Pieter Borger

Pieter Borger
W+W Research Association

MSc, PhD
Currently, I am assessing the hypothesis that transposable elements can mutate into (retro)viruses in only a few steps.

About

109
Publications
331,609
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
2,331
Citations
Introduction
PB (MSc Biology, PhD Medical Sciences) worked for several research institutes, incl. the University of Groningen (Netherlands), the University of Sydney (Australia), the University of Basel and Zurich (Switzerland). An expert on molecular biology of gene expression and signal transduction networks, PB published over 70 articles in leading international journals, including the New Eng. J. Med. Currently, PB works on the non-protein coding part of the genome and how it is involved in generating variation and speciation.
Additional affiliations
October 2019 - present
Wort & Wissen Studiengemeinschaft
Position
  • Research Officer
January 2015 - October 2019
University of Zurich
Position
  • Groupleader
January 2004 - December 2014
University of Basel
Position
  • Project Manager

Publications

Publications (109)
Article
Full-text available
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Article
Full-text available
In the scientific community, but also among non-scientists, there is a belief that with current biological knowledge it must be possible to design a living dividing cell. This school of thought believed they can design a dividing cell from scratch, that it would take 200-300 genes--maybe even less. The Craig J Venter Institute studies now show that...
Article
Full-text available
Recently, Andreas Beyer published an article on the german evangelical platform EZW with the title „Radikalisiert sich „Wort und Wissen“ [1]. It is clear that this article is the latest of a series of rants Beyer started in January 2021, after ICLSS published their critique on the RT-qPCR test [2]. Andreas Beyer falsely believes that ICLSS, an inte...
Article
Full-text available
LINE1 retrotransposons, which are thought to be the remnants of ancient integrations of retrovirus-like elements, are aberrantly (re)activated in many cancer cells. Due to LINE1-induced alterations in target gene expression and/or chromosomal rearrangements, they may be important drivers of tumorigenesis. Moreover, LINE1 encoded proteins, Open Read...
Preprint
Full-text available
If you really need a vaccine it is important to know how they work and what the potential adverse effects might be. This pre-print briefly discusses this for DNA- and RNA vaccines currently administered to major part of the human population. An earlier version of this pre-print was dishonestly discussed by Dr. Andreas Beyer who claimed two referen...
Article
Full-text available
The sequence of the 3 billion DNA letters of the entire human genome was published in 2001 after more than ten years of intensive work. But what information and thus functions do these sequences contain? The decoding of the functional elements of the human genome by ENCODE has changed the view of the human genome enormously. It turns out to be an a...
Article
Full-text available
After publication of our Corman-Drosten Critique, a small group of dyed-in-the-whool Darwinians gathered around Dr. Andreas Beyer, germany´s most vocal defender of the Darwinian narrative (the most tested and failed hypothesis of biology). Why did Beyer include them? They are not PCR experts at all, so what could the reason be? It appears that the...
Article
Full-text available
Nick Lane is a British biochemist and professor of evolutionary biochemistry at University College London, UK. With his book "The Vital Question" Lane seeks to offer a new perspective on the evolutionary history of life and devises solutions to some of the unexplained mysteries of evolution that have puzzled scientists for decades. His answer to th...
Article
Full-text available
Als u een vaccin nodig heeft, is het belangrijk te weten wat de verschillende soorten zijn, hoe ze werken en welke mogelijke gevaren er kunnen bestaan.
Negative Results
Full-text available
When an article—or essay—commences with several unsubstantiated statements it should be read with caution, because we might not be dealing with a scientific paper. Rather, such articles are written for personal goals or gains, or simply to stir up public opinion. The article by Dr Andreas Beyer, indisputably the most vocal defender of Drosten´s PCR...
Article
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Article
Full-text available
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Preprint
Full-text available
Background:: After submitting our review report on Corman et al. (referred hereinafter as CD-report) and republishing it on a scientific preprint server (http://doi.org/10.5281/zenodo.4298004) and Researchgate.net we offered the report for public discussion at cormandrostenreview.com on 27th November 2020. The scientific community provided addition...
Preprint
Full-text available
After submitting our review report on Corman et al. (referred hereinafter as CD-report) andrepublishing it on a scientific preprint server [50] and Researchgate.net [51] we offered thereport for public discussion at cormandrostenreview.com on 27th November 2020. Thescientific community provided additional literature, references, and analyses concer...
Article
Full-text available
The genetic code as we find it in nature—the canonical code—has been shown to be highly optimal according to various criteria. It is commonly believed the genetic code was optimised during the course of an evolutionary process (for various purposes). We evaluate this claim and find it wanting. We identify difficulties related to the three families...
Article
Full-text available
In 1970, Susumo Ohno proposed gene and genome duplications as the principal forces that drove the increasing complexity during the evolution from microbes to microbiologists.1 Today, evolutionists assume duplication followed by neo-functionalization is the major source of new genes. Since life is claimed to have started simple and evolved new funct...
Article
Full-text available
In the standard genetic code, 64 codons map to 20 amino acids and a stop signal. The particular assignments show clear evidence that the coding convention used protects against the deleterious effects of mutations. Evolutionists believe the standard code went through multiple refining stages preceding the Last Universal Common Ancestor (LUCA). Vari...
Preprint
Full-text available
This extensive review report has been officially submitted to Eurosurveillance editorial board on 27th November 2020 via their submission-portal, enclosed to this review report is a retraction request letter, signed by all the main & co-authors. First and last listed names are the first and second main authors. All names in between are co-authors....
Article
Full-text available
Background: bladder cancer is one of the most common urinary tract malignancies. Establishment of robust predictors of disease progression and outcome is important for personalizing treatment of non-muscular invasive bladder carcinoma (NMIBC). In this study we evaluated association of PD-L1 expression with other prognostic biomarkers, such as expr...
Article
Full-text available
Heterostyly is a fascinating feature of the flowers of a variety of plant families. It both helps to promote sexual reproduction and prevents inbreeding. In the most common form of heterostyly, plants develop either flowers with a short style and long stamens or with a long style and short stamens. The fact that in nature only plants with either of...
Article
Full-text available
Despite numerous studies addressing normal liver regeneration, we still lack comprehensive understanding of the biological processes underlying failed liver regeneration. Therefore, we analyzed the activity of 271 intracellular signaling pathways (ISPs) by genome wide profiling of differentially expressed RNAs in murine liver tissue biopsies after...
Article
Full-text available
It was common knowledge that some strain of coronavirus-sooner or later-was going to cause a pandemic. It was known since the SARS-CoV-outbreak in 2003. In 2013 and 2015, the world was informed that a variant of SARS-CoV in bats was emerging as a threat for humans. Why was no action taken by our governments and the World Health Organization (WHO)?...
Article
Full-text available
Transposable and Transposed Elements are an integral part of all higher genomes and were long regarded junk DNA. It was--and still is--believed they were they are remnants of ancient virus invasions. In the light of current knowledge this vision is untenable. In this perspective a few recent insight on the functions of Lines and ERVs are reported....
Thesis
Full-text available
Science and dogmatic ideology don’t go very well together. Two biological concepts, "Junk DNA" "pseudogenes" were derived from the darwinian philosophy and have been taught as dogmas for over 40 years. A recent article in Nature argued that the old darwinian idea that pseudogenes are functionless is clearly false. There is now ample evidence--and m...
Article
Full-text available
Background and Aims: ALPPS (associating liver partition and portal vein ligation for staged hepatectomy), a novel 2-staged hepatectomy, dramatically accelerates liver regeneration and thus enables extensive liver tumor resection. The signaling networks underlying the ALPPS-induced accelerated regeneration process are largely unknown. Methods: We pe...
Article
Full-text available
In the article ‘Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution,’ a number of transcription factor binding sites (TFBS) mapped on all retroelement classes were incorrectly calculated as sum of TFBS numbers separately mapped on LINEs, SINEs and LTR retrotransposons/endogenou...
Article
Full-text available
Background: Intracellular molecular pathways (IMPs) control all major events in the living cell. They are considered hotspots in contemporary oncology because knowledge of IMPs activation is essential for understanding mechanisms of molecular pathogenesis in oncology. Profiling IMPs requires RNA-seq data for tumors and for a collection of reference...
Article
e13143 Background: Anticancer Targeted Drugs (ATDs) specifically target one or a few types of tumor-related molecules in a cell. More than two hundred of ATDs were approved worldwide. They have different mechanisms of action and are effective for different cohorts of patients. However, many individual cases remain poorly responsive and it is of gre...
Article
Full-text available
Background: Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulation evolution. This approach allows for interrogating the regulatory evolution of organisms with RE-...
Article
Full-text available
Despite the significant achievements in chemotherapy, cancer remains one of the leading causes of death. Target therapy revolutionized this field, but efficiencies of target drugs show dramatic variation among individual patients. Personalization of target therapies remains, therefore, a challenge in oncology. Here, we proposed molecular pathway-ba...
Data
The complete clinical status information for 128 target drugs in eight cancer localizations.
Data
Mutation profiles for 3800 TCGA tumor samples obtained from COSMIC v76.
Data
Mutation drug scores for 3800 TCGA tumor samples for 10 versions of drug scoring algorithm. The dataset contains 10 tables that match the 10 methods of drug scoring.
Data
Normalized mutation rate for genes that mutated in 18273 tumor samples from COSMIC v76.
Data
Mutation Drug Scores for 8736 virtual drugs specific to the same number of genes.
Article
Full-text available
Citation: Miglino N, Tamm M, Borger (2018) Fast Up-regulation of The LINE-1 ORF2 Proteins in Pulmonary Cells after Exposure to Cigarette Smoke. J Pulm Respir Med 8: 454.
Article
Full-text available
In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because...
Article
Full-text available
Humans have 2x23 chromosomes, modern apes 2x24. The human chromosome 2 (Chr2) is typically interpreted as the result of a fusion, involving two smaller chromosomes that still occur separately in great apes. A similar banding pattern between human Chr2 and chimpanzee chromosomes Chr2A and Chr2B, as well as a sequence segment that is thought to be a...
Article
Background: Temporary portal vein embolization may be a safe alternative to permanent portal vein embolization. Such a new approach could be applied in living-related liver transplantation to increase graft volume before procurement. The impact of temporary portal vein embolization on occluded liver after recanalization, however, has never been as...
Article
Background & Aims ALPPS, a novel two-staged approach for the surgical removal of large/multiple liver tumors, combines portal vein ligation (PVL) with parenchymal transection. This causes acceleration of compensatory liver growth, enabling faster and more extensive tumor removal. We sought to identify the plasma factors thought to mediate the regen...
Article
Full-text available
Background: Bronchial smooth muscle (BSM) cells from asthmatic patients maintain in vitro a distinct hyper-reactive ("primed") phenotype, characterized by increased release of pro-inflammatory factors and mediators, as well as hyperplasia and/or hypertrophy. This "primed" phenotype helps to understand pathogenesis of asthma, as changes in BSM func...
Article
Full-text available
Aberrant expression of small noncoding RNAs (sncRNAs), microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) in particular, define several pathologic processes. Asthma is characterized by airway hyperreactivity, chronic inflammation, and airway wall remodeling. Asthma-specific miRNA profiles were reported for bronchial epithelial cells, whereas snc...
Article
Full-text available
Asthma affects more than 300 million people worldwide and its prevalence is still rising. Acute asthma attacks are characterized by severe symptoms such as breathlessness, wheezing, tightness of the chest, and coughing, which may lead to hospitalization or death. Besides the acute symptoms, asthma is characterized by persistent airway inflammation...
Article
Full-text available
Background. Bronchial smooth muscle cells (BSMC) are a major source of proinflammatory and proangiogenic cytokines and chemokines, including VEGF and CXC-chemokines. CXC-chemokines act primarily on neutrophils, mediating their recruitment to and activation at the site of inflammation. In humans, house-dust mite (HDM) allergens can cause asthmatic e...
Article
Full-text available
For oxygen supply, airway wall cells depend on diffusion though the basement membrane, as well as on delivery by micro-vessels. In the asthmatic lung, local hypoxic conditions may occur due to increased thickness and altered composition of the basement membrane, as well as due to edema of the inflamed airway wall. In our study we investigated the e...
Article
Full-text available
Airway wall remodelling is a key pathology of asthma. It includes thickening of the airway wall, hypertrophy and hyperplasia of bronchial smooth muscle cells (BSMC), as well as an increased vascularity of the sub-epithelial cell layer. BSMC are known to be the effector cells of bronchoconstriction, but they are increasingly recognized as an importa...
Article
Full-text available
Background Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving functional information from a s...
Article
Full-text available
Transforming growth factor β (TGF-β), a key mediator of fibrotic responses, is increased in asthma and drives airway remodeling by inducing expression of extracellular matrix (ECM) proteins. We investigated the molecular mechanisms underlying TGF-β-induced ECM expression by airway smooth muscle cells and demonstrate a novel link between TGF-β and W...
Article
Full-text available
Background Airway wall remodelling is a key pathology of asthma. It includes thickening of the airway wall, hypertrophy and hyperplasia of bronchial smooth muscle cells (BSMC), as well as an increased vascularity of the sub-epithelial cell layer. BSMC are known to be the effector cells of bronchoconstriction, but they are increasingly recognized as...
Article
Full-text available
Asthma is a complex disease characterised by inflammation and remodelling of the airways. Over the past few decades enormous progress has been made to understand which genes are associated with asthma development and several interactions between genes and environmental factors have been elucidated. Investigations into genetic and gene expression pr...
Article
Full-text available
Asthma is a highly complex disease, involving both environmental factors and genetics. The origin and aetiology of asthma remain elusive. Dr Pieter Borger hypothesises that variation in transposable elements that act as genetic switches (promoter/enhancers) present in asthma susceptibility genes may be the genetic component of asthma.
Article
Full-text available
Asthma and chronic obstructive pulmonary disease (COPD) are the two most prominent chronic inflammatory lung diseases with increasing prevalence. Both diseases are associated with mild or severe remodeling of the airways. In this review, we postulate that the pathologies of asthma and COPD may result from inadequate responses and/or a deregulated b...
Article
Full-text available
Background. Calreticulin controls the C/EBPαp42/p30 at the translational level trough a cis-regulatory CNG rich loop in the CEBPA mRNA. We determined the effects of steroids and long-acting beta-agonists on the p42/p30 ratio and on calreticulin expression in primary human bronchial smooth muscle (BSM) cells. Methods. The effects of budesonide (10(-...
Article
Full-text available
Cigarette smoke is a major cause of chronic obstructive pulmonary disease (COPD) and emphysema. Although cigarette smoke represses cellular proliferation, the molecular mechanisms underlying this phenomenon are unknown. CCAAT/enhancer-binding proteins (C/EBPs) are key regulators of cell cycle progression, differentiation and pro-inflammatory gene e...
Article
Full-text available
Reduced translation of CEBPA mRNA has been associated with increased proliferation of bronchial smooth muscle (BSM) cells of asthma patients. Here, we assessed the effect of house dust mite (HDM) extracts on the cell proliferation ([(3)H]-thymidine incorporation), inflammation (interleukin (IL)-6 release) and upstream translation regulatory protein...
Article
Full-text available
Mutations are a fact of life. Darwin gave mutations, which he called natural variation between individuals, a key role to explain the origin of species. The origin and nature of mutations is one of the most fundamental questions of biology, and are a hot topic in origin debates. If mutations are merely a matter of chance, then the alignment of muta...
Thesis
Full-text available
In 2001, molecular biologist Dr. Peter Borger left for a study trip to Australia. The journey that followed was unexpected. Not only did it change his life, but it also fundamentally changed his view of biology. He discovered that living systems are very differently from what he was taught in the academia. Biology is very different from what Darwin...
Article
Full-text available
Rationale: Inflammation, increased fibroblast proliferation, and increased deposition of extracellular matrix (ECM) are hallmarks of early lung fibrosis and asthma. Transforming growth factor-(TGF-) has been suggested as a key regulator of lung tissue homeostasis with several and often opposite effects on fibroblast proliferation and ECM production...
Article
Full-text available
Bronchial smooth muscle (BSM) cells of asthmatic patients have an impaired expression of CCAAT/enhancer binding protein (C/EBP) alpha, which is associated with increased proliferation. We sought to assess the translational regulation of CEBPA mRNA in cultured BSM cells of healthy control subjects (n = 11) and asthmatic patients (n = 12). Translatio...
Article
Full-text available
The major difference between the evolution and creation paradigms is that the evolutionist believes that the natural variation found in populations can explain microbe-to-man evolution via natural selection (Darwinism), while the creationist believes it cannot. This is because the evolutionary, naturalistic framework requires something creationists...
Article
Full-text available
Knockout strategies have demonstrated that the function of many genes cannot be studied by disrupting them in model organisms because the inactivation of these genes does not lead to a phenotypic effect. For living systems, this peculiar phenomenon of genetic redundancy seems to be the rule rather than the exception. Genetic redundancy is now defin...