bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antihistone Autoantibodies in Dobermans With Hepatitis
Authors: Dyggve H. , Meri S. , Spillmann T. , Jarva H. , Speeti M. 
Published: September 2017

BackgroundImmune system involvement is suggested as an underlying cause for Doberman hepatitis (DH) based on female predisposition, lymphocyte infiltration, abnormal hepatocyte expression of major histocompatibility complex class II antigens, and homozygosity for dog leukocyte antigen DRB1*00601.ObjectiveTo measure serum antinuclear antibodies (ANA) and serum antihistone antibodies (AHA) in Dobermans with hepatitis. To determine whether increased serum ANA or serum AHA could be used to support the diagnosis of Doberman hepatitis (DH).AnimalsPrivately owned 25 subclinically and 13 clinically affected DH Dobermans and 17 healthy control Dobermans.MethodsCase–control study. Indirect immunofluorescence (IIF) microscopy and line blot tests were employed for the ANA pilot studies and an enzyme‐linked immunosorbent assay (ELISA) assay for detection of IgG AHA.ResultsIndirect immunofluorescence revealed ANA‐positive cases, and line blot showed AHA reactivity. In ELISA, importantly increased concentrations of AHA were found in 92% (23/25) of dogs in the subclinical stage and 84.6% (11 of 13) of dogs in the clinical stage of DH compared with no control dogs (0/17) (P < 0.0005). The mean AHA absorbance values of the blood samples obtained from the 25 subclinical DH dogs (1.36 ± 0.60, mean ± SD) and the 13 clinically affected dogs (1.46 ± 0.49) were significantly higher than in 17 control dogs (0.51 ± 0.18; P < 0.0001).Conclusions and Clinical ImportanceAs the presence of AHA indicates autoimmune activity, our results favor an autoimmune background as one cause for DH. Antihistone antibody could represent a novel means for screening Dobermans with increased serum alanine transaminase concentrations and suspicion of DH.
Body mass index trajectories in young adulthood predict non‐alcoholic fatty liver disease in middle age: The CARDIA cohort study
Authors: VanWagner Lisa B. , Khan Sadiya S. , Ning Hongyan , Siddique Juned , Lewis Cora E. , Carr John J. , Vos Miriam B. , Speliotes Elizabeth , Terrault Norah A. , Rinella Mary E. , Lloyd‐Jones Donald M. , Allen Norrina B. 
Published: September 2017

AbstractBackground & AimsNon‐alcoholic fatty liver disease is an epidemic. Identifying modifiable risk factors for non‐alcoholic fatty liver disease development is essential to design effective prevention programmes. We tested whether 25‐year patterns of body mass index change are associated with midlife non‐alcoholic fatty liver disease.MethodsIn all, 4423 participants from Coronary Artery Risk Development in Young Adults, a prospective population‐based biracial cohort (age 18‐30), underwent body mass index measurement at baseline (1985‐1986) and 3 or more times over 25 years. At Year 25, 3115 had liver fat assessed by non‐contrast computed tomography. Non‐alcoholic fatty liver disease was defined as liver attenuation ≤40 Hounsfield Units after exclusions. Latent mixture modelling identified 25‐year trajectories in body mass index per cent change (%Δ) from baseline.ResultsWe identified four distinct trajectories of BMI%Δ: stable (26.2% of cohort, 25‐year BMI %Δ = 3.1%), moderate increase (46.0%, BMI%Δ = 21.7%), high increase (20.9%, BMI%Δ = 41.9%) and extreme increase (6.9%, BMI%Δ = 65.9%). Y25 non‐alcoholic fatty liver disease prevalence was higher in groups with greater BMI %Δ: 4.1%, 9.3%, 13.0%, and 17.6%, respectively (P‐trend <.0001). In multivariable analyses, participants with increasing BMI%Δ had increasingly greater odds of non‐alcoholic fatty liver disease compared to the stable group: OR: 3.35 (95% CI: 2.07‐5.42), 7.80 (4.60‐13.23) and 12.68 (6.68‐24.09) for moderate, high and extreme body mass index increase, respectively. Associations were only moderately attenuated when adjusted for baseline or Y25 body mass index.ConclusionsTrajectories of weight gain during young adulthood are associated with greater non‐alcoholic fatty liver disease prevalence in midlife independent of metabolic covariates and baseline or concurrent body mass index highlighting the importance of weight maintenance throughout adulthood as a target for primary non‐alcoholic fatty liver disease prevention.
Clinical and virological heterogeneity of hepatitis delta in different regions world‐wide: The Hepatitis Delta International Network (HDIN)
Authors: Wranke Anika , Pinheiro Borzacov Lourdes M. , Parana Raymundo , Lobato Cirley , Hamid Saeed , Ceausu Emanoil , Dalekos George N. , Rizzetto Mario , Turcanu Adela , Niro Grazia A. , Lubna Farheen , Abbas Minaam , Ingiliz Patrick , Buti Maria , Ferenci Peter , Vanwolleghem Thomas , Hayden Tonya , Dashdorj Naranjargal , Motoc Adriana , Cornberg Markus , Abbas Zaigham , Yurdaydin Cihan , Manns Michael P. , Wedemeyer Heiner , Hardtke Svenja ,   the Hepatitis Delta International Network
Published: September 2017

AbstractBackground & AimsChronic hepatitis D (delta) is a major global health burden. Clinical and virological characteristics of patients with hepatitis D virus (HDV) infection and treatment approaches in different regions world‐wide are poorly defined.MethodsThe Hepatitis Delta International Network (HDIN) registry was established in 2011 with centres in Europe, Asia, North‐ and South America. Here, we report on clinical/ virological characteristics of the first 1576 patients with ongoing or past HDV infection included in the database until October 2016 and performed a retrospective outcome analysis. The primary aim was to investigate if the region of origin was associated with HDV replication and clinical outcome.ResultsThe majority of patients was male (n = 979, 62%) and the mean age was 36.7 years (range 1‐79, with 9% of patients younger than 20 years). Most patients were HBeAg‐negative (77%) and HDV‐RNA positive (85%). Cirrhosis was reported in 48.7% of cases which included 13% of patients with previous or ongoing liver decompensation. Hepatocellular carcinoma (HCC) developed in 30 patients (2.5%) and 44 (3.6%) underwent liver transplantation. Regions of origin were independently associated with clinical endpoints and detectability of HDV RNA. Antiviral therapy was administered to 356 patients with different treatment uptakes in different regions. Of these, 264 patients were treated with interferon‐a and 92 were treated with HBV‐Nucs only.ConclusionsThe HDIN registry confirms the severity of hepatitis delta but also highlights the heterogeneity of patient characteristics and clinical outcomes in different regions. There is an urgent need for novel treatment options for HDV infection.
Zap1‐dependent transcription from an alternative upstream promoter controls translation of RTC4 mRNA in zinc‐deficient Saccharomyces cerevisiae
Authors: Taggart Janet , MacDiarmid Colin W. , Haws Spencer , Eide David J. 
Published: September 2017

SummaryMaintaining zinc homeostasis is an important property of all organisms. In the yeast Saccharomyces cerevisiae, the Zap1 transcriptional activator is a central player in this process. In response to zinc deficiency, Zap1 activates transcription of many genes and consequently increases accumulation of their encoded proteins. In this report, we describe a new mechanism of Zap1‐mediated regulation whereby increased transcription of certain target genes results in reduced protein expression. Transcription of the Zap1‐responsive genes RTC4 and RAD27 increases markedly in zinc‐deficient cells but, surprisingly, their protein levels decrease. We examined the underlying mechanism further for RTC4 and found that this unusual regulation results from altered transcription start site selection. In zinc‐replete cells, RTC4 transcription begins near the protein‐coding region and the resulting short transcript leader allows for efficient translation. In zinc‐deficient cells, RTC4 RNA with longer transcript leaders are expressed that are not efficiently translated due to the presence of multiple small open reading frames upstream of the coding region. This regulation requires a potential Zap1 binding site located farther upstream of the promoter. Thus, we present evidence for a new mechanism of Zap1‐mediated gene regulation and another way that this activator protein can repress protein expression.
Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain
Authors: Qu Yuanyuan , Ma Qiao , Liu Ziyan , Wang Weiwei , Tang Hongzhi , Zhou Jiti , Xu Ping 
Published: September 2017

SummaryIndole, an important signaling molecule as well as a typical N‐heterocyclic aromatic pollutant, is widespread in nature. However, the biotransformation mechanisms of indole are still poorly studied. Here, we sought to unlock the genetic determinants of indole biotransformation in strain Cupriavidus sp. SHE based on genomics, proteomics and functional studies. A total of 177 proteins were notably altered (118 up‐ and 59 downregulated) in cells grown in indole mineral salt medium when compared with that in sodium citrate medium. RT‐qPCR and gene knockout assays demonstrated that an indole oxygenase gene cluster was responsible for the indole upstream metabolism. A functional indole oxygenase, termed IndA, was identified in the cluster, and its catalytic efficiency was higher than those of previously reported indole oxidation enzymes. Furthermore, the indole downstream metabolism was found to proceed via the atypical CoA‐thioester pathway rather than conventional gentisate and salicylate pathways. This unusual pathway was catalyzed by a conserved 2‐aminobenzoyl‐CoA gene cluster, among which the 2‐aminobenzoyl‐CoA ligase initiated anthranilate transformation. This study unveils the genetic determinants of indole biotransformation and will provide new insights into our understanding of indole biodegradation in natural environments and its functional studies.
Beyond immune escape: a variant surface glycoprotein causes suramin resistance in Trypanosoma brucei
Authors: Wiedemar Natalie , Graf Fabrice E. , Zwyer Michaela , Ndomba Emiliana , Kunz Renggli Christina , Cal Monica , Schmidt Remo S. , Wenzler Tanja , Mäser Pascal 
Published: September 2017

SummarySuramin is one of the first drugs developed in a medicinal chemistry program (Bayer, 1916), and it is still the treatment of choice for the hemolymphatic stage of African sleeping sickness caused by Trypanosoma brucei rhodesiense. Cellular uptake of suramin occurs by endocytosis, and reverse genetic studies with T. b. brucei have linked downregulation of the endocytic pathway to suramin resistance. Here we show that forward selection for suramin resistance in T. brucei spp. cultures is fast, highly reproducible and linked to antigenic variation. Bloodstream‐form trypanosomes are covered by a dense coat of variant surface glycoprotein (VSG), which protects them from their mammalian hosts' immune defenses. Each T. brucei genome contains over 2000 different VSG genes, but only one is expressed at a time. An expression switch to one particular VSG, termed VSGSur, correlated with suramin resistance. Reintroduction of the originally expressed VSG gene in resistant T. brucei restored suramin susceptibility. This is the first report of a link between antigenic variation and drug resistance in African trypanosomes.
How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region?
Authors: Marques I. , Loureiro J. , Draper D. , Castro M. , Castro S. 
Published: September 2017

AbstractNatural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora (Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region.
Cell density and airspace patterning in the leaf can be manipulated to increase leaf photosynthetic capacity
Authors: Lehmeier Christoph , Pajor Radoslaw , Lundgren Marjorie R. , Mathers Andrew , Sloan Jen , Bauch Marion , Mitchell Alice , Bellasio Chandra , Green Adam , Bouyer Daniel , Schnittger Arp , Sturrock Craig , Osborne Colin P. , Rolfe Stephen , Mooney Sacha , Fleming Andrew J. 
Published: September 2017

SummaryThe pattern of cell division, growth and separation during leaf development determines the pattern and volume of airspace in a leaf. The resulting balance of cellular material and airspace is expected to significantly influence the primary function of the leaf, photosynthesis, and yet the manner and degree to which cell division patterns affect airspace networks and photosynthesis remains largely unexplored. In this paper we investigate the relationship of cell size and patterning, airspace and photosynthesis by promoting and repressing the expression of cell cycle genes in the leaf mesophyll. Using microCT imaging to quantify leaf cellular architecture and fluorescence/gas exchange analysis to measure leaf function, we show that increased cell density in the mesophyll of Arabidopsis can be used to increase leaf photosynthetic capacity. Our analysis suggests that this occurs both by increasing tissue density (decreasing the relative volume of airspace) and by altering the pattern of airspace distribution within the leaf. Our results indicate that cell division patterns influence the photosynthetic performance of a leaf, and that it is possible to engineer improved photosynthesis via this approach.
Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04-02, a Strain Toxic to
Plutella xylostella
Authors: Fu Yajuan , Wu Yan , Yuan Yihui , Gao Meiying 
Published: September 2017

ABSTRACT

Bacillus thuringiensis
(Bt) is widely used to control agricultural and forestry pests, though there are only a few available complete genome sequences of the Bt reference strain. Here, we report the complete genome sequence of
B. thuringiensis
serovar rongseni reference strain SCG04-02, which is toxic to
Plutella xylostella
.
Complete Genome Sequence of Bacillus thuringiensis subsp.
jinghongiensis
Reference Strain YGd22-03
Authors: Wu Yan , Fu Yajuan , Yuan Yihui , Gao Meiying 
Published: September 2017

ABSTRACT

Bacillus thuringiensis
is widely used in producing ecofriendly microbial agents for the purpose of controlling insect pests. In this study, we determined the complete genome sequence of
B. thuringiensis
subsp.
jinghongiensis
reference strain YGd22-03, which contains three
cry
genes and one cerecidin biosynthetic gene cluster.
Draft Genome Sequences of
Trichophyton rubrum
CMCC(F)T
1i
and
Trichophyton violaceum
CMCC(F)T
3l
by Illumina 2000 and Pacific Biosciences
Authors: Zhan Ping , de Hoog Sybren , Liu Weida 
Published: September 2017

ABSTRACT

One strain of
Trichophyton rubrum
CMCC(F)T
1i
(=CBS 139224) isolated from onychomycosis and one strain of
Trichophyton violaceum
CMCC(F)T
3l
(=CBS 141829) isolated from tinea capitis in China were whole-genome sequenced by Illumina/Solexa, while the former was also sequenced by Pacific Biosciences sequencing in parallel.
Complete Draft Genome Sequence of Escherichia coli KRX, a Strain for Efficient Cloning and High-Yield Expression of Proteins under Control of the T7 RNA Polymerase
Authors: Schwarzhans Jan-Philipp , Wibberg Daniel , Winkler Anika , Kalinowski Jörn , Friehs Karl 
Published: September 2017

ABSTRACT

Escherichia coli
KRX is a strain offering both a high transformation efficiency and the possibility to produce the target protein to high yields in one host, avoiding additional cloning steps. Here, the draft genome sequence of
E. coli
KRX is presented and provides the genetic basis for additional biotechnological applications.
Draft Genome Sequences of Historical Strains of Coxiella burnetii Isolated from Cow’s Milk and a Goat Placenta
Authors: Beare Paul A. , Jeffrey Brendan M. , Martens Craig A. , Pearson Talima , Heinzen Robert A. 
Published: September 2017

ABSTRACTHere, we report draft genome sequences of historical strains ofCoxiella burnetiiderived from cow’s milk and the placenta of a goat that had aborted. The California and Ohio milk strains display a different sequence type than do contemporary milk strains.
Complete Genome Sequence of Mycoplasma bovirhinis Strain HAZ141_2 from Bovine Nasal Discharge in Japan
Authors: Hata Eiji , Nagai Kazuya , Murakami Kenji 
Published: September 2017

ABSTRACT

Mycoplasma bovirhinis
, a mycoplasmal species involved in bovine respiratory diseases, is also a commensal microorganism that inhabits the bovine respiratory and reproductive organs. We present the complete 948,039-bp genome sequence of
M. bovirhinis
strain HAZ141_2, which was isolated from bovine nasal discharge in Japan.
Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii
Authors: Tettelin Hervé , Hooven Thomas A. , Zhao Xuechu , Su Qi , Sadzewicz Lisa , Tallon Luke J. , Fraser Claire M. , Ratner Adam J. 
Published: September 2017

ABSTRACT

Bordetella holmesii
causes respiratory and invasive diseases in humans, but its pathogenesis remains poorly understood. We report here the genome sequences of seven bacteremia isolates of
B. holmesii
, including the type strain. Comparative analysis of these sequences may aid studies of
B. holmesii
biology and assist in the development of species-specific diagnostic strategies.
Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611
Authors: Furmanczyk Ewa M. , Kaminski Michal A. , Dziembowski Andrzej , Lipinski Leszek , Sobczak Adam 
Published: September 2017

ABSTRACT

Here, we report the draft genome sequence of
Pseudomonas umsongensis
type strain DSM 16611. The assembly consists of 14 contigs containing 6,701,403 bp with a GC content of 59.73%.
Draft Genome Sequence of a
Gordonia
sp. Isolated from the Soil of a Red Alder Plant
Authors: Devitt Nicholas P. , Herman Barrington , Luchterhand Randi A. , Costa Michael A. , Jacobi Jennifer L. , Davin Laurence B. , Lewis Norman G. , Bell Callum J. 
Published: September 2017

ABSTRACT

A
Gordonia
species was cultured from soil of a red alder (
Alnus rubra
) plant. Here we present the assembled and annotated genome sequence to aid investigations into the potential of this organism as a symbiont and comparative studies of the genus
Gordonia
.
Draft Genome Sequence of an Acid-Tolerant Yeast,
Candida zemplinina
NP2, a Potential Producer of Organic Acids
Authors: Ko Hyeok-Jin , Park Hyun Joo , Lee Sun Hee , Jeong Haeyoung , Bae Jung-Hoon , Sung Bong Hyun , Choi In-Geol , Sohn Jung-Hoon 
Published: September 2017

ABSTRACT

Here, we report the draft genome sequence of the acid-tolerant yeast
Candida zemplinina
NP2, which was isolated from peach peels. This genome sequence will aid in the understanding of the organism’s physiological properties as a potential producer of organic acids in acidic environments.
Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample
Authors: Jennings Matthew E. , Chia Nicholas , Boardman Lisa A. , Metcalf William W. 
Published: September 2017

ABSTRACT

Methanobrevibacter smithii
is a common inhabitant of the human gut. Here, we present a draft genome sequence of
M. smithii
isolate WWM1085, obtained from a human stool sample. This sequence will improve our understanding of the genetic diversity of this human-associated methanogen.
Draft Genome Sequences of Salmonella enterica Isolates Containing Incompatibility Group I1 Plasmids from Swine, Poultry, and Human Sources
Authors: Kaldhone Pravin R. , Khajanchi Bijay K. , Han Jing , Nayak Rajesh , Ricke Steven C. , Foley Steven L. 
Published: September 2017

ABSTRACT

The draft genome sequences of eight
Salmonella enterica
isolates from various sources were evaluated for the influence of incompatibility group I1 (IncI1) plasmids on virulence. Strains SE142, SE143, SE144, and SE146 originated from swine, SE36N and SE89N from poultry-related sources, and SE991 and SE1148 from human patients.
Draft Genome Sequence of Marinobacter vinifirmus Type Strain FB1
Authors: Stepanov Victor G. , Roberts Deborah J. , Fox George E. 
Published: September 2017

ABSTRACT

The gammaproteobacterium
Marinobacter vinifirmus
is associated with moderately saline environments and is often found in marine ecosystems. Here, we report the draft genome sequence of
M. vinifirmus
type strain FB1 (3.8 Mbp, 3,588 predicted genes). The presented sequence will improve our understanding of the taxonomy and evolution of the genus
Marinobacter
.
Draft Genome Sequences of Biofilm-Forming and Non-Biofilm-Forming Nontyphoidal Salmonella enterica Serovars
Authors: Shetty Deeksha , Grigoryan Alexander A. , Alshalchi Sahar , Withana Gamage Niradha , Roy Julie , Lawrence John R. , Vidovic Sinisa , Korber Darren R. 
Published: September 2017

ABSTRACT
The genetic basis for biofilm formation among nontyphoidal salmonellae (NTS) remains poorly understood. This draft genome submission provides initial insights on the genetic differences between biofilm-forming and non-biofilm-forming clinical and environmental NTS serovars.
Draft Genome Sequence of Xanthomonas arboricola pv. juglandis J303, Isolated from Infected Walnut Trees in Southern Chile
Authors: Retamales Julio , Segovia Cristopher , Alvarado Romina , Nuñez Pablo , Santander Javier 
Published: September 2017

ABSTRACT

Here, we report the draft genome sequence of
Xanthomonas arboricola
pv. juglandis J303, isolated from infected walnut trees in southern Chile. The size of the genome is 5,066,424 bp with a G+C content of 65.4%.
X. arboricola
pv. juglandis J303 has several genes related to virulence, antibiotic resistance, and copper resistance.