Destroyed documents: uncovering the science that Imperial Tobacco Canada sought to conceal

Background

In 1992, British American Tobacco had its Canadian affiliate, Imperial Tobacco Canada, destroy internal research documents that could expose the company to liability or embarrassment. Sixty of these destroyed documents were subsequently uncovered in British American Tobacco’s files.

Methods

Legal counsel for Imperial Tobacco Canada provided a list of 60 destroyed documents to British American Tobacco. Information in this list was used to search for copies of the documents in British American Tobacco files released through court disclosure. We reviewed and summarized this information.

Results

Imperial Tobacco destroyed documents that included evidence from scientific reviews prepared by British American Tobacco’s researchers, as well as 47 original research studies, 35 of which examined the biological activity and carcinogenicity of tobacco smoke. The documents also describe British American Tobacco research on cigarette modifications and toxic emissions, including the ways in which consumers adapted their smoking behaviour in response to these modifications. The documents also depict a comprehensive research program on the pharmacology of nicotine and the central role of nicotine in smoking behaviour. British American Tobacco scientists noted that “… the present scale of the tobacco industry is largely dependent on the intensity and nature of the pharmacological action of nicotine,” and that “... should nicotine become less attractive to smokers, the future of the tobacco industry would become less secure.”

Interpretation

The scientific evidence contained in the documents destroyed by Imperial Tobacco demonstrates that British American Tobacco had collected evidence that cigarette smoke was carcinogenic and addictive. The evidence that Imperial Tobacco sought to destroy had important implications for government regulation of tobacco.On May 8, 1998, the US State of Minnesota reached a historic settlement with the tobacco industry.¹ As part of the settlement, the 7 tobacco manufacturers named in the trial were ordered to pay more than $200 billion dollars and to make public over 40 million pages of internal tobacco industry documents. These documents have provided a wealth of information about the conduct of the tobacco industry, the health effects of smoking and the role of cigarette design in promoting addiction.²A number of the most sensitive documents were concealed or destroyed before the trial as the threat of litigation grew.^3,4 Based on advice from their lawyers, companies such as British American Tobacco instituted a policy of document destruction.⁵ A.G. Thomas, the head of Group Security at British American Tobacco, explained the criteria for selecting reports for destruction: “In determining whether a redundant document contains sensitive information, holders should apply the rule of thumb of whether the contents would harm or embarrass the Company or an individual if they were to be made public.”⁶British American Tobacco’s destruction policy was most rigorously pursued by its subsidiaries in the United States, Canada and Australia, likely because of the imminent threat of litigation in these countries. The policy was developed following the 1989 decision by a Canadian judge to give Canadian government representatives access to scientific research conducted by Imperial Tobacco Canada and its principal shareholder, British American Tobacco.⁷ This ruling prompted British American Tobacco to undertake steps to prevent scientists in its affiliate companies from retaining industry studies and to require the destruction of sensitive documents.^8,9 Canadian scientists were the most resistant to this policy,¹⁰ but they too agreed to destroy their copies of British American Tobacco’s scientific research.¹¹In a letter dated June 5, 1992, a lawyer working on behalf of Imperial Tobacco Canada informed British American Tobacco that Imperial would destroy copies of 60 documents in compliance with the document destruction policy, and he provided reference numbers for each of these documents.¹² This memo was one of the earlier industry documents to be made public, and it became a key document in legal arguments about the destruction of evidence.¹³ The contents of the destroyed documents to which it referred, however, had never been analyzed. All that was known was that they contained what British American Tobacco considered “sensitive” research results.¹⁴ A list of the 60 documents is available in Appendix 1 (www.cmaj.ca/cgi/content/full/cmaj.080566/DC1). Appendix 2 (www.cmaj.ca/cgi/content/full/cmaj.080566/DC1) includes summaries of 3 documents not otherwise discussed that explore the transfer of the flavouring additive coumarin to tobacco smoke.^15–17What was the nature of the 60 reports that Imperial and British American Tobacco wanted destroyed? Although Imperial dutifully destroyed its copies of these sensitive documents, other copies of the same documents were stored at British American Tobacco headquarters in the United Kingdom and were released in 1998 through court disclosure in the Minnesota Trial and subsequent legal proceedings.¹ We searched British American Tobacco’s archives for each of the 60 reports using the research numbers included in the original letter.¹² In this article, we present the contents of these research reports.     

Human IgG detection in serum on polymer based Mach‐Zehnder interferometric biosensors

We report a new method for detecting human IgG (hIgG) in serum on integrated‐optical Mach‐Zehnder interferometer biosensors realized in a high index contrast polymer material system. In the linear range of the sensor (5–200 nM) we observed excellent signal recoveries (95–110%) in buffer and serum samples, which indicate the absence of matrix effects. Signal enhancement was reached by using secondary anti‐human IgG antibodies, which bind to immobilized target IgGs and allow detecting concentrations down to 100 pM. This polymer based optical sensor is fully compatible with cost‐efficient mass production technologies, which makes it an attractive alternative to inorganic optical sensors.

Graphical abstract of the hIgG measured on polymer based photonic sensors using a direct binding assay and a signal enhancement strategy with secondary antibodies.     

Identification of new Presenilin‐1 phosphosites: implication for γ‐secretase activity and Aβ production

An important pathological hallmark of Alzheimer's disease (AD) is the deposition of amyloid‐beta (Aβ) peptides in the brain parenchyma, leading to neuronal death and impaired learning and memory. The protease γ‐secretase is responsible for the intramembrane proteolysis of the amyloid‐β precursor protein (APP), which leads to the production of the toxic Aβ peptides. Thus, an attractive therapeutic strategy to treat AD is the modulation of the γ‐secretase activity, to reduce Aβ42 production. Because phosphorylation of proteins is a post‐translational modification known to modulate the activity of many different enzymes, we used electrospray (LC‐MS/MS) mass spectrometry to identify new phosphosites on highly purified human γ‐secretase. We identified 11 new single or double phosphosites in two well‐defined domains of Presenilin‐1 (PS1), the catalytic subunit of the γ‐secretase complex. Next, mutagenesis and biochemical approaches were used to investigate the role of each phosphosite in the maturation and activity of γ‐secretase. Together, our results suggest that the newly identified phosphorylation sites in PS1 do not modulate γ‐secretase activity and the production of the Alzheimer's Aβ peptides. Individual PS1 phosphosites shall probably not be considered therapeutic targets for reducing cerebral Aβ plaque formation in AD.

     

Hippocampal proteoglycans brevican and versican are linked to spatial memory of Sprague–Dawley rats in the morris water maze

Proteoglycans (PGs) are major constituents of the extracellular matrix and have recently been proposed to contribute to synaptic plasticity. Hippocampal PGs have not yet been studied or linked to memory. The aim of the study, therefore, was to isolate and characterize rat hippocampal PGs and determine their possible role in spatial memory. PGs were extracted from rat hippocampi by anion‐exchange chromatography and analyzed by nano LC‐MS/MS. Twenty male Sprague–Dawley rats were tested in the morris water maze. PGs agrin, amyloid beta A4 protein, brevican, glypican‐1, neurocan, phosphacan, syndecan‐4, and versican were identified in the hippocampi. Brevican and versican levels in the membrane fraction were higher in the trained group, correlating with the time spent in the target quadrant. α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate receptor GluR1 was co‐precipitated with brevican and versican. Levels for a receptor complex containing GluR1 was higher in trained while GluR2 and GluR3‐containing complex levels were higher in yoked rats. The findings provide information about the PGs present in the rat hippocampus, demonstrating that versican and brevican are linked to memory retrieval in the morris water maze and that PGs interact with α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate receptor GluR1, which is linked to memory retrieval.

     

The extracellular fragment of GPNMB (Glycoprotein nonmelanosoma protein B,osteoactivin) improves memory and increases hippocampal GluA1 levels in mice

Glycoprotein nonmelanoma protein B (GPNMB, alias osteoactivin), a type I transmembrane glycoprotein, is cleaved by extracellular proteases, resulting in release of an extracellular fragment (ECF). GPNMB is widely expressed by neurons within the CNS, including the hippocampus; however, its function in the brain remains unknown. Here, we investigated the role of GPNMB in memory and learning by using transgenic (Tg) mice over‐expressing GPNMB (Tg mice on a BDF‐1 background) and ECF‐treated mice. In the hippocampus of both wild‐type and Tg mice, GPNMB was highly expressed in neurons and astrocytes. Tg mice exhibited memory improvements in two types of learning tasks but were impaired in a passive‐avoidance test. In Tg mice, the hippocampus displayed increased levels of the α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate receptor subunit GluA1. Intracerebroventricular administration of ECF (50 ng) to Institute of Cancer Research (ICR) mice also improved memory in a passive‐avoidance test and increased hippocampal GluA1 levels 24 h after treatment. In Tg mice and ECF (0.25 μg/mL)‐treated hippocampal slices, long‐term potentiation was promoted. These findings suggest that GPNMB may be a novel target for research on higher order brain functions.

     

An algebraic model of an associative noise-like coding memory

A mathematical model of an associative memory is presented, sharing with the optical holography memory systems the properties which establish an analogy with biological memory. This memory system-developed from Gabor's model of memoryis based on a noise-like coding of the information by which it realizes a distributed, damage-tolerant, equipotential storage through simultaneous state changes of discrete substratum elements. Each two associated items being stored are coded by each other by means of two noise-like patterns obtained from them through a randomizing preprocessing. The algebraic braic transformations operating the information storage and retrieval are matrix-vector products involving Toeplitz type matrices. Several noise-like coded memory traces are superimposed on a common substratum without crosstalk interference; moreover, extraneous noise added to these memory traces does not injure the stored information. The main performances shown by this memory model are: i) the selective, complete recovering of stored information from incomplete keys, both mixed with extraneous information and translated from the position learnt; ii) a dynamic recollection where the information just recovered acts as a new key for a sequential retrieval process; iii) context-dependent responses. The hypothesis that the information is stored in the nervous system through a noise-like coding is suggested. The model has been simulated on a digital computer using bidimensional images.     

Insulin induces phosphorylation of the AMPA receptor subunit GluR1, reversed by ZIP,and over‐expression of Protein Kinase M zeta,reversed by amyloid beta

Insulin receptor (IR) in the brain plays a role in synaptic plasticity and cognitive functions. Phosphorylation of α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA) receptors GluR1 subunit at Serine 831 is regulated by calcium–calmodulin‐dependent protein kinase II and protein kinase C that underlie long‐term potentiation and learning/memory. Recent studies have shown that the novel Protein Kinase M zeta (PKMζ) underlies synaptic plasticity and may regulate AMPAr. In this study, we show that insulin induces phosphorylation of Serine 831 GluR1 subunit of AMPAr and induces over‐expression of PKMζ; pre‐treatment with either the IR inhibitor 3‐Bromo‐5‐t‐butyl‐4‐hydroxy‐benzylidenemalonitrile (AG1024) or PKMζ inhibitor protein kinase C zeta pseudo‐substrate inhibitor returned the phosphorylation value of GluR1 to control level. Amyloid beta (Aβ) peptide in the form of oligomers interferes with IR signaling. Pre‐treating neuronal cultures with Aβ following incubation with insulin, we found a reduction of insulin‐dependent PKMζ over‐expression and MAPK/Erk (1/2) phosphorylation, i.e., signaling pathways involved in synaptic plasticity and learning/memory. These results indicate a new intracellular insulin signaling pathway, and, additionally, that insulin resistance in Alzheimer's disease is a response to the production and accumulation of Aβ.

     

Enzyme reversal to explore the function of yeast E3 ubiquitin‐ligases

The covalent attachment of ubiquitin onto proteins can elicit a variety of downstream consequences. Attachment is mediated by a large array of E3 ubiquitin ligases, each thought be subject to regulatory control and to have a specific repertoire of substrates. Assessing the biological roles of ligases, and in particular, identifying their biologically relevant substrates has been a persistent yet challenging question. In this study, we describe tools that may help achieve both of these goals. We describe a strategy whereby the activity of a ubiquitin ligase has been enzymatically reversed, accomplished by fusing it to a catalytic domain of an exogenous deubiquitinating enzyme. We present a library of 72 “anti‐ligases” that appear to work in a dominant‐negative fashion to stabilize their cognate substrates against ubiquitin‐dependent proteasomal and lysosomal degradation. We then used the ligase‐deubiquitinating enzyme (DUb) library to screen for E3 ligases involved in post‐Golgi/endosomal trafficking. We identify ligases previously implicated in these pathways (Rsp5 and Tul1), in addition to ligases previously localized to endosomes (Pib1 and Vps8). We also document an optimized workflow for isolating and analyzing the “ubiquitome” of yeast, which can be used with mass spectrometry to identify substrates perturbed by expression of particular ligase‐DUb fusions.      

KIBRA (KIdney/BRAin protein) regulates learning and memory and stabilizes Protein kinase Mζ

The WWC1 gene has been genetically associated with human episodic memory performance, and its product KIdney/BRAin protein (KIBRA) has been shown to interact with the atypical protein kinase protein kinase M ζ (PKMζ). Although recently challenged, PKMζ remains a candidate postsynaptic regulator of memory maintenance. Here, we show that PKMζ is subject to rapid proteasomal degradation and that KIBRA is both necessary and sufficient to counteract this process, thus stabilizing the kinase and maintaining its function for a prolonged time. We define the binding sequence on KIBRA, a short amino acid motif near the C‐terminus. Both hippocampal knock‐down of KIBRA in rats and KIBRA knock‐out in mice result in decreased learning and memory performance in spatial memory tasks supporting the notion that KIBRA is a player in episodic memory. Interestingly, decreased memory performance is accompanied by decreased PKMζ protein levels. We speculate that the stabilization of synaptic PKMζ protein levels by KIBRA may be one mechanism by which KIBRA acts in memory maintenance.

     

Hippocampal chromatin‐modifying enzymes are pivotal for scopolamine‐induced synaptic plasticity gene expression changes and memory impairment

The amnesic potential of scopolamine is well manifested through synaptic plasticity gene expression changes and behavioral paradigms of memory impairment. However, the underlying mechanism remains obscure and consequently ideal therapeutic target is lacking. In this context, chromatin‐modifying enzymes, which regulate memory gene expression changes, deserve major attention. Therefore, we analyzed the expression of chromatin‐modifying enzymes and recovery potential of enzyme modulators in scopolamine‐induced amnesia. Scopolamine administration drastically up‐regulated DNA methyltransferases (DNMT1) and HDAC2 expression while CREB‐binding protein (CBP), DNMT3a and DNMT3b remained unaffected. HDAC inhibitor sodium butyrate and DNMT inhibitor Aza‐2′deoxycytidine recovered scopolamine‐impaired hippocampal‐dependent memory consolidation with concomitant increase in the expression of synaptic plasticity genes Brain‐derived neurotrophic factor (BDNF) and Arc and level of histone H3K9 and H3K14 acetylation and decrease in DNA methylation level. Sodium butyrate showed more pronounced effect than Aza‐2′deoxycytidine and their co‐administration did not exhibit synergistic effect on gene expression. Taken together, we showed for the first time that scopolamine‐induced up‐regulation of chromatin‐modifying enzymes, HDAC2 and DNMT1, leads to gene expression changes and consequent decline in memory consolidation. Our findings on the action of scopolamine as an epigenetic modulator can pave a path for ideal therapeutic targets.

     

Optical anisotropy of polypeptide chains

Optical anisotropies γ² of N-t-butylacetamide (tBA), N-Methylacetamide (MA), and N, N-dimethylacetamide (DMA) have been determined from the Rayleigh ratios for depolarzed scattering by dilute solutions of the amides in p-dioxane. Traceless optical polarizability tensors \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for the amides are derived from these results in conjunction with the Kerr constant for tBA determined by LeGèvre and co-workers. It is shown that the tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}_i for the glycyle unit in a polypeptide chain may be identified with \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}MA . Methods for deriving corresponding tensors for other peptide units are indicated and the traceless polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for a polypeptide chain in any specified configuration is formulated.     

Transcriptional co‐repressor SIN3A silencing rescues decline in memory consolidation during scopolamine‐induced amnesia

Epigenetic modifications through methylation of DNA and acetylation of histones modulate neuronal gene expression and regulate long‐term memory. Earlier we demonstrated that scopolamine‐induced decrease in memory consolidation is correlated with enhanced expression of hippocampal DNA methyltransferase 1 (DNMT 1) and histone deacetylase 2 (HDAC 2) in mice. DNMT 1 and HDAC 2 act together by recruiting a co‐repressor complex and deacetylating the chromatin. The catalytic activity of HDAC s is mainly dependent on its incorporation into multiprotein co‐repressor complexes, among which SIN 3A‐HDAC 2 co‐repressor is widely studied to regulate synaptic plasticity. However, the involvement of co‐repressor complex in regulating memory loss or amnesia is unexplored. This study examines the role of co‐repressor SIN 3A in scopolamine‐induced amnesia through epigenetic changes in the hippocampus. Scopolamine treatment remarkably enhanced hippocampal SIN 3A expression in mice. To prevent such increase in SIN 3A expression, we used hippocampal infusion of SIN 3A‐siRNA and assessed the effect of SIN 3A silencing on scopolamine‐induced amnesia. Silencing of SIN 3A in amnesic mice reduced the binding of HDAC 2 at neuronal immediate early genes (IEG s) promoter, but did not change the expression of HDAC 2. Furthermore, it increased acetylation of H3K9 and H3K14 at neuronal IEG s (Arc, Egr1, Homer1 and Narp) promoter, prevented scopolamine‐induced down‐regulation of IEG s and improved consolidation of memory during novel object recognition task. These findings together suggest that SIN 3A has a critical role in regulation of synaptic plasticity and might act as a potential therapeutic target to rescue memory decline during amnesia and other neuropsychiatric pathologies.

     

Quantitative and rapid estimations of human sub‐surface skin mass using ultra‐high‐resolution spectral domain optical coherence tomography

Non‐invasive and quantitative estimations for the delineation of sub‐surface tumor margins could greatly aid in the early detection and monitoring of the morphological appearances of tumor growth, ensure complete tumor excision without the unnecessary sacrifice of healthy tissue, and facilitate post‐operative follow‐up for recurrence. In this study, a high‐speed, non‐invasive, and ultra‐high‐resolution spectral domain optical coherence tomography (UHR‐SDOCT) imaging platform was developed for the quantitative measurement of human sub‐surface skin mass. With a proposed robust, semi‐automatic analysis, the system can rapidly quantify lesion area and shape regularity by an en‐face‐oriented algorithm. Various sizes of nylon sutures embedded in pork skin were used first as a phantom to verify the accuracy of our algorithm, and then in vivo, feasibility was proven using benign human angiomas and pigmented nevi. Clinically, this is the first step towards an automated skin lesion measurement system.

In vivo optical coherence tomography (OCT) image of angioma (A). Thin red arrows point to a blood vessel (BV).     

In vivo testing of a bioresorbable phosphate‐based optical fiber

Optical fibers have recently attracted a noticeable interest for biomedical applications because they provide a minimally invasive method for in vivo sensing, imaging techniques, deep‐tissue photodynamic therapy or optogenetics. The silica optical fibers are the most commonly used because they offer excellent optical properties, and they are readily available at a reasonable price. The fused silica is a biocompatible material, but it is not bioresorbable so it does not decompose in the body and the fibers must be ex‐planted after in vivo use and their fragments can present a considerable risk to the patient when the fiber breaks. In contrast, optical fibers made of phosphate glasses can bring many benefits because such glasses exhibit good transparency in ultraviolet‐visible and near‐infrared regions, and their solubility in water can be tailored by changing the chemical composition. The bioresorbability and toxicity of phosphate glass–based optical fibers were tested in vivo on male laboratory rats for the first time. The fiber was spliced together with a standard graded‐index multi‐mode fiber pigtail and an optical probe for in vitro pH measurement was prepared by the immobilization of a fluorescent dye on the fiber tip by a sol‐gel method to demonstrate applicability and compatibility of the fiber with common fiber optics.      

Elemental fingerprint as a cerebrospinal fluid biomarker for the diagnosis of Parkinson's disease

The diagnosis of Parkinson's disease (PD) still lacks objective diagnostic markers independent of clinical criteria. Cerebrospinal fluid (CSF) samples from 36 PD and 42 age‐matched control patients were subjected to inductively coupled plasma‐sector field mass spectrometry and a total of 28 different elements were quantified. Different machine learning algorithms were applied to the dataset to identify a discriminating set of elements yielding a novel biomarker signature. Using 19 stably detected elements, the extreme gradient tree boosting model showed the best performance in the discrimination of PD and control patients with high specificity and sensitivity (78.6% and 83.3%, respectively), re‐classifying the training data to 100%. The 10 times 10‐fold cross‐validation yielded a good area under the receiver operating characteristic curve of 0.83. Arsenic, magnesium, and selenium all showed significantly higher mean CSF levels in the PD group compared to the control group (p  = 0.01, p  = 0.04, and p  = 0.03). Reducing the number of elements to a discriminating minimum, we identified an elemental cluster (Se, Fe, As, Ni, Mg, Sr), which most importantly contributed to the sample discrimination. Selenium was identified as the element with the highest impact within this cluster directly followed by iron. After prospective validation, this elemental fingerprint in the CSF could have the potential to be used as independent biomarker for the diagnosis of PD. Next to their value as a biomarker, these data also argue for a prominent role of these highly discriminating six elements in the pathogenesis of PD.

     

Surface functionalization allowing repetitive use of optical sensors for real‐time detection of antibody‐bacteria interaction

In this study, sensor surface functionalization allowing the repetitive use of a sensing device was evaluated for antibody‐based detection of living bacteria using an optical planar Bragg grating sensor. To achieve regenerable immobilization of bacteria specific antibodies, the heterobifunctional cross‐linker N‐succinimidyl 3‐(2‐pyridyldithio) propionate (SPDP) was linked to an aminosilanized sensor surface and subsequently reduced to expose sulfhydryl groups enabling the covalent conjugation of SPDP‐activated antibodies via disulfide bonds. The immobilization of a capture antibody specific for Staphylococcus aureus on the sensor surface as well as specific binding of S. aureus could be monitored, highlighting the applicability of optical sensors for the specific detection of large biological structures. Reusability of bacteria saturated sensors was successfully demonstrated by cleaving the antibody along with bound bacteria through reduction of disulfide bonds and subsequent re‐functionalization with activated antibody, resulting in comparable sensitivity towards S. aureus.

     

Functional analysis and purification of a Pen‐2 fusion protein for γ‐secretase structural studies

The 19‐transmembrane, multisubunit γ‐secretase complex generates the amyloid β‐peptide (Aβ) of Alzheimer's disease (AD) by an unusual intramembrane proteolysis of the β‐amyloid precursor protein. The complex, which similarly processes many other type 1 transmembrane substrates, is composed of presenilin, Aph1, nicastrin, and presenilin enhancer (Pen‐2), all of which are necessary for proper complex maturation and enzymatic activity. Obtaining a high‐resolution atomic structure of the intact complex would greatly aid the rational design of compounds to modulate activity but is a very difficult task. A complementary method is to generate structures for each individual subunit to allow one to build a model of the entire complex. Here, we describe a method by which recombinant human Pen‐2 can be purified from bacteria to > 95% purity at milligram quantities per liter, utilizing a maltose binding protein tag to both increase solubility and facilitate purification. Expressing the same construct in mammalian cells, we show that the large N‐terminal maltose binding protein tag on Pen‐2 still permits incorporation into the complex and subsequent presenilin‐1 endoproteolysis, nicastrin glycosylation and proteolytic activity. These new methods provide valuable tools to study the structure and function of Pen‐2 and the γ‐secretase complex.

     

Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins

Background

Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification of quantitative trait loci (QTL) associated with milk, fat, and protein yield and the genetic and molecular mechanisms underlying them. Copy number variation (CNV) is an emerging class of variants which may be associated with complex traits.

Results

In this study, we performed a genome-wide association between CNVs and milk production traits in 26,362 Holstein bulls and cows. A total of 99 candidate CNVs were identified using Illumina BovineSNP50 array data, and association tests for each production trait were performed using a linear regression analysis with PCA correlation. A total of 34 CNVs on 22 chromosomes were significantly associated with at least one milk production trait after false discovery rate (FDR) correction. Some of those CNVs were located within or near known QTL for milk production traits. We further investigated the relationship between associated CNVs with neighboring SNPs. For all 82 combinations of traits and CNVs (less than 400 kb in length), we found 17 cases where CNVs directly overlapped with tag SNPs and 40 cases where CNVs were adjacent to tag SNPs. In 5 cases, CNVs located were in strong linkage disequilibrium with tag SNPs, either within or adjacent to the same haplotype block. There were an additional 20 cases where CNVs did not have a significant association with SNPs, suggesting that the effects of those CNVs were probably not captured by tag SNPs.

Conclusion

We conclude that combining CNV with SNP analyses reveals more genetic variations underlying milk production traits than those revealed by SNPs alone.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-683) contains supplementary material, which is available to authorized users.     

Government vote for optical cards

The Italian Government has awarded Drexler Technology Corporation an initial US$2.4 million order to supply combined optical memory chip cards for use as Italy’s national ID card. Called the Carta d’Identita Elettronica (CIE), they represent the first use of a LaserCard national identification card within the European Union. The citizen’s demographics, colour photograph, digitised signature, and other biometrics, such as the holder’s fingerprint, are to be contained in the optical memory stripe.This is a short news story only. Visit www.compseconline.com for the latest computer security industry news.     

CaMKII activity is essential for improvement of memory‐related behaviors by chronic rivastigmine treatment

Because the cholinergic system is down‐regulated in the brain of Alzheimer's disease patients, cognitive deficits in Alzheimer's disease patients are significantly improved by rivastigmine treatment. To address the mechanism underlying rivastigmine‐induced memory improvements, we chronically treated olfactory bulbectomized (OBX) mice with rivastigmine. The chronic rivastigmine treatments for 12–13 days starting at 10 days after OBX operation significantly improved memory‐related behaviors assessed by Y‐maze task, novel object recognition task, passive avoidance task, and Barnes maze task, whereas the single rivastigmine treatment failed to improve the memory. Consistent with the improved memory‐related behaviors, long‐term potentiation in the hippocampal CA1 region was markedly restored by rivastigmine treatments. In immunoblotting analyses, the reductions of calcium/calmodulin‐dependent protein kinase II (CaMKII) autophosphorylation and calcium/calmodulin‐dependent protein kinase IV (CaMKIV) phosphorylation in the CA1 region in OBX mice were significantly restored by rivastigmine treatments. In addition, phosphorylation of AMPAR subunit glutamate receptor 1 (GluA1) (Ser‐831) and cAMP‐responsive element‐binding protein (Ser‐133) as downstream targets of CaMKII and CaMKIV, respectively, in the CA1 region was also significantly restored by chronic rivastigmine treatments. Finally, we confirmed that rivastigmine‐induced improvements of memory‐related behaviors and long‐term potentiation were not obtained in CaMKIIα^+/? mice. On the other hand, CaMKIV^?/? mice did not exhibit the cognitive impairments. Taken together, the stimulation of CaMKII activity in the hippocampus is essential for rivastigmine‐induced memory improvement in OBX mice.