Plaque deposition and microglia response under the influence of hypoxia in a murine model of Alzheimer\'s disease

Clinical findings have linked multiple risk factors and associated pathologies to Alzheimer\''s disease (AD). Amongst them are vascular risk factors such as hypertension and pathologies such as stroke. Coexistence of AD and these associated pathologies worsenes dementia, the clinical hallmark of the disease, as compared to pure AD. One general common denominator of these associated pathologies is the presence of hypoxic tissue conditions. It was asked the question, whether there exists a mutual, causal interaction between hypoxia and AD pathology, that could explain the clinical observations. Alternatively, the worsened clinical state of multiple brain pathologies could \"simply\" be the consequence of multimorbidity, i.e. accumulated disease load, without any causal interaction between the constituents. To approach this question whether hypoxia influences AD progression, use was made of a murine animal model of AD (transgenic mice: APPswe, PSEN1dE). Animals of two ages (8 and 14 months, \"young\" and \"old\" respectively) and two genotypes (transgenic and wild- type) were either treated under hypoxia or normoxia, corresponding to 8% and 21% oxygen, for 20 consecutive days. The resulting changes in the brain were assessed with a variety of techniques, namely by histology, ELISA, dot and Western blotting. Additional experiments in primary cell cultures were performed. Animals exposed to hypoxia showed an increased hematocrit (HCT), weight loss, reactive angiogenesis, but no infarctions. This illustrates that our hypoxic treatment put significant stress on the animals, without causing major pathologies. A large number of variables exists that could potentially be measured to assess the effect of hypoxia on AD. The focus was put on three of them: First, there is the Abeta1-42- protein, known to be the Abeta- isoform associated with the most detrimental disease progression. In AD, the self-combinatory Amyloid- beta peptide (Abeta) accumulates in the brain in so- called plaques, which is a main histologic finding of the disease. Its quantity was determined through histology and ELISA. Secondly, it was attempted to estimate the structural quality of the Abeta- protein by assessing the amount of A!- oligomers present. Abeta- protein does self- accumulate in various grades of complexity, i.e. as monomer, oligomer or fibril. Since oligomers are known to be the most neurotoxic \"species\" of the Abeta- protein, it was hypothesized that under hypoxic treatment their quantity could increase. And third, the organism\''s response to the Abeta- protein stimulus was investigated. Microglial cells have been described as the first cells to encounter the Abeta- protein \"threat\" in the shape of plaques, i.e. Abeta- protein aggregates. They then try to encapsulate and subsequently degrade them. Therefore, the attention was put on this cellular population. It was asked whether hypoxia could change the Abeta- protein quantity in the brain. This was assessed in two ways: First histologically, by staining for Abeta- protein depositions and quantifying them. Second, an ELISA was performed. Our findings state that hypoxic treatment does not alter the Abeta1-42 protein load in the brain, neither in young nor old animals, as assessed by histology and by total ELISA quantification of Abeta1-42 protein. Since hypoxia did not alter the quantity of the Abeta- protein, it was asked whether it influenced it qualitatively? If hypoxia increased oligomer formation, this change in the spectrum of the Abeta- species could, without any change in total Abeta- protein load, lead to increased neurotoxicity in animals under hypoxia. Initial experiments showed that oligomer formation in the brain seems to increase. However, this was not statistically significant and future experiments are necessary to evaluate this hypothesis further. It was then asked, whether hypoxia alters the cellular response to the protein. The total number of microglia in the hippocampal dentate gyrus, our structure of interest for practical purposes, and, it can be argued, by extension the brain, changes dynamically with various factors. First, transgenic animals present an increase in microglia. Second, microglia increase with age. Third, microglia decrease under hypoxia, but only do so significantly in old animals. Next, a parameter called \"plaque occupancy\" was coined to assess the microglia function to confront Abeta- plaques. Plaque occupancy is defined as the number of microglia in spatial proximity to one square millimeter of Abeta- plaque. This means, that microglia restricting one plaque are counted, and then normalized to this plaque\''s area. It was hypothesized that hypoxia would decrease plaque occupancy. Indeed, plaque occupancy roughly halved under hypoxia. Summarizing, our results demonstrate that long- term exposure to hypoxia significantly reduces the number of microglia. The reduced number results in significantly reduced plaque occupancy and compromizes the function of microglia to confront Abeta- plaques. The Abeta1-42 load, however, is not affected. On the other hand, Abeta shows an increased trend towards oligomer formation. A variety of possible explanations to these phenomena have been presented, that in our opinion deserve further investigation

Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.Peer Reviewe

What the Phage: a scalable workflow for the identification and analysis of phage sequences

Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage)

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes

BackgroundLipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different timepoints of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation.ResultsWe observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in beta-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2-glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD(+)-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed.ConclusionsWe suspect that the physiological reason for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy

Assessing genetic diversity and similarity of 435 KPC-carrying plasmids.

Brandt C, Viehweger A, Singh A, et al. Assessing genetic diversity and similarity of 435 KPC-carrying plasmids. Scientific reports. 2019;9(1): 11223.The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over the last decade in the health care setting. blaKPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes

Chronic hypoxia aggravates Alzheimer’s disease pathology by causing microglial dysfunction

Trabajo presentado en el XXXVII Congreso de la Sociedad Española de Bioquímica y Biología Molecular (SEBBM), celbrado en Granada del 9 al 12 de septiembre de 2014.Alzheimer’s disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia. In many cases AD patients present concomitant vascular pathology. Low oxygen levels are also frequently found in the brain of AD patients. The most accepted hypothesis to explain the correlation between hypoxia and AD is the deposition of amyloid ß (Aß) occurring in the microvasculature (amyloid angiopathy) and the affectation by the disease of the locus coeruleus, a brain region involved in the control of brain blood flow. However, few data has been collected to understand the relation between hypoxia and AD progression. We show here the accumulation of the hypoxic marker HIF1 α (Hypoxia-inducible-factor 1α), the major transcription factor for the adaptation to hypoxic conditions, in the brain of AD patients by western blot. We have also characterized the consequences of chronic exposition to hypoxia in the progression of the disease using a widely accepted AD mice model. AD mice were exposed to physiologic hypoxia (8.5% oxygen, 21 days) at initial and advances stages of the pathology. Brains from hypoxic animals showed no differences in the Aß content and number of plaques, but they showed a clear reduction in the total number of microglial cells that was even more evident around the Aß plaques. In vitro analyses suggest that hypoxia slows down proliferation and chemotaxis towards polymeric Aß in both cell line and primary microglial cultures. Interestingly, the brain cortex from the hypoxic animals showed a high increase in the number of dystrophic neurites surrounding the microglia- free Aß plaques. We observed also a decrease in the mRNA levels of two markers of interneurons, Somatostatin and Neuropeptide-Y, in the hippocampus of hypoxic mice. These data suggest that hypoxia accelerates the progression of AD pathology. The pathway underlying microglial affectation by hypoxia has an enormous potential in neurodegenerative disorders where microglia function is correlated with the progression of the disease.N

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available

Systemic and Local Hypoxia Synergize Through HIF1 to Compromise the Mitochondrial Metabolism of Alzheimer's Disease Microglia

Microglial cells are key contributors to Alzheimer’s disease (AD), constituting the first cellular line against Aß plaques. Local hypoxia and hypoperfusion, which are typically present in peripheral inflammatory foci, are also common in the AD brain. We describe here that Aß deposits are hypoxic and hypoperfused and that Aß plaque-associated microglia (AßAM) are characterized by the expression of hypoxia-inducible factor 1 (HIF1)-regulated genes. Notably, AßAM simultaneously upregulate the expression of genes involved in anaerobic glycolysis and oxidative mitochondrial metabolism, show elongated mitochondria surrounded by rough endoplasmic reticulum, and blunt the HIF1-mediated exclusion of pyruvate from the mitochondria through the pyruvate dehydrogenase kinase 1 (PDK1). Overstabilization of HIF1 –by genetic (von Hippel-Lindau deficient microglia) or systemic hypoxia (an AD risk factor)– induces PDK1 in microglia and reduces microglial clustering in AD mouse models. The human AD brain exhibits increased HIF1 activity and a hypoxic brain area shows reduced microglial clustering. The loss of the microglial barrier associates with augmented Aß neuropathology both in the chronic hypoxia AD mouse model and the human AD brain. Thus, the synergy between local and systemic AD risk factors converges with genetic susceptibility to cause microglial dysfunction.Peer reviewe

Hypoxia compromises the mitochondrial metabolism of Alzheimer’s disease microglia via HIF1

Genetic Alzheimer’s disease (AD) risk factors associate with reduced defensive amyloid β plaque-associated microglia (AβAM), but the contribution of modifiable AD risk factors to microglial dysfunction is unknown. In AD mouse models, we observe concomitant activation of the hypoxia-inducible factor 1 (HIF1) pathway and transcription of mitochondrial-related genes in AβAM, and elongation of mitochondria, a cellular response to maintain aerobic respiration under low nutrient and oxygen conditions. Overactivation of HIF1 induces microglial quiescence in cellulo, with lower mitochondrial respiration and proliferation. In vivo, overstabilization of HIF1, either genetically or by exposure to systemic hypoxia, reduces AβAM clustering and proliferation and increases Aβ neuropathology. In the human AD hippocampus, upregulation of HIF1α and HIF1 target genes correlates with reduced Aβ plaque microglial coverage and an increase of Aβ plaque-associated neuropathology. Thus, hypoxia (a modifiable AD risk factor) hijacks microglial mitochondrial metabolism and converges with genetic susceptibility to cause AD microglial dysfunction.R.M.-D. was the recipient of a Sara Borrell fellowship from Instituto de Salud Carlos III (ISCIII) (CD09/0007). N.L.-U., C.O.-d.S.L., C.R.-M. and M.I.A.-V. were the recipients of FPU fellowships from Spanish Ministry of Education, Culture and Sport (FPU14/02115, AP2010‐1598, FPU16/02050 and FPU15/02898, respectively). A.H.-G. was the recipient of an FPI fellowship from the Spanish Ministry of Education, Culture and Sport (BES-2010-033886). This work was supported by grants from the Spanish MINEICO, ISCIII and FEDER (European Union) (SAF2012‐33816, SAF2015‐64111‐R, SAF2017-90794-REDT and PIE13/0004 to A.P.); by the Regional Government of Andalusia co-funded by CEC and FEDER funds (European Union) (‘Proyectos de Excelencia’; P12‐CTS‐2138 and P12‐CTS‐2232 to A.P.); by the ‘Ayuda de Biomedicina 2018’, Fundación Domingo Martínez (to A.P.) ; by the ISCIII of Spain, co-financed by FEDER funds (European Union) through grants PI18/01556 (to J.V.) and PI18/01557 (to A. Gutierrez); by Junta de Andalucía, co-financed by FEDER funds (grants UMA18-FEDERJA-211 (to A. Gutierrez) and US‐1262734 (to J.V.)); and by Spanish MINEICO (BFU2016-76872-R and BES-2011-047721 to E.B.).Peer reviewe