTANCEDeciphering the mechanisms of pathogenicity island excision is necessary for understanding the evolution and spread of these elements to their nonpathogenic counterparts. Such mechanistic insight would assist in predicting the mobility of uncharacterized genetic elements. This study identified extensive RDF-mediated cross talk between two nonhomologous VPIs and demonstrated the dual functionality of RDF proteins: (i) inducing PAI excision and (ii) acting as transcriptional regulators. Findings from this study may be implicated in determining the mobilome contribution of other bacteria with multiple MIGEs.
Reexamining the Germination Phenotypes of Several Clostridium difficile Strains Suggests Another Role for the CspC Germinant Receptor
Authors: Bhattacharjee Disha , Francis Michael B. , Ding Xicheng , McAllister Kathleen N. , Shrestha Ritu , Sorg Joseph A. 
Published: December 2015

ABSTRACT

Clostridium difficile
spore germination is essential for colonization and disease. The signals that initiate
C. difficile
spore germination are a combination of taurocholic acid (a bile acid) and glycine. Interestingly, the chenodeoxycholic acid class (CDCA) bile acids competitively inhibit taurocholic acid-mediated germination, suggesting that compounds that inhibit spore germination could be developed into drugs that prophylactically prevent
C. difficile
infection or reduce recurring disease. However, a recent report called into question the utility of such a strategy to prevent infection by describing
C. difficile
strains that germinated in the apparent absence of bile acids or germinated in the presence of the CDCA inhibitor. Because the mechanisms of
C. difficile
spore germination are beginning to be elucidated, the mechanism of germination in these particular strains could yield important information on how
C. difficile
spores initiate germination. Therefore, we quantified the interaction of these strains with taurocholic acid and CDCA, the rates of spore germination, the release of DPA from the spore core, and the abundance of the germinant receptor complex (CspC, CspB, and SleC). We found that strains previously observed to germinate in the absence of taurocholic acid correspond to more potent 50% effective concentrations (EC
50
values; the concentrations that achieve a half-maximum germination rate) of the germinant and are still inhibited by CDCA, possibly explaining the previous observations. By comparing the germination kinetics and the abundance of proteins in the germinant receptor complex, we revised our original model for CspC-mediated activation of spore germination and propose that CspC may activate spore germination and then inhibit downstream processes.

IMPORTANCE
Clostridium difficile
forms metabolically dormant spores that persist in the health care environment. In susceptible hosts,
C. difficile
spores germinate in response to certain bile acids and glycine. Blocking germination by
C. difficile
spores is an attractive strategy to prevent the initiation of disease or to block recurring infection. However, certain
C. difficile
strains have been identified whose spores germinate in the absence of bile acids or are not blocked by known inhibitors of
C. difficile
spore germination (calling into question the utility of such strategies). Here, we further investigate these strains and reestablish that bile acid activators and inhibitors of germination affect these strains and use these data to suggest another role for the
C. difficile
bile acid germinant receptor.
MEDICATION USE IN NEONATAL INTENSIVE CARE UNITS ACROSS EUROPE
Authors: Mesek Inge , Nellis Georgi , Lass Jana , Lutsar Irja 
Published: December 2015

ObjectivesThis is the first Europe-wide study aiming to describe the medication use in Neonatal Intensive Care Units and to analyse the factors that might influence the prescription pattern.MethodsA pan-European one day point-prevalence study was conducted in 2012 where all of the prescriptions for hospitalised neonates were recorded. A trade name, manufacturer, active pharmaceutical ingredients (API), strength, galenic form and route of administration were registered.ResultsAltogether 2173 prescriptions were administered to 726 neonates from 21 countries, of whom 66% (477/726) were preterm, 12% (84/726) extremely preterm. There was inverse correlation between gestational age (GA) and median number of prescriptions per neonate (group median 2/IQR 1–4, extremely preterm 4/3–6, very preterm 3/2–5, late preterm 2/1–3, full-term 2/1–3). Median number of prescriptions per neonate was highest in the eastern region, among extremely preterm neonates (median=6.5/IQR 6–8.5). Highest prescription rate was for alimentary medicines (93/per 100 admissions), systemic antiinfectives (79/100) and medicines for blood (71/100). Antiinfectives were most frequently prescribed in the southern region (103/100). Multivitamins were most frequently used medications in most regions (western 74, southern 31, northern 31/100), except in eastern region (5/100). Most commonly prescribed API-s were multivitamins (32/100), caffeine (19/100), gentamicin (18/100), amino acids (18/100) and colecalciferol (15/100). Most frequently prescribed medications among extremely preterm neonates were caffeine (60/100), among very preterms multivitamins and caffeine (45 and 43/100), among late preterms multivitamins (44/100) and among full-terms phytomenadione (26/100) and gentamicin (24/100).ConclusionsOur study revealed the most commonly used medications in neonates. Higher prescription rate among preterm neonates calls for further analysis of the suitability and safety of medications for infants with lower GA.