How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ...ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.
The processing of verbal fluency tasks relies on the coordinated activity of a number of brain areas, particularly in the frontal and temporal lobes of the left hemisphere. Recent studies using ...functional magnetic resonance imaging (fMRI) to study the neural networks subserving verbal fluency functions have yielded divergent results especially with respect to a parcellation of the inferior frontal gyrus for phonemic and semantic verbal fluency. We conducted a coordinate-based activation likelihood estimation (ALE) meta-analysis on brain activation during the processing of phonemic and semantic verbal fluency tasks involving 28 individual studies with 490 healthy volunteers.
For phonemic as well as for semantic verbal fluency, the most prominent clusters of brain activation were found in the left inferior/middle frontal gyrus (LIFG/MIFG) and the anterior cingulate gyrus. BA 44 was only involved in the processing of phonemic verbal fluency tasks, BA 45 and 47 in the processing of phonemic and semantic fluency tasks.
Our comparison of brain activation during the execution of either phonemic or semantic verbal fluency tasks revealed evidence for spatially different activation in BA 44, but not other regions of the LIFG/LMFG (BA 9, 45, 47) during phonemic and semantic verbal fluency processing.
The human pathogen Yersinia enterocolitica strain W22703 is characterized by its toxicity towards invertebrates that requires the insecticidal toxin complex (Tc) proteins encoded by the pathogenicity ...island Tc-PAIYe. Molecular and pathophysiological details of insect larvae infection and killing by this pathogen, however, have not been dissected. Here, we applied oral infection of Galleria mellonella (Greater wax moth) larvae to study the colonisation, proliferation, tissue invasion, and killing activity of W22703. We demonstrated that this strain is strongly toxic towards the larvae, in which they proliferate by more than three orders of magnitude within six days post infection. Deletion mutants of the genes tcaA and tccC were atoxic for the insect. W22703 ΔtccC, in contrast to W22703 ΔtcaA, initially proliferated before being eliminated from the host, thus confirming TcaA as membrane-binding Tc subunit and TccC as cell toxin. Time course experiments revealed a Tc-dependent infection process starting with midgut colonisation that is followed by invasion of the hemolymph where the pathogen elicits morphological changes of hemocytes and strongly proliferates. The in vivo transcriptome of strain W22703 shows that the pathogen undergoes a drastic reprogramming of central cell functions and gains access to numerous carbohydrate and amino acid resources within the insect. Strikingly, a mutant lacking a phage-related holin/endolysin (HE) cassette, which is located within Tc-PAIYe, resembled the phenotypes of W22703 ΔtcaA, suggesting that this dual lysis cassette may be an example of a phage-related function that has been adapted for the release of a bacterial toxin.
Abstract
Key message
Mining genome-wide DNA sequences enabled the discovery of near-diagnostic markers for species assignment in four European white oaks (
Quercus petraea
(Matt.) Liebl.,
Quercus ...pubescens
Willd.,
Quercus pyrenaica
Willd., and
Quercus robur
L.) despite their low interspecific differentiation. Near-diagnostic markers are almost fully fixed in one species and absent in the three others. As a result, only a handful of markers are needed for species identification, making this genetic assay a very promising operational taxonomic assignment procedure in research and forestry.
Context
Identifying species in the European white oak complex has been a long-standing concern in taxonomy, evolution, forest research, and management.
Quercus petraea
(Matt.) Liebl.,
Q. robur
L.,
Q. pubescens
Willd., and
Q. pyrenaica
Willd. are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification.
Aims
Our aim was to identify near-diagnostic single-nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry.
Methods
We first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, i.e., genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step).
Results
We found a subset of 38 SNPs (10 for
Q. petraea
, 7 for
Q. pubescens
, 9 for
Q. pyrenaica
, and 12 for
Q. robur
) that showed near-diagnostic features across their species distribution ranges with
Q. pyrenaica
and
Q. pubescens
exhibiting the highest (0.876) and lowest (0.747) diagnosticity, respectively.
Conclusions
We provide a new, efficient, and reliable molecular tool for the identification of the species
Q. petraea
,
Q. robur
,
Q. pubescens
, and
Q. pyrenaica
, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design near-diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.
The hard template method for the preparation of monodisperse mesoporous silica microspheres (MPSMs) has been established in recent years. In this process, in situ-generated silica nanoparticles ...(SNPs) enter the porous organic template and control the size and pore parameters of the final MPSMs. Here, the sizes of the deposited SNPs are determined by the hydrolysis and condensation rates of different alkoxysilanes in a base catalyzed sol-gel process. Thus, tetramethyl orthosilicate (TMOS), tetraethyl orthosilicate (TEOS), tetrapropyl orthosilicate (TPOS) and tetrabutyl orthosilicate (TBOS) were sol-gel processed in the presence of amino-functionalized
(glycidyl methacrylate-
-ethylene glycol dimethacrylate) (
(GMA-
-EDMA)) templates. The size of the final MPSMs covers a broad range of 0.5-7.3 µm and a median pore size distribution from 4.0 to 24.9 nm. Moreover, the specific surface area can be adjusted between 271 and 637 m
g
. Also, the properties and morphology of the MPSMs differ according to the SNPs. Furthermore, the combination of different alkoxysilanes allows the individual design of the morphology and pore parameters of the silica particles. Selected MPSMs were packed into columns and successfully applied as stationary phases in high-performance liquid chromatography (HPLC) in the separation of various water-soluble vitamins.
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; ...providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
In contrast to biological invasions, translocations of individuals within a species range are understudied, due to difficulties in systematically detecting them. This results in limited knowledge ...about the corresponding processes and uncertainties regarding the status of extant populations. European larch, a forest tree whose fragmented native distribution is restricted to the Alps and to other Central European mountains, has been massively planted for at least 300 years. Here we focus on the genetic characterization of translocations having taken place within its native range. Microsatellite variation at 13 nuclear loci and sequence data of two mitochondrial DNA fragments were analyzed on the basis of a comprehensive range-wide population sample. Two complementary methods (Geneclass and Structure) were used to infer translocation events based on nuclear data whereas mitochondrial data were used for validation of these inferences. Using Geneclass, we found translocation events in a majority of populations. Additional cases of translocation and many instances of admixture were identified using Structure, thanks to the clear-cut ancestral genetic structure detected in this species. In particular, a strong divide between Alpine and Central European populations, also apparent at mitochondrial markers, helped uncover details on translocation events and related processes. Translocations and associated admixture events were found to be heterogeneously distributed across the species range, with a particularly high frequency in Central Europe. Furthermore, translocations frequently involved multiple geographic sources, some of which were over-represented. Our study illustrates the importance of range-wide investigations for tracing translocations back to their origins and for revealing some of their consequences. It provides some first clues for developing suitable conservation and management strategies.
Monodisperse porous poly(glycidyl methacrylate-
-ethylene glycol dimethacrylate) particles are widely applied in different fields, as their pore properties can be influenced and functionalization of ...the epoxy group is versatile. However, the adjustment of parameters which control morphology and pore properties such as pore volume, pore size and specific surface area is scarcely available. In this work, the effects of the process factors monomer:porogen ratio, GMA:EDMA ratio and composition of the porogen mixture on the response variables pore volume, pore size and specific surface area are investigated using a face centered central composite design. Non-linear effects of the process factors and second order interaction effects between them were identified. Despite the complex interplay of the process factors, targeted control of the pore properties was possible. For each response a response surface model was derived with high predictive power (all R
> 0.85). All models were tested by four external validation experiments and their validity and predictive power was demonstrated.
Genetic Architecture of the APM1 Gene and Its Influence on Adiponectin Plasma Levels and Parameters of the Metabolic Syndrome in 1,727 Healthy Caucasians
Iris M. Heid 1 2 ,
Stefanie A. Wagner 1 3 ,
...Henning Gohlke 1 ,
Bernhard Iglseder 4 ,
Jakob C. Mueller 5 ,
Paula Cip 3 ,
Günther Ladurner 4 ,
Raphael Reiter 3 ,
Andreas Stadlmayr 3 ,
Vitolds Mackevics 3 ,
Thomas Illig 1 ,
Florian Kronenberg 6 and
Bernhard Paulweber 3
1 GSF-National Research Center for Environment and Health, Institute of Epidemiology, Neuherberg, Germany
2 Department of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
3 First Department of Internal Medicine, St. Johann Spital, Paracelsus Private Medical University Salzburg, Salzburg, Austria
4 Department of Neurology, Paracelsus Private Medical University Salzburg, Salzburg, Austria
5 Institute for Medical Statistics and Epidemiology & Institute for Psychiatry and Psychotherapy, Clinic “Rechts der Isar,“
Technical University, Munich, Germany
6 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University,
Innsbruck, Austria
Address correspondence and reprint requests to Florian Kronenberg MD, Division of Genetic Epidemiology, Department of Medical
Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Schöpfstr. 41, A-6020 Innsbruck, Austria. E-mail:
florian.kronenberg{at}i-med.ac.at
Abstract
The associations of the adiponectin ( APM1 ) gene with parameters of the metabolic syndrome are inconsistent. We performed a systematic investigation based on fine-mapped
single nucleotide polymorphisms (SNPs) highlighting the genetic architecture and their role in modulating adiponectin plasma
concentrations in a particularly healthy population of 1,727 Caucasians avoiding secondary effects from disease processes.
Genotyping 53 SNPs (average spacing of 0.7 kb) in the APM1 gene region in 81 Caucasians revealed a two-block linkage disequilibrium (LD) structure and enabled comprehensive tag SNP
selection. We found particularly strong associations with adiponectin concentrations for 11 of the 15 tag SNPs in the 1,727
subjects (five P values <0.0001). Haplotype analysis provided a thorough differentiation of adiponectin concentrations with 9 of 17 haplotypes
showing significant associations (three P values <0.0001). No significant association was found for any SNP with the parameters of the metabolic syndrome. We observed
a two-block LD structure of APM1 pointing toward at least two independent association signals, one including the promoter SNPs and a second spanning the relevant
exons. Our data on a large number of healthy subjects suggest a clear modulation of adiponectin concentrations by variants
of APM1 , which are not merely a concomitant effect in the course of type 2 diabetes or coronary artery disease.
CCA, common carotid artery
HWE, Hardy-Weinberg equilibrium
LD, linkage disequilibrium
MAF, minor allele frequency
SAPHIR, Salzburg Atherosclerosis Prevention Program in Subjects at High Individual Risk
SNP, single nucleotide polymorphism
Footnotes
I.M.H. and S.A.W. have contributed equally to this article.
Additional information for this article can be found in an online appendix at http://diabetes.diabetesjournals.org .
Accepted October 19, 2005.
Received June 9, 2005.
DIABETES
There is evidence that symptomatology in patients with major depressive disorder (MDD) changes with age. However, studies comparing depressive symptomatology between different age groups during ...antidepressant therapy are rare. We compared demographic and clinical characteristics in depressed patients of different age groups at baseline and during treatment.
889 MDD inpatients were divided into four age groups (18–29, 30–39, 40–49, 50–65 yrs.). Demographic and clinical characteristics including depressive symptomatology (assessed by the Inventory of Depressive Symptoms) were assessed at baseline and weekly during treatment.
At baseline, young patients (18–29 years) significantly more often reported cognitive symptoms like irritability, suicidality, negative self-concept and interpersonal sensitivity and more often suffered from drug abuse and comorbid personality disorders. Late middle aged patients (50–65 years) significantly more often suffered from neuro-vegetative symptoms such as reduced general interest, sexual interest and sleep disturbances and more often showed a recurrent MDD and comorbid physical disorders. During therapy, symptoms such as interpersonal sensitivity in young patients and low interest in sex in late middle aged patients persisted until the end of treatment while all other symptoms declined until day 56.
The herein presented age differences in depressive symptomatology only hold true for the study medication and are not generalizable to other antidepressants agents.
There are substantial differences in the clinical presentation of depression between age groups. Whereas many of these differences disappear during treatment, some differences persisted until the end of treatment. These findings my help to more specifically tailor the treatment of depressed patients.
•First study investigating the course of depressive symptoms during inpatient antidepressant treatment in different age groups•Older patients (50-65 yrs.) more often suffered from recurrent MDD, comorbid physical disorders and neuro-vegetative symptoms.•Younger patients (18 -29 yrs.) more often suffered from comorbid drug abuse and personality disorders and more often reported of cognitive symptoms.•Symptoms such as interpersonal sensitivity in young patients and low interest in sex in older patients persisted until the end of treatment.•The findings my help to more specifically tailor the treatment of depressed patients.
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