Evolution of a Core Gene Network for Skeletogenesis in Chordates

The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB) and from dogfish as representative of jawed cartilaginous fish (ScRunx1–3). According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets) Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view that teeth and placoid scales evolved from a homologous developmental module

Response of Methicillin-Resistant Staphylococcus aureus to Amicoumacin A

Amicoumacin A exhibits strong antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), hence we sought to uncover its mechanism of action. Genome-wide transcriptome analysis of S. aureus COL in response to amicoumacin A showed alteration in transcription of genes specifying several cellular processes including cell envelope turnover, cross-membrane transport, virulence, metabolism, and general stress response. The most highly induced gene was lrgA, encoding an antiholin-like product, which is induced in cells undergoing a collapse of Δψ. Consistent with the notion that LrgA modulates murein hydrolase activity, COL grown in the presence of amicoumacin A showed reduced autolysis, which was primarily caused by lower hydrolase activity. To gain further insight into the mechanism of action of amicoumacin A, a whole genome comparison of wild-type COL and amicoumacin A-resistant mutants isolated by a serial passage method was carried out. Single point mutations generating codon substitutions were uncovered in ksgA (encoding RNA dimethyltransferase), fusA (elongation factor G), dnaG (primase), lacD (tagatose 1,6-bisphosphate aldolase), and SACOL0611 (a putative glycosyl transferase). The codon substitutions in EF-G that cause amicoumacin A resistance and fusidic acid resistance reside in separate domains and do not bring about cross resistance. Taken together, these results suggest that amicoumacin A might cause perturbation of the cell membrane and lead to energy dissipation. Decreased rates of cellular metabolism including protein synthesis and DNA replication in resistant strains might allow cells to compensate for membrane dysfunction and thus increase cell survivability

Measuring the Environmental Sustainability Performance of Global Supply Chains: a Multi-Regional Input-Output analysis for Carbon, Sulphur Oxide and Water Footprints

Measuring the performance of what an environmentally sustainable supply chain has become a challenge despite the convergence of the underlining principles of sustainable supply chain management. This challenge is exacerbated by the fact that supply chains are inherently dynamic and complex and also because multiple measures can be used to characterize performances. By identifying some of the critical issues in the literature regarding performance measurements, this paper contributes to the existing body of literature by adopting an environmental performance measurement approach for economic sectors (primary, secondary and tertiary sectors). It uses economic sectors and evaluates them on a sectoral level in specific countries as well as part of the Global Value Chain based on the established multi-regional input-output (MRIO) modelling framework. The MRIO model has been used to calculate direct and indirect (that is supply chain or upstream) environmental effects such as CO2, SO2, biodiversity, water consumption and pollution to name just a few of the applications. In this paper we use MRIO to calculate emissions and resource consumption intensities and footprints, direct and indirect impacts, and net emission flows between countries. These are exemplified by using carbon emissions, sulphur oxide emissions and water use in two highly polluting industries; Electricity production and Chemical industry in 33 countries, including the EU-27, Brazil, India and China, the USA, Canada and Japan from 1995 to 2009. Some of the results highlights include: On average, direct carbon emissions in the electricity sector across all 27 member states of the EU was estimated to be 1368 million tonnes and indirect carbon emissions to be 470.7 million tonnes per year representing 25.6% of the EU-27 total carbon emissions related to this sector. It was also observed that from 2004, sulphur oxide emissions intensities in electricity production in India and China have remained relatively constant at about 62.8 gSOx/$and 84.4 gSOx/$ although being higher than in other countries. In terms of water use, the high water use intensity in China (1040.27 litres/$) and India (961.63 litres/$), which are among the highest in the sector in the electricity sector is exacerbated by both countries being ranked as High Water Stress Risk countries. The paper also highlights many merits of the MRIO including: a 15-year time series study (which provides a measurement of environmental performance of key industries and an opportunity to assess technical and technological change during the investigated time period), a supply chain approach that provides a consistent methodological framework and accounts for all upstream supply chain environmental impacts throughout entire global supply chains. The paper also discusses the implications of the study to environmental sustainability performance measurement in terms of the level of analysis from a value chain hierarchy perspective, methodological issues, performance indicators, environmental exchanges and policy relevance

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

The Guide: A Journey Through Holistic Healing

The Graphic Journalism genre is emerging with influences from war reportage with authors like Joe Sacco. I would like to address and report the “War on Drugs” from small first hand experiences, personal connections, and a genuine deep desire to see the healthcare and justice system change. The war on Drugs started in the 1970s during Richard Nixon’s term in the U.S. Presidency. Nixon’s influence to launch the “War on Drugs'' campaign began shortly after two congressmen released a report on the growing heroin epidemic that affected hundreds to thousands of servicemen who fought in the Vietnam War, who used heroin to treat PTSD. Nixon launched unfair disconnected political policy and passed laws that disproportionately targeted those against him and his values (minorities, specifically African Americans and anyone belonging to the counterculture “subwhite”). The War on Drugs movement started as a way to outcast and control minorities through unrealistic and systemically racist and oppressive laws. As the movement evolved so did its focus, the War on Drugs eventually metamorphosed into the “War on Class”, or a war against the economically disadvantaged. The War on Drugs has done way more harm than good and immediate action needs to be taken to begin to restart drug policy in America and within the World. The incomparable Billie Holiday, world renowned jazz singer and creator of “Strange Fruit” once said “I need help. Not jail time.” Shortly after her arrest for heroin possession in 1947. In my opinion, these famous words that Billie Holiday shared during the day of her arrest should be the leading quote in the much needed movement against the criminalization of drug abuse victims. Not only does the War on Drugs disproportionately disenfranchise black and brown communities, it makes researching the benefits of any type of narcotic that was not fully understood nearly impossible. My goal is to reverse the taboos that currently exist throughout our society with a graphic novel/ zine aimed at high school students. I believe that future generations can benefit from natural hallucinogens and other forms of holistic medicines in a safe way that doesn’t involve them having to access illegal avenues of receiving narcotics in order to remedy their pain. Afterall, there is a far greater risk in taking street narcotics due to one’s ability to use an incorrect dosage according to their size and bodily chemistry which can ultimately lead to an overdose and street narcotics may include an unknown amount of ingredients, some of which include fentanyl, a synthetic product of prohibition that is cheaper than heroin, but far more powerful. Fentanyl is used pharmacologically in anesthesia and neuroleptanalgesia and can be extremely harmful to the mind and body. I believe extremely deadly drugs like fentanyl would never exist if it wasn’t for the War on Drugs and its consistent agenda to demonize the usage of all narcotics without exploring the benefits of holistic medicines like hallucinogens and regulating the usage of these medicines through legalization, supervision, FDA regulation, and accessibility within the U.S, Healthcare System

Consulting, independence and quality in audit

Background: An accountant is supposed to secure that the information from a company is true and fair. Recently consulting, or giving advice, has grown to be a major part of an accountants daily work particularly in smaller companies which may have insufficient financial competence themselves. This means that an accountant occupies two parts, as an independent reviewer and as an initiated advisor, which have caused controversy. Purpose: The purpose is to outline and explain how the accountants and audit customers regard an eventual discrepancy between performing the audit and consulting, and to give suggestions how to manage this. The purpose is also to define what customers perceive as quality in consulting an auditor. Method: Interviews were preformed with Chief financial officers from four companies, together with each company's auditor and head of quality from the audit firm. Conclusion: The conclusion is that there are no conflicting interests from auditing and consulting in small companies. Receiving advice is on the contrary what smaller companies perceive as quality in employing an auditor. For the auditor to give advice therefore grants advantages to all stakeholders

Consulting, independence and quality in audit

Background: An accountant is supposed to secure that the information from a company is true and fair. Recently consulting, or giving advice, has grown to be a major part of an accountants daily work particularly in smaller companies which may have insufficient financial competence themselves. This means that an accountant occupies two parts, as an independent reviewer and as an initiated advisor, which have caused controversy. Purpose: The purpose is to outline and explain how the accountants and audit customers regard an eventual discrepancy between performing the audit and consulting, and to give suggestions how to manage this. The purpose is also to define what customers perceive as quality in consulting an auditor. Method: Interviews were preformed with Chief financial officers from four companies, together with each company's auditor and head of quality from the audit firm. Conclusion: The conclusion is that there are no conflicting interests from auditing and consulting in small companies. Receiving advice is on the contrary what smaller companies perceive as quality in employing an auditor. For the auditor to give advice therefore grants advantages to all stakeholders