Serum levels of 4-hydroxynonenal adducts and responding autoantibodies correlate with the pathogenesis from hyperglycemia to Alzheimer's disease.

OBJECTIVE: Hyperglycemia leads to lipid peroxidation, producing 4-hydroxynonenal (HNE) adducts which correlate with the production of amyloid-beta (Aß), one of the hallmarks of Alzheimer's disease (AD). This study is to investigate the interactions of Aß, HNE adducts and responding autoantibodies during the pathogenesis from hyperglycemia to AD. METHODS: A total of 239 Taiwanese serum samples from a healthy control group and patients with hyperglycemia, and AD with and without hyperglycemia were analyzed. Aß was immunoprecipitated from randomly pooled serum in each group and immunoblotted. Synthetic Aß1-16 and Aß17-28 peptides were modified with HNE in vitro and verified with LC-MS/MS. The levels of Aß, HNE adducts, and autoantibody isotypes IgG and IgM against either native or HNE-modified Aß were determined with ELISA. The diagnostic power of potential biomarkers was evaluated. RESULTS: Increased fasting glucose and decreased high-density-lipoprotein cholesterol in AD groups indicated abnormal metabolism in the pathogenesis progression from hyperglycemia to AD. Indeed, serum Aß, HNE adducts and most of the autoantibodies recognizing either native or HNE-modified Aß were increased in the diseased groups. However, HNE adducts had better diagnostic performances than Aß for both hyperglycemia and AD. Additionally, HNE-Aß peptide levels were increased, and the responding autoantibodies (most notably IgM) were decreased in hyperglycemic AD group compared to the hyperglycemia only group, suggesting an immunity disturbance in the pathogenesis progression from hyperglycemia to AD. CONCLUSION: Hyperglycemia increases the level of HNE adducts which may be neutralized by responding autoantibodies. Depletion of these autoantibodies promotes AD-like pathogenesis. Thus, levels of a patient's HNE adducts and associated responding autoantibodies are potential biomarkers for AD with diabetes.

Patenting a living microbial cell: 40th anniversary of US Supreme Court decision Diamond versus Chakrabarty.

Patents for microbiology and biotechnology are generally for a process (for example DNA cloning; and polymerase chain reaction, PCR) and not for the microbe itself. The patent for oil degrading bacteria was different in that it covered the modified microbial cell itself, a Pseudomonas strain with laboratory-assembled plasmids that encoded the bacterial degradation of multiple components of crude oil. It was first applied for in 1972, initially refused by the patent office on the basis that it was a living organism, and then eight years later in June 1980 allowed by the US Supreme Court ruling that this did not matter and the only issue was whether it was a novel manufactured product.

Death of scientific journals after 350 years.

Scientific journals have virtually disappeared as subscription-based familiar paper copies. These have been replaced by article by article access on internet sites (either subscription based paid for by libraries in multi-journal often million dollar 'Big Deal' packages or by author prepayments of thousand dollars 'article processing fees' (Omary and Lawrence, Dealing with rising publication costs. The Scientist 2017;31:29-31), followed by open access. The result appears to be the death of the traditional scientific journal as a familiar means of communication, after nearly 350 years from the time of Anton van Leeuwenhoek and Robert Hooke (for two early microbiology examples). Rather than journals with page numbers, individual reports are accessed using titles or manuscript file code numbers. This commentary is knowingly provocative, describing the rapidly changing situation in scientific publication at the beginning of the 21st century and predicting a bad future, basically the end of the long-time most-used vehicles for scientific communication, the paper scientific journal with volumes and pages. This view is not particular to this author and appears frequently today (e.g. The Scientist 2012; https://scholarlykitchen.sspnet.org/2016/10/26/revisiting-why-hasnt-scientific-publishing-been-disrupted-already/). This negative conclusion offers no better possibilities, as it is concluded that it is already too late and too far along this pathway for any meaningful middle ground. This commentary is intended for a broad group of potential readers, including authors and readers of this journal (who are active microbial scientists who need to adapt to individual manuscript identification numbers replacing page numbers), as well as the larger community interested broadly in scientific communication, and even our institutional librarians (who have experienced the disappearance of paper copies from their shelves, and especially unsustainable rapid increases in money costs at a time of very limited resources).

Mercury resistance transposons in Bacilli strains from different geographical regions.

A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.

Laboratory-acquired lethal infections by potential bioweapons pathogens including Ebola in 2014.

Researchers studying both cellular and viral disease agents in the laboratory have become infected since the early days of microbiology 150 years ago. However, in the early 21st century, new concerns about bioweapons being used to generate terror and also with a series of newly emerging or newly understood disease-causing microbes have resulted in infections and deaths of workers studying these microbes in the laboratory, generally to gain understanding and to develop treatments and vaccines. Here, five examples are summarized: (i) smallpox virus escaped from a UK laboratory where it was being maintained and stored, (ii) the 2014 infections and deaths of five researchers who were isolating West African Ebola virus for DNA sequencing epidemiology studies, (iii) and (iv) two recent infections that happened in the same US laboratory where researchers were infected with agents causing septicemic Yersinia plague and Bacillus anthrax and (v) the 2012 death in California from laboratory infection by Neisseria meningitidis resulting in spinal meningitis.

Beyond the fringe: when science moves from innovative to nonsense.

Microbiology has experienced examples of highly productive researchers who have gone beyond just interpreting their experimental results with hypotheses and published nonsense that was readily recognized as such by readers. Although the most discussed cases of this pathology come from physics, studies of single-celled microorganisms, virology, and immunology have provided many examples. Five cases are described here along with some generalizations. These are the Lamarckian inheritance of acquired characteristics reported by distinguished and experienced researchers, vectorless DNA transfer and incorporation of bacterial DNA into chromosomes of plants years before vector construction of genetically modified plants was invented, water with memory of immunoglobulin IgE, a new electromagnetic radiation method for identifying bacterial and viral pathogens by the discoverer of human immunodeficiency virus, and the claim of isolation of a new bacterial isolate with arsenic replacing phosphorus in DNA. These examples represent very dissimilar areas, and the only common factor is hubris on the part of experienced researchers. Secondarily, failure of peer review sometimes happens, and journal editors do not step in, sometimes even when alerted before publication. These failures of the publishing process teach us that unnecessary mistakes occur and should warn us all to watch our own enthusiasms.

Antimicrobial silver: uses, toxicity and potential for resistance.

This review gives a comprehensive overview of the widespread use and toxicity of silver compounds in many biological applications. Moreover, the bacterial silver resistance mechanisms and their spread in the environment are discussed. This study shows that it is important to understand in detail how silver and silver nanoparticles exert their toxicity and to understand how bacteria acquire silver resistance. Silver ions have shown to possess strong antimicrobial properties but cause no immediate and serious risk for human health, which led to an extensive use of silver-based products in many applications. However, the risk of silver nanoparticles is not yet clarified and their widespread use could increase silver release in the environment, which can have negative impacts on ecosystems. Moreover, it is shown that silver resistance determinants are widely spread among environmental and clinically relevant bacteria. These resistance determinants are often located on mobile genetic elements, facilitating their spread. Therefore, detailed knowledge of the silver toxicity and resistance mechanisms can improve its applications and lead to a better understanding of the impact on human health and ecosystems.

Draft genome sequence of Agrobacterium albertimagni strain AOL15.

Agrobacterium albertimagni strain AOL15 is an alphaproteobacterium isolated from arsenite-oxidizing biofilms whose draft genome contains 5.1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene arsenic gene island. This is the first available genome for this species and the second Agrobacterium arsenic gene island.

Draft genome sequence of Achromobacter piechaudii strain HLE.

Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes faecalis) that was an early isolate with arsenite oxidase activity. This draft genome of 6.89 Mb is the second available genome for this species in the opportunistic pathogen Alcaligenaceae family.

Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).

Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and the first "arsenate gene island" identified, provided a draft genome of 3.9 Mb in 186 contigs (with the largest 15 comprising 90% of the total) for this opportunistic pathogen species.

Draft genome of halomonas species strain GFAJ-1 (ATCC BAA-2256).

Halomonas strain GFAJ-1 was reported in Science magazine to be a remarkable microbe for which there was "arsenate in macromolecules that normally contain phosphate, most notably nucleic acids." The draft genome of the bacterium was determined (NCBI accession numbers AHBC01000001 through AHBC01000103). It appears to be a typical gamma proteobacterium.

BioMetals: a historical and personal perspective.

Understanding of BioMetals developed basically from a starting point about 60 years ago to current mechanistic understanding of the biological behavior of many metal ions from protein structural and functional studies. Figure 1 shows a Biochemical Periodic Table, element by element, with requirements, roles and biochemistry of the specific ions indicated. With few exceptions, the biology is of the ions formed and not of the elemental state of each. Early BioMetals efforts defined nutritional growth needs for animals, plants and microbes for inorganic "macro-nutrients" such as magnesium, calcium, potassium, sodium, and phosphate and of "micronutrients" such as copper, iron, manganese and zinc. Surprises came early with regard to microbes, for example the finding that Escherichia coli (then and now the standard microbial model) grows happily in the apparent total absence of calcium, sodium, and chloride, which are certainly major animal nutrients. Some elements such as mercury and arsenic are never required by living cells, but are always toxic, often at very low levels. Therefore, the division into nutrient elements and toxic elements came soon. For most inorganic nutrients, excessive amounts can be toxic as well, for example for copper and iron.

Interactions between two MerR regulators and three operator/promoter regions in the mercury resistance module of Bacillus megaterium.

The mercury resistance module of Bacillus transposon TnMERI1 is regulated by three operator/promoter regions (O/P merB3, O/P merR1, and O/P merR2) and two regulatory proteins (MerR1 and MerR2) encoded by the module itself. To clarify the roles of MerR1 and MerR2 in the regulatory mechanism, both proteins were overexpressed and purified. MerR1 bound the regulatory regions O/P merB3 and O/P merR1, with a preference for O/P merB3 as measured on in vitro gel shift assays. However, MerR2 bound O/P merR2, as revealed by gel shift and restriction endonuclease protection assays. The transcriptional start sites of O/P merB3 and O/P merR2 were determined by rapid amplification of 5'-cDNA ends (5'-RACE) in the TnMERI1 original host, Bacillus megaterium strain MB1. Real-time reverse transcription polymerase chain reaction (RT-PCR) assays showed that O/P merB3 and O/P merR1 were induced in the presence of Hg2+ but not O/P merR2. It was concluded that MerR1 regulates O/P merB3 and O/P merR1, while MerR2 regulates O/P merR2.

Arsenate reduction: thiol cascade chemistry with convergent evolution.

The frequent abundance of arsenic in the environment has guided the evolution of enzymes for the reduction of arsenate. The arsenate reductases (ArsC) from different sources have unrelated sequences and structural folds, and can be divided into different classes on the basis of their structures, reduction mechanisms and the locations of catalytic cysteine residues. The thioredoxin-coupled arsenate reductase class is represented by Staphylococcus aureus pI258 ArsC and Bacillus subtilis ArsC. The ArsC from Escherichia coli plasmid R773 and the eukaryotic ACR2p reductase from Saccharomyces cerevisiae represent two distinct glutaredoxin-linked ArsC classes. All are small cytoplasmic redox enzymes that reduce arsenate to arsenite by the sequential involvement of three different thiolate nucleophiles that function as a redox cascade. In contrast, the ArrAB complex is a bacterial heterodimeric periplasmic or a surface-anchored arsenate reductase that functions as a terminal electron acceptor and transfers electrons from the membrane respiratory chain to arsenate. Finally, the less well documented arsenate reductase activity of the monomeric arsenic(III) methylase, which is an S-adenosylmethionine (AdoMet)-dependent methyltransferase. After each oxidative methylation cycle and before the next methylation step, As(V) is reduced to As(III). Methylation by this enzyme is also considered an arsenic-resistance mechanism for bacteria, fungi and mammals.