Alexandra Bettina Graf

Alexandra Bettina Graf
FH Campus Wien · Bioinformatics

PhD

About

58
Publications
17,977
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1,477
Citations
Citations since 2016
8 Research Items
927 Citations
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
Introduction
Alexandra Graf currently works at the Bioinformatics, FH Campus Wien. Their current research interest is urban metagenomics, de-novo assembly, annotation and comparative genomics of microorganisms as well as transcriptome analysis.

Publications

Publications (58)
Article
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic...
Preprint
Full-text available
Advancements in DNA methods and biotechnology have enabled forensic scientists to explore the DNA evidence found as part of a criminal investigation on a much more comprehensive and predictive level. This has led to a rise in research into DNA intelligence tools such as phenotypic prediction (i.e., eye and hair colour) and inference of biogeographi...
Preprint
Full-text available
Although studies have shown that urban environments and mass-transit systems have geospatially distinct metagenomes, no study has ever systematically studied these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit syste...
Article
Full-text available
Background: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in sili...
Article
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Background Pichia pastoris is a widely used eukaryotic expression host for recombinant protein production. Adaptive laboratory evolution (ALE) has been applied in a wide range of studies in order to improve strains for biotechnological purposes. In this context, the impact of long-term carbon source adaptation in P. pastoris has not been addressed...
Article
As manually curated and non-automated BLAST analysis of the published Pichia pastoris genome sequences revealed many differences between the gene annotations of the strains GS115 and CBS7435, RNA-Seq analysis, supported by proteomics, was performed to improve the genome annotation. Detailed analysis of sequence alignment and protein domain predicti...
Article
Full-text available
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning...
Article
Full-text available
The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the prese...
Article
Full-text available
Background Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledg...
Article
Full-text available
Oxidative folding of secretory proteins in the endoplasmic reticulum (ER) is a redox active process, which also impacts the redox conditions in the cytosol. As the transcription factor Yap1 is involved in the transcriptional response to oxidative stress, we investigate its role upon the production of secretory proteins, using the yeast Pichia pasto...
Article
Full-text available
MicroRNAs are short non-coding RNAs that play an important role in the regulation of gene expression. Hence, microRNAs are considered as potential targets for engineering of Chinese hamster ovary (CHO) cells to improve recombinant protein production. Here, we analyzed and compared the microRNA expression patterns of high, low, and non-producing rec...
Article
Full-text available
Protein production in yeasts is related to the specific growth rate μ. To elucidate on this correlation, we studied the transcriptome of Pichia pastoris at different specific growth rates by cultivating a strain secreting human serum albumin at μ = 0.015 h(-1) to 0.15 h(-1) in glucose-limited chemostats. Genome-wide regulation revealed that transla...
Article
Chinese hamster ovary (CHO) cells are currently the most important mammalian host for the manufacture of biopharmaceuticals. To enhance our understanding of cellular processes, pathways, and the genetic setup of CHO cell lines, we predicted PIWI interacting RNAs (piRNAs) from small RNA sequencing data. Although piRNAs are the least understood class...
Article
Chinese hamster ovary (CHO) cells are currently the most important mammalian host for the manufacture of biopharmaceuticals. To enhance our understanding of cellular processes, pathways, and the genetic setup of CHO cell lines, we predicted PIWI interacting RNAs (piRNAs) from small RNA sequencing data. Although piRNAs are the least understood class...
Article
Protein secretion is an essential process for living organisms. In eukaryotes this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle mediated secretion are similar from yeasts to hig...
Poster
Chinese Hamster Ovary Cells (CHO) are used as an important mammalian cell factory for therapeutic proteins since 1987 [1]. In 2011 the transcriptome and the genome of CHO were published [1], [2]. Because Mus musculus is a near relative of Chinese Hamster (Cricetulus griseus) its sequence was used as a substitute in CHO microarray experiments until...
Article
Full-text available
Megasphaera elsdenii is a Gram-negative ruminal bacterium. It is being investigated as a probiotic supplement for ruminants as it may provide benefits for energy balance and animal productivity. Furthermore, it is of biotechnological interest due to its capability of producing various volatile fatty acids. Here we report the complete genome sequenc...
Data
MATLAB implementation of the kinetic model. Time courses of the intracellular and extracellular labeled Fab concentrations after start of labeling are modeled dependent of the kinetic parameters of protein formation, degradation and secretion. Continuous cultivation (constant YDM and dilution rate) are prerequisits for numerically solving the diffe...
Data
Sensitivity analysis of the kinetic parameters. At a time two of the parameters, namely degradation, secretion and intracellular protein formation are varied against each other to determine the effect on extracellular Fab3H6 concentrations. Three dimensional plots are automatically created using the MATLAB functions meshgrid and surf.
Article
Full-text available
The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein formation, degradation and secretion defines...
Article
Full-text available
Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins. Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, thus mimicking not only perturbations and adaptations which occur in their n...
Data
List of orthologues. List of the orthologues (2891 gene IDs) between S. cerevisiae and P. pastoris used for the direct comparison of the results of the transcriptional analysis. Orthology was determined using a reciprocal best hit strategy based on protein BLASTs (E-value cut-off < 10-5 and filtering for at least one high scoring segment > 50 amino...
Data
qRT-PCR primer sequences used in this study. Table showing the primer sequences of the genes analyzed by qRT-PCR and characteristics of the corresponding amplicons. Calculated copy numbers and the dilution factors in order to obtain 109 copies μl-1 are indicated (see main text for explanation).
Data
Identified protein spots. List of the 45 identified proteins with different abundances comparing hypoxic (8) and normoxic (21) conditions in the P. pastoris expressing and control strain. Proteins were identified by MALDI-TOF MS and grouped into 6 different biological processes. The protein name, short name and accession number, theoretical Mw and...
Data
Metabolic fluxes Metabolic fluxes in the central carbon metabolism of P. pastoris Fab-producing and control strain in glucose-limited chemostats at a D = 0.1 h-1 in different oxygenation conditions. The standard deviations of each net flux are given.
Data
Stoichiometric model of the central carbon metabolism of P. pastoris. Reactions in the stoichiometric model of the central carbon metabolism of P. pastoris applied in the 13C-MFA determination of the metabolic fluxes under different oxygenation conditions; it also includes anabolic reactions from metabolic intermediates to biosynthesis, transport r...
Data
MetaCyc Data Saccharomyces cerevisiae. Regulated S. cerevisiae pathways in hypoxia vs. normoxia. Individual S. cerevisiae (recombinant strain) pathways that were transcriptionally regulated (i e. exceeding the log2 FC threshold of 0.59) in the comparison hypoxic vs. normoxic conditions, as resulting from the MetaCyc analysis presented in Figure 3 h...
Data
Relative abundances of intact carbon fragments in proteinogenic amino acids. Relative abundances of intact C2 and C3 fragments (f-values) in proteinogenic amino acids describing the conservation of carbon chain fragments in P. pastoris Fab-producing and control strains growing in glucose-limited chemostats at a D = 0.1 h-1 in different oxygenation...
Data
Metabolic network model of the central carbon metabolism of P. pastoris. Bioreaction network model of the central carbon metabolism of P. pastoris used in the 13C-metabolic flux analysis for the determination of net fluxes under the different oxygenation conditions. Fluxes are represented as net fluxes and the directions of the arrows indicate the...
Article
Full-text available
Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pich...
Article
The methylotrophic yeast Pichia pastoris has gained much attention during the last decade as a platform for producing heterologous recombinant proteins of pharmaceutical importance, due to its ability to reproduce post-translational modification similar to higher eukaryotes. With the recent release of the full genome sequence for P. pastoris, in-de...
Data
Full-text available
Fisher's exact test of the up/down regulated gene groups upon DTT treatment and HAC1 overexpression. Fisher's exact test was applied to test significance of the up- and downregulated gene groups displayed in figure 4. padj values are given for each GO group. Legend of headers: group – Gene Ontology term; Description – Gene Ontology description; odd...
Data
Fold-change and one-way ANOVA data for all contrasts of the 2D-DIGE experiment. contains 2D-DIGE data of all comparisons (low to medium, low to high and medium to high) of both strains. Tables contain protein master numbers, short protein names, protein descriptions, fold-changes and corresponding one-way ANOVA values as described for Table 2.
Data
Differences between the non-expressing wt strain and the Fab 3H6 expressing strain of P. pastoris at low osmolarity at the transcript level. contains microarray data on the gene expression differences between the two strains. Spreadsheet 1 contains microarray data for differentially regulated genes (p-value ≤ 0.001). Spreadsheet 2 contains results...
Data
Determination of intracellular polyol and trehalose content in P. pastoris upon growth at different osmolarities. contains data on methodology of HPLC measurements, retention times of analytes and analyte concentrations with corresponding standard errors of the mean.
Data
Differential expression values of all annotated genes upon DTT treatment and HAC1 overexpression. Differential expression values and adjusted p-values of all annotated genes of P. pastoris, denominated with the gene name of their respective S. cerevisiae homolog. Genes that were tested with TRAC as a different method for transcript quantification a...
Data
Full-text available
Quality of microarray experiments and statistical test for osmolarity experiments. contains supplemental data on microarray analysis: Signal intensity plots, correlation of intensities, standard deviations and variations of the microarray experiment. Additionally, results of Hierarchical Cluster Analysis (HCA), Gene Set Analysis (GSA) and Fisher's...
Data
Microarray results of interesting genes. contains gene expression results of interesting genes, which are described and discussed in the manuscript.
Article
Full-text available
The effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on re...
Article
Full-text available
The first genome sequences of the important yeast protein production host Pichia pastoris have been released into the public domain this spring. In order to provide the scientific community easy and versatile access to the sequence, two web-sites have been installed as a resource for genomic sequence, gene and protein information for P. pastoris: A...
Article
Background: Pichia pastoris is widely used as a production platform for heterologous proteins and model organism for organelle proliferation. Without a published genome sequence available, strain and process development relied mainly on analogies to other, well studied yeasts like Saccharomyces cerevisiae.
Article
Full-text available
Pichia pastoris is widely used as a production platform for heterologous proteins and model organism for organelle proliferation. Without a published genome sequence available, strain and process development relied mainly on analogies to other, well studied yeasts like Saccharomyces cerevisiae. To investigate specific features of growth and protein...
Data
Summary of identified proteins. List of mass spectrometry identified proteins on both 1D and 2D gels, including protein scores and all individual peptides with corresponding peptide scores.
Article
Systems biotechnology has been established as a highly potent tool for bioprocess development in recent years. The applicability to complex metabolic processes such as protein synthesis and secretion, however, is still in its infancy. While yeasts are frequently applied for heterologous protein production, more progress in this field has been achie...
Article
Full-text available
While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora....
Article
Full-text available
DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely...

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Projects (4)