Cryo-EM structures of amyloid-ß and tau filaments in Down syndrome.

Adult individuals with Down syndrome (DS) develop Alzheimer disease (AD). Whether there is a difference between AD in DS and AD regarding the structure of amyloid-ß (Aß) and tau filaments is unknown. Here we report the structure of Aß and tau filaments from two DS brains. We found two Aß40 filaments (types IIIa and IIIb) that differ from those previously reported in sporadic AD and two types of Aß42 filaments (I and II) identical to those found in sporadic and familial AD. Tau filaments (paired helical filaments and straight filaments) were identical to those in AD, supporting the notion of a common mechanism through which amyloids trigger aggregation of tau. This knowledge is important for understanding AD in DS and assessing whether adults with DS could be included in AD clinical trials.

Cross-ß helical filaments of Tau and TMEM106B in Gray and White Matter of Multiple System Tauopathy with presenile Dementia.

Background: The Microtubule-Associated Protein Tau (MAPT) is one of the proteins that are central to neurodegenerative diseases. The nature of intracellular tau aggregates is determined by the cell types whether neuronal or glial, the participating tau isoforms, and the structure of the amyloid filament. The transmembrane protein 106B (TMEM106B) has recently emerged as another significant player in neurodegeneration and aging. In the central nervous system, the composition of the gray and white matter differs considerably. The gray matter consists of nerve cell bodies, dendrites, unmyelinated axons, synaptic terminals, astrocytes, oligodendrocytes (satellite cells) and microglia. The white matter differs from the gray for the presence of axonal tracts as the only neuronal component and for the absence of nerve cell bodies, dendrites and synaptic terminals. Cryogenic electron microscopy (cryo-EM) studies have unveiled the structure of tau and TMEM106B, from the cerebral cortex, in several neurodegenerative diseases; however, whether tau and TMEM106B filaments from the gray and white matter share a common fold requires additional investigation. Methods: We isolated tau and TMEM106B from the cerebral cortex and white matter of the frontal lobes of two individuals affected by multiple system tauopathy with presenile dementia (MSTD), a disease caused by the MAPT intron 10 mutation +3. We used immunostaining, biochemical, genetics and cryo-EM methods to characterize tau and TMEM106B. Results: We determined that tau filaments in the gray and the white matter of MSTD individuals can induce tau aggregation and have identical AGD type 2 folds. TMEM106B amyloid filaments were also found in the gray and white matter of MSTD; the filament folds were identical in the two anatomical regions. Conclusions: Our findings show for the first time that in MSTD two types of amyloid filaments extracted from the gray matter have identical folds to those extracted from the white matter. Whether in this genetic disorder there is a relationship in the pathogenesis of the tau and TMEM106B filaments, remains to be determined. Furthermore, additional studies are needed for other proteins and other neurodegenerative diseases to establish whether filaments extracted from the gray and white matter would have identical folds.

Development of CryoVR, a virtual reality training system for hands-on cryoEM operations.

Cryogenic electron microscopy (cryoEM) has emerged as a revolutionary method for solving high-resolution structures and studying the dynamics of macromolecular complexes and viruses in near-native states. However, the availability of the equipment, and the time and cost needed for training, severely limit the opportunities for training. To solve these problems, a virtual reality-based training system, CryoVR, has been developed to prepare trainees before operating real-world cryoEM equipment. This paper describes the design and assessment of CryoVR (available at https://www.purdue.edu/cryoVR), which helps users learn cryoEM experimental procedures in a virtual environment, allowing immersive training with step-by-step tutorials with vivid visual, audio and text guidance. Implemented as a training step before a novice user interacts with the expensive real-world cryoEM equipment, CryoVR can help users to become familiar with hands-on operational procedures through multiple training modules and earning certificates after passing the built-in Exam mode. Qualitative evaluation and feedback of CryoVR from users with various levels of cryoEM experience indicate the substantial value of CryoVR as a tool for a comprehensive cryoEM procedural training.

Cryo-EM structures of prion protein filaments from Gerstmann-Sträussler-Scheinker disease.

Prion protein (PrP) aggregation and formation of PrP amyloid (APrP) are central events in the pathogenesis of prion diseases. In the dominantly inherited prion protein amyloidosis known as Gerstmann-Sträussler-Scheinker (GSS) disease, plaques made of PrP amyloid are present throughout the brain. The c.593t > c mutation in the prion protein gene (PRNP) results in a phenylalanine to serine amino acid substitution at PrP residue 198 (F198S) and causes the most severe amyloidosis among GSS variants. It has been shown that neurodegeneration in this disease is associated with the presence of extracellular APrP plaques and neuronal intracytoplasmic Tau inclusions, that have been shown to contain paired helical filaments identical to those found in Alzheimer disease. Using cryogenic electron microscopy (cryo-EM), we determined for the first time the structures of filaments of human APrP, isolated post-mortem from the brain of two symptomatic PRNP F198S mutation carriers. We report that in GSS (F198S) APrP filaments are composed of dimeric, trimeric and tetrameric left-handed protofilaments with their protomers sharing a common protein fold. The protomers in the cross-ß spines consist of 62 amino acids and span from glycine 80 to phenylalanine 141, adopting a previously unseen spiral fold with a thicker outer layer and a thinner inner layer. Each protomer comprises nine short ß-strands, with the ß1 and ß8 strands, as well as the ß4 and ß9 strands, forming a steric zipper. The data obtained by cryo-EM provide insights into the structural complexity of the PrP filament in a dominantly inherited human PrP amyloidosis. The novel findings highlight the urgency of extending our knowledge of the filaments' structures that may underlie distinct clinical and pathologic phenotypes of human neurodegenerative diseases.

The effects of molecular crowding and CpG hypermethylation on DNA G-quadruplexes formed by the C9orf72 nucleotide repeat expansion.

A nucleotide repeat expansion (NRE), (G4C2)n, located in a classically noncoding region of C9orf72 (C9), is the most common genetic mutation associated with ALS/FTD. There is increasing evidence that nucleic acid structures formed by the C9-NRE may both contribute to ALS/FTD, and serve as therapeutic targets, but there is limited characterization of these nucleic acid structures under physiologically and disease relevant conditions. Here we show in vitro that the C9-NRE DNA can form both parallel and antiparallel DNA G-quadruplex (GQ) topological structures and that the structural preference of these DNA GQs can be dependent on the molecular crowding conditions. Additionally, 5-methylcytosine DNA hypermethylation, which is observed in the C9-NRE locus in some patients, has minimal effects on GQ topological preferences. Finally, molecular dynamic simulations of methylated and nonmethylated GQ structures support in vitro data showing that DNA GQ structures formed by the C9-NRE DNA are stable, with structural fluctuations limited to the cytosine-containing loop regions. These findings provide new insight into the structural polymorphic preferences and stability of DNA GQs formed by the C9-NRE in both the methylated and nonmethylated states, as well as reveal important features to guide the development of upstream therapeutic approaches to potentially attenuate C9-NRE-linked diseases.

Bending of the BST-2 coiled-coil during viral budding.

BST-2/tetherin is a human extracellular transmembrane protein that serves as a host defense factor against HIV-1 and other viruses by inhibiting viral spreading. Structurally, BST-2 is a homo-dimeric coiled-coil that is connected to the host cell membrane by N and C terminal transmembrane anchors. The C-terminal membrane anchor of BST-2 is inserted into the budding virus while the N-terminal membrane anchor remains in the host cell membrane creating a viral tether. The structural mechanism of viral budding and tethering as mediated by BST-2 is not clear. To more fully describe the mechanism of viral tethering, we created a model of BST-2 embedded in a membrane and used steered molecular dynamics to simulate the transition from the host cell membrane associated form to the cell-virus membrane bridging form. We observed that BST-2 did not transition as a rigid structure, but instead bent at positions with a reduced interface between the helices of the coiled-coil. The simulations for the human BST-2 were then compared with simulations on the mouse homolog, which has no apparent weak spots. We observed that the mouse homolog spread the bending across the ectodomain, rather than breaking at discrete points as observed with the human homolog. These simulations support previous biochemical and cellular work suggesting some flexibility in the coiled-coil is necessary for viral tethering, while also highlighting how subtle changes in protein sequence can influence the dynamics and stability of proteins with overall similar structure.

Histopathologic, biochemical and genotoxic investigations on chronic sodium nitrite toxicity in mice.

The aim of this study was to investigate the effects of long term Sodium nitrite (NaNO2) consumption. Swiss albino mice were given NaNO2 (0, 10 and 20 mg/kg/day) as mixed in feed for 8 months. At the end of treatments, animals were sacrificed and selected organs were processed for histopathologic, imunohistochemical, biochemical and genotoxic investigations. Mild to moderate degenerative changes were observed in liver, kidney, intestine, lung and spleen of NaNO2-given mice. Inducible nitric oxide synthase and nitrotyrosine activities increased in liver and kidney of NaNO2-given mice. Proliferating cell nuclear antigen activity increased in liver. Apoptotic cell death was observed in livers of the treatment groups. Liver malondialdehyde level was higher in the treatment groups while no change was seen in kidney. Nitric oxide levels in both liver and kidney of the treatment groups were lower than those of the control group. In genotoxic investigations, the number of chromosome and chromatid breaks, chromatid association, and polyploidy increased while mitotic index decreased in NaNO2-given mice. The results showed that NaNO2 would cause histopathologic changes, nitrosative tissue damage, and lipid peroxidation in liver and kidney, as well as induce chromosomal aberrations even if it was given at low levels for long time.

Detection of myocardial degeneration with point-of-care cardiac troponin assays and histopathology in lambs with white muscle disease.

The aim of this study was to evaluate the use of human cardiac troponin-I (cTn-I) and cardiac troponin-T (cTn-T) kits for the determination of myocardial degeneration in lambs suffering from white muscle disease (WMD). Cardiac troponin (cTn) analyses and necropsy were performed on 12 lambs with acute WMD. Only cTn analyses were tested in six healthy lambs. cTn-I and cTn-T tests were positive for all lambs with WMD, but negative in healthy lambs. Necropsy revealed that the cardiac and skeletal muscles of lambs with WMD had chalky white lesions, which appeared as necrosis and calcification in histopathology. The histopathological findings of the heart muscle and increased cTn in lambs with WMD suggested that marked myocardial degeneration may be detected by point-of-care cTn assays in lambs.

Histomoniasis in turkeys: pathological observations and PCR detection.

Histomoniasis was detected and described in naturally affected 35 turkeys. A polymerase chain reaction, which amplified a 209 bp region from the small subunit ribosomal RNA gene of H. meleagridis, was used and compared to the detection by histopathological observation of the histomonad trophozoits. In gross examination, typical histomoniasis lesions of hyperaemia and thickening of the cecal wall with grayish-yellow cecal cores were seen. In livers and kidneys, variably sized multiple foci of circumscribed necrotic areas were observed. Microscopically, varying amounts of histomonad trophozoits were detected in cecum (100%), liver (91.4%), kidney (17.1%), spleen (11.4%), proventriculus (5.7%) and bursa of Fabricius (2.8%). Mononuclear cell infiltration often containing giant cells in ceca, livers, kidneys and a proventriculus was observed. Lymphoid depletion was present in spleen and bursa of Fabricius. PCR assay detected the agent in cecum (100%), liver (100%), kidney (31.4%), spleen (25.7%), proventriculus (11.4%), bursa of Fabricius (11.4%) and lung (17.1%). This study describes histomoniasis lesions especially in several unusual locations such as kidney, spleen, bursa of Fabricius and proventriculus and could provide a help in the diagnosis of the natural histomoniasis in turkeys. It was also shown that PCR based detection was a more sensitive technique than detection based on histopathological observation.

Effectiveness of melatonin on aflatoxicosis in chicks.

The efficacy of melatonin co-administration on aflatoxicosis in chicks was investigated. Ross PM3 breed chicks were divided into groups of 10 and given conventional feed. One of the groups was kept as a control (C), and the others were given 150ppb aflatoxin (AF1), 300ppb aflatoxin (AF2), 150ppb aflatoxin plus 10mg/kg/bwt melatonin (AF1+M), 300ppb aflatoxin plus 10mg/kg/bwt melatonin (AF2+M), 10mg/kg/bwt melatonin (M), and 1% ethanol (E). After 21 day-treatment period, the chicks were sacrificed, liver and kidney tissues were collected, processed for immuno-histochemical staining, in situ TUNEL method, and biochemical analyses. Vacuolar degeneration, necrosis, bile duct hyperplasia in liver, and mild tubular degeneration in kidney were detected in AF groups. Pathological changes were markedly reduced in AF+M groups, and a microscopic view similar to group C was observed. Increased immunoreactivity against inducible nitric oxide synthase (iNOS) and nitrotyrosine was detected in AF groups compared to weak immunoreactivity in group C. Immunoreactivity in AF+M groups was markedly reduced compared to AF groups and was similar to group C in liver and kidney. Many apoptotic cells were detected in the livers of AF groups, whereas there were no apoptotic cells in AF+M groups. While reduced glutathione (GSH) levels in liver and kidney of AF groups were greatly reduced, malondialdehyde (MDA) levels increased. With melatonin co-administration, the levels of GSH and MDA approached to the values of group C. These results indicated that nitrosative tissue degeneration caused by aflatoxin could be greatly reduced by melatonin supplementation in chicks.

Diprosopus, craniorachischisis, arthrogryposis, and other associated anomalies in a stillborn lamb.

Congenital malformations with multiple anomalies have been described infrequently in the veterinary literature. A stillborn male crossbred lamb with diprosopus, craniorachischisis, and arthrogryposis was examined macroscopically and histopathologically in this study. The left head was smaller than the right head. Micrencephaly, agnathia, and a rudimentary tongue, which was adherent to the palate, were present in the left head. Micrencephaly, brachygnathia superior, and cleft palate were present in the right head. Cerebellar agenesis and spinal cord hypoplasia were observed. The cerebrums and the spinal cord were covered with a tapering membranous structure. Neural and dermal tissues were noted to intervene upon microscopic examination of this structure. Disorganization of neurons was observed in both cerebrums, though it was more severe in the left one. This case demonstrates many congenital defects occurring together in a lamb.

Occurrence of Helicobacter Infection in the gastric mucosa of free-living red foxes (Vulpes vulpes).

We studied gastric Helicobacter spp. in five red foxes (Vulpes vulpes). Samples of stomach from the cardia, corpus, pyloric antrum, and duodenum were subjected to histopathologic, immunohistochemical, and transmission electron microscopy (TEM) examination for the presence of Helicobacter and gastritis. All foxes had gastric Helicobacter-like organisms (GHLOs) on examination by light microscopy and TEM. Gastric Helicobacter-like organisms were present in all areas of the stomachs. Chronic mild or moderate gastric inflammation was associated with infection by GHLOs in one or more regions of the stomach, but there was no correlation between inflammation and infection. It is not clear whether the organisms were causing the minimal histologic lesions observed, but the gastric mucosa of free-living foxes appears to be commonly colonized with GHLOs. The frequent colonization of free-living foxes with distinct GHLOs possibly reflects their special characteristic in feeding and/or social behavior or the potential commensal nature of the bacteria in free-ranging foxes.