Genetic and phenotypic variation of foot-and-mouth disease virus during serial passages in a natural host

Foot-and-mouth disease virus (FMDV), like other RNA viruses, exhibits high mutation rates during replication that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses and, more specifically, FMDV has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little is known regarding the generation and effects of genetic variability of virus replication in the natural host under experimental conditions and no genetic data are available regarding the effects of serial passage in natural hosts. Here, we present the results of 20 serial contact transmissions of the highly pathogenic, pig-adapted O Taiwan 97 (O Tw97) isolate of FMDV in swine. We examined the virus genomic consensus sequences for a total of 37 full-length viral genomes recovered from 20 in vivo passages. The characteristics and distributions of changes in the sequences during the series of pig infections were analyzed in comparison to the O Tw97 genomes recovered from serially infected BHK-21 cell cultures. Unexpectedly, a significant reduction of virulence upon pig passages was observed, and finally, interruption of the viral transmission chain occurred after the14th pig passage (T14). Virus was, however, isolated from the tonsils and nasal swabs of the asymptomatic T15 pigs at 26 days postcontact, consistent with a natural establishment of the carrier state previously described only for ruminants. Surprisingly, the region encoding the capsid protein VP1 (1D) did not show amino acid changes during in vivo passages. These data demonstrate that contact transmission of FMDV O Tw97 in pigs mimics the fitness loss induced by the bottleneck effect, which was previously observed by others during plaque-to-plaque FMDV passage in vitro, suggesting that unknown mechanisms of virulence recovery might be necessary during the evolution and perpetuation of FMDV in nature.

Mutations in the carboxyl terminal region of E2 glycoprotein of classical swine fever virus are responsible for viral attenuation in swine

We have previously reported [Risatti, G.R., Borca, M.V., Kutish, G.F., Lu, Z., Holinka, L.G., French, R.A., Tulman, E.R., Rock, D.L. 2005a. The E2 glycoprotein of classical swine fever virus is a virulence determinant in swine. J. Virol. 79, 3787-3796] that chimeric virus 319.1v containing the E2 glycoprotein gene from Classical Swine Fever Virus (CSFV) vaccine strain CS with the genetic background of highly virulent CSFV strain Brescia (BICv) was markedly attenuated in pigs. To identify the amino acids mediating 319.1v attenuation a series of chimeric viruses containing CS E2 residues in the context of the Brescia strain were constructed. Chimera 357v, containing CS E2 residues 691 to 881 of CSFV polyprotein was virulent, while chimera 358v, containing CS E2 residues 882 to 1064, differing in thirteen amino acids from BICv, was attenuated in swine. Single or double substitutions of those amino acids in BICv E2 to CS E2 residues did not affect virulence. Groups of amino acids were then substituted in BICv E2 to CS E2 residues. Mutant 32v, with six substitutions between residues 975 and 1059, and mutant 33v, with six substitutions between 955 and 994, induced disease indistinguishable from BICv. Mutant 31v, with seven substitutions between residues 882 and 958, induced a delayed onset of lethal disease. Amino acids abrogating BICv virulence were then determined by progressively introducing six CS residues into 31v. Mutant 39v, containing nine residue substitutions, was virulent. Mutant 40v, containing ten residue substitutions, induced mild disease. Mutant 42v, containing twelve substitutions, and mutant 43v, with an amino acid composition identical to 358v, were attenuated in swine indicating that all substitutions were necessary for attenuation of the highly virulent strain Brescia. Importantly, 358v protected swine from challenge with virulent BICv at 3 and 28 days post-infection.

Emulsion PCR-based method to detect Y chromosome microdeletions

Deletions in Y chromosome are thought to be pathologically involved in some cases of male infertility associated with azoospermia or oligozoospermia. An emulsion-based multiplex PCR method was developed for detecting Y chromosome microdeletions in infertile men and a plasma sample of pregnant women carrying a male fetus. The sensitivity of multiplex PCR in emulsion was evaluated. Conventional PCR was also carried out for comparison. A total of 13 sequence-tagged sites (STSs) distributed in the AZF region were analyzed simultaneously with this method. The SRY gene was also detected as the inner control. Results showed that Y chromosome microdeletions were found in 4 of 19 infertile patients. Also, in 1 of 63 samples collected from pregnant women, microdeletions were found in some of the detected sites. It is suggested that the emulsion PCR assay was proven to be a promising diagnostic tool and could be widely used in further clinical and academic research.

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features

To distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs), a hybrid feature which consists of local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure and P-value of randomization test is used. Besides, a novel machine-learning algorithm, random forest (RF), is introduced. The results suggest that our method predicts at 98.21% specificity and 95.09% sensitivity. When compared with the previous study, Triplet-SVM-classifier, our RF method was nearly 10% greater in total accuracy. Further analysis indicated that the improvement was due to both the combined features and the RF algorithm. The MiPred web server is available at http://www.bioinf.seu.edu.cn/miRNA/. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one.

An outbreak of pig rabies in Hunan province, China

The first dog-associated outbreak of rabies in swine in China (Hunan province) has been diagnosed and the related virus isolated. Sequence analysis showed that the pig isolate was a genotype 1 rabies virus with a very high nucleotide identity to local dog isolates.

Melatonin inhibits fatty acid-induced triglyceride accumulation in ROS17/2.8 cells: implications for osteoblast differentiation and osteoporosis

Melatonin is produced not only by the pineal gland but by cells of the bone marrow. Moreover, melatonin is known to promote osteogenic differentiation in several cell line models and in multipotential bone marrow mesenchymal stem cells. Fatty acids have been independently shown to direct such cells to acquire the phenotype and molecular characteristics of adipocytes. To examine the effect of melatonin on intracellular triglyceride accumulation, an indicator of adipogenic differentiation in the rat osteoblast-like ROS17/2.8 cell line, cells were incubated with added oleic acid (100 μM), fixed and stained with Oil Red O. Cellular lipid accumulation was quantitated by an Oil Red O method highly specific for triglycerides and expressed as a triglyceride accumulation index (TGAI, triglyceride per cell). Melatonin in nanomolar concentrations inhibited oleic acid-induced triglyceride accumulation. To identify the mechanism by which melatonin reduces triglyceride accumulation, cells were incubated with the two melatonin receptor antagonists, luzindole and S20928, or forskolin, a stimulator of adenylyl cyclase and cAMP production. These compounds prevented the inhibitory effect of melatonin on triglyceride accumulation, indicating that melatonin acts through known melatonin receptor-mediated mechanisms. In view of the previously demonstrated positive effects of melatonin in promoting osteoblastic differentiation in ROS17/2.8 cells and their reciprocal adipocytic differentiation induced by fatty acids, our observations may serve to relate the known age-related decreases of melatonin production, the shift in the bone marrow toward an adipocytic line of cell development, and the development of osteoporosis during aging.

RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features

In the yeast, meiotic recombination is initiated by double-strand DNA breaks (DSBs) which occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Although observations concerning individual hot/cold spots have given clues as to the mechanism of recombination initiation, the prediction of hot/cold spots from DNA sequence information is a challenging task. In this article, we introduce a random forest (RF) prediction model to detect recombination hot/cold spots from yeast genome. The out-of-bag (OOB) estimation of the model indicated that the RF classifier achieved high prediction performance with 82.05% total accuracy and 0.638 Mattew's correlation coefficient (MCC) value. Compared with an alternative machine-learning algorithm, support vector machine (SVM), the RF method outperforms it in both sensitivity and specificity. The prediction model is implemented as a web server (RF-DYMHC) and it is freely available at http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm. Given a yeast genome and prediction parameters (RI-value and non-overlapping window scan size), the program reports the predicted hot/cold spots and marks them in color.

Application of atomic force microscopy on observing the ultra-fine structure of the neoproterozoic microfossils from China

Phosphatic microfossils from the Doushantuo Formation, Guizhou, China, have been reported with preserved cellular structure or even sub-cellular structure in micron scale. However, more details in sub-micro scale have not been reported as having been found. The Fossil embryos from the acid residue of the phosphorite rocks of the Neoproterozoic Doushantuo Formation in south China have been studied with a scanning electron microscope (SEM) and an atomic force microscope (AFM). Some ultra-structures in sub-micro scale have been found by AFM on the surface of the fossil embryos. There are four types of structures found on the surface of the selected fossil embryos, the sizes of which vary from 30 to 645 nm in diameter under our AFM. One of the structures is composed of several big sub-units integrated with each other, and the size of the big sub-units is from 250 to 645 nm. Meanwhile, we also found an ultra-layer structure on the surface of the big sub-units, the thickness of which was about 10 nm. Thus we speculate that it could most probably be of biological origin. Therefore, AFM provides a new method for direct observation of the ultra-structure of the Doushantuo fossils in the sub-micro scale.

The LIM-only factor LMO4 regulates expression of the BMP7 gene through an HDAC2-dependent mechanism, and controls cell proliferation and apoptosis of mammary epithelial cells

The nuclear LIM-only protein 4 (LMO4) is upregulated in breast cancer, especially estrogen receptor-negative tumors, and its overexpression in mice leads to hyperplasia and tumor formation. Here, we show that deletion of LMO4 in the mammary glands of mice leads to impaired lobuloalveolar development due to decreased epithelial cell proliferation. With the goal of discovering potential LMO4-target genes, we also developed a conditional expression system in MCF-7 cells for both LMO4 and a dominant negative (DN) form of its co-regulator, cofactor of LIM domains (Clim/Ldb/Nli). We then used DNA microarrays to identify genes responsive to LMO4 and DN-Clim upregulation. One of the genes common to both data sets was bone morphogenic protein 7 (BMP7), whose expression is also significantly correlated with LMO4 transcript levels in a large dataset of human breast cancers, suggesting that BMP7 is a bona fide target gene of LMO4 in breast cancer. Inhibition of BMP7 partially blocks the effects of LMO4 on apoptosis, indicating that BMP7 mediates at least some functions of LMO4. Gene transfer studies show that LMO4 regulates the BMP7 promoter, and chromatin immunoprecipitation studies show that LMO4 and its cofactor Clim2 are recruited to the BMP7 promoter. Furthermore, we demonstrate that HDAC2 recruitment to the BMP7 promoter is inhibited by upregulation of LMO4 and that HDAC2 knockdown upregulates the promoter. These studies suggest a novel mechanism of action for LMO4: LMO4, Clim2 and HDAC2 are part of a transcriptional complex, and increased LMO4 levels can disrupt the complex, leading to decreased HDAC2 recruitment and increased promoter activity.

Real-time PCR Assay for Ultrasensitive Quantification of DNA-Binding Proteins

Background: The specific binding of proteins to DNA is a key step for many cellular activities, such as transcription regulation, DNA replication, recombination, repair, and restriction. The detection of DNA-binding proteins, as well as the identification of specific binding sites, is therefore important to understand gene expression mechanisms and cellular function. We describe an ultrasensitive method for quantification of DNA-binding proteins.

Methods: We combined the common exonuclease III (ExoIII) footprinting assay and real-time PCR for quantification of DNA-binding proteins, for an assay that does not require antibodies against the target proteins. Double-strand DNA probes were designed to monitor the activities of DNA-binding protein. The protein-binding site is at the 5′ end of the forward primer. When a target protein is present, it will specifically bind to the protein-binding site and produce a physical hindrance to ExoIII, which protects the reverse DNA strand from digestion by ExoIII. The remaining single-strand DNA template can be quantitatively detected by real-time PCR. Conversely, in the absence of the target protein, the naked primer regions will be degraded by ExoIII, which then cannot be amplified by real-time PCR.

Results: We detected the binding of 10 different transcription factors in crude cell extracts. The assay quantitatively detected binding at femtomolar concentrations of protein.

Conclusions: This technique is customizable and easy to establish. It has potential applications in research, medical diagnosis, and drug discovery.

Altered expression of HOXA10 in endometriosis: potential role in decidualization

Endometriosis is a poorly understood gynaecologic disorder that is associated with infertility. In this study, we examined the expression of HOXA10 in the eutopic endometrium of baboons with induced endometriosis. A decrease in HOXA10 mRNA was observed after 3, 6, 12 and 16 months of disease, which reached statistical significance at 12 and 16 months. HOXA10 protein levels were decreased in both the epithelial and stromal cells of the endometrium. Furthermore, expression of beta3 integrin (ITGB3), which is upregulated by HOXA10, was decreased, whereas EMX2, a gene that is inhibited by HOXA10, was increased. Next, methylation patterns of the HOXA10 gene were analysed in the diseased and control animals. The F1 region on the promoter was found to be the most significantly methylated in the endometriosis animals and this may account for the decrease in HOXA10 expression. Finally, we demonstrate that stromal cells from the eutopic endometrium of baboons with endometriosis expressed significantly higher levels of insulin-like growth factor binding protein-1 (IGFBP1) mRNA than disease-free animals in response to estradiol, medroxyprogesterone acetate and dibutyryl cAMP (H + dbcAMP). The functional role of HOXA10 in IGFBP1 expression was further explored using human endometrial stromal cells (HSC). Overexpression of HOXA10 in HSC resulted in a decrease of IGFBP1 mRNA, whereas silencing HOXA10 caused an increase of IGFBP1 mRNA, even in the presence of H + dbcAMP. These data demonstrate that HOXA10 negatively influences IGFBP1 expression in decidualizing cells. Thus, the decrease in HOXA10 levels may in part be involved with the altered uterine environment associated with endometriosis.

Gender difference in hemodynamic responses of prefrontal area to emotional stress by near-infrared spectroscopy

Presentation of negative pictures was used as emotional stress to assess gender differences in prefrontal area activation in a functional near-infrared spectroscopy (NIRS) study. Compared with neutral condition, the response of oxy-HB for men yielded no significant difference during stress period, but the response induced by stress pictures for women showed significant enhancement. It was indicated that it is crucial to take gender difference into account when negative stimuli are used in functional brain imaging.

An evaluation of the vitamin D3 content in fish: Is the vitamin D content adequate to satisfy the dietary requirement for vitamin D?

It has been suggested that the major source of vitamin D should come from dietary sources and not sun exposure. However, the major fortified dietary source of vitamin D is milk which often does not contain at least 80% of what is stated on the label. Fish has been touted as an excellent source of vitamin D especially oily fish including salmon and mackerel. Little is known about the effect of various cooking conditions on the vitamin D content in fish. We initiated a study and evaluated the vitamin D content in several species of fish and also evaluated the effect of baking and frying on the vitamin D content. Surprisingly, farmed salmon had approximately 25% of the vitamin D content as wild salmon had. The vitamin D content in fish varied widely even within species. These data suggest that the tables that list the vitamin D content are out-of-date and need to be re-evaluated.

The response of the metabolic network of the red blood cell to pyruvate kinase deficiency

The response of the metabolic network of human red blood cell is investigated using the E-Cell simulation system when pyruvate kinase (PK) is deficient. The results that several downstream metabolites of the glycolysis pathway accumulate are in a good agreement with experimental data reported in literatures. This accumulation results in the reaction that phosphoglycerate kinase (PGK) catalyzes reversing its direction. Mathematical analysis to the simulation results shows that the PGK-catalyzing reaction reversing its direction happens simultaneously with an abrupt change of the second derivative of the ATP quantity.

Theoretical and experimental studies on filtering tumor cells from blood cell mixtures with dam structure in microfluidic devices

Here, a filter with series of pools and dams structures was designed and fabricated, utilizing size difference between tumor and blood cells. The cell mixtures were successfully filtrated out by the filter, and separation efficiency was up to 99.9%. To evaluate the filter, physical models were made to describe the behaviors of different cells in microfluidic systems. As the ability of cell deformation depends on both cells' size and excess surface index (ESI), we measured the excess membrane area of different cells, and got tumor cell's ESI is 61.7% ~ 81% comparing with red blood cell (RBC) (44%) and white blood cell (WBC) (84%~137%). Then from the formulas we deduced, we get the filtering limitations of RBC, WBC, and tumor cell are respectively, around 1.8μm, 1.0-1.6μm and 3.7-4.4μm for dam structure; and 1.3μm, 0.9-1.3μm and 3-3.4μm radius for pipes, which actually show conditions for separation. The accuracy and high flux of the filter provide possibilities to isolate cancer cells directly from the blood in real-time, which could become a potential therapy to cancers.

Post-hybridisation by Electrophoresis for Reinforcing the Hybridization Result

In this paper, we developed an electrophoresis method for reinforcing hybridization efficiency, and distinguishing the perfectly matched sequences from the mismatched ones. The non-specific binding labeled targets in the hybridization were effectively removed by electrophoresis instead of the conventional washing procedure in the post-hybridisation process. During electrophoresis, the hybrids (the dual-spiral structures formed in hybridization) would be unchained when targets were continuously removed. In this case, not only the non-specific binding labeled targets, but also the targets participating in hybridization would be removed. Therefore, only the perfectly matched sequences had the distinct hybridization signals, the perfectly matched probes from the single-base mismatched ones could more easily be distinguished, and the single nucleotide polymorphisms (SNP) genotypes were also easily determined by dual-color fluorescence targets.

Novel microarray technology for post-genomic studies

There are great challenges of developing high-throughput analytic tools in the post-genomic era. The microarray technology, as one of the most poowerful high-throughput tools, has a lot of opportunities in meeting increasing enormous demands in the discovery of the molecular mechanisms of life systems. A number of the new concept microarrays will be developed and used in fundamental and medical researches in the near future. We developed several kinds of the new microarray chips for detecting DNA methylation patterns, double strands DNA microarray for sequence-specific DNA binding proteins (such as transcription factors), the PCR procduct microarray for screening disease related SNPs, a cap-array assay (lab-in-a-tube system), and quantitative detection microarray for mulit-viruses detection and clinical applications. In this presentation, I will give brief introductions on these biochip platforms developed in our laboratory recently. Our results show that the innovations in high-throughput tools could be promoted through the combination between life science and engineering researches.

Blood vessels and desmin control the positioning of nuclei in skeletal muscle fibers

Skeletal muscle fibers contain hundreds to thousands of nuclei which lie immediately under the plasmalemma and are spaced out along the fiber, except for a small cluster of specialized nuclei at the neuromuscular junction. How the nuclei attain their positions along the fiber is not understood. Here we show that the nuclei are preferentially localized near blood vessels (BV), particularly in slow-twitch, oxidative fibers. Thus, in rat soleus muscle fibers, 81% of the nuclei appear next to BV. Lack of desmin markedly perturbs the distribution of nuclei along the fibers but does not prevent their close association with BV. Consistent with a role for desmin in the spacing of nuclei, we show that denervation affects the organization of desmin filaments as well as the distribution of nuclei. During chronic stimulation of denervated muscles, new BV form, along which muscle nuclei align themselves. We conclude that the positioning of nuclei along muscle fibers is plastic and that BV and desmin intermediate filaments each play a distinct role in the control of this positioning.

A Simple Method of Fabricating Weir-type Filters with Interdigital Aligned Full-polymer Microfluidic Channels for Blood Cell Fractionation

This paper describes a new method to fabricate large scale 3D weir-type filter for cell fractionation. The 3D structure is realized by a conformal bonding of two separate PDMS (poly-dimethyloxane) layers with in-situ microchannels which are formed by the conventional soft lithographic techniques. Moreover, the microfluidics channels on the two PDMS are set to cross to each other to increase weir numbers and flow throughput. The gap space of the weir filters depends on the thickness of the photoresist coated for the master formation, thereby it can be defined as required from submicron to hundreds micron scale. A white blood cells (WBCs) extraction experiments with the full polymer fabricated filters are conducted to validate the proposed method.. The experimental results show that the weir-type filter array can fractionate the WBCs well from blood samples. Due to its intrinsic advantages of rapid process, high throughput and low cost, the proposed method is very promising for being integrated into Micro Total analysis System (μTAS).

Non-invasive monitoring of left ventricular contractility and ventilatory mechanics

The maximum left ventricular elastance (E^max<inf>iv</inf>) is a valuable index of ventricular contractility. However, conventional methods for its measurements are too invasive for routine use. We propose a non-invasive technique for tracking changes in E^max<inf>iv</inf>by mathematically determining the dynamic coupling between beat-to-beat fluctuations in instantaneous lung volume and arterial blood pressure measured during random-interval breathing. The mathematical technique also provides an estimate of the dominant time constant of the ventilatory system (), which is equal to the product of the airway resistance and lung compliance. We then describe a theoretical evaluation of the technique with respect to realistic beat-to-beat variability generated by a cardiovascular simulator. Our results show that the technique is able to detect actual changes in the E^max<inf>iv</inf>and values of the simulator. With successful experimental testing, the technique may ultimately be employed to help guide therapy in heart failure patients.

Cardiac output monitoring in intensive care patients by radial artery pressure waveform analysis

We have developed a novel technique for monitoring cardiac output (CO) changes by mathematically analyzing a single peripheral arterial blood pressure (ABP) waveform. In contrast to all previous techniques, our technique analyzes the ABP waveform over time scales greater than a cardiac cycle in which complex wave reflections are attenuated. We have previously validated the technique in swine instrumented with aortic flow probes. We present here an initial evaluation of the technique in 16 patient records of the MIMIC (Multi-parameter Intelligent Monitoring for Intensive Care) database, consisting of 122 simultaneous pairs of radial ABP waveforms and thermodilution CO. We report an overall error in the technique of 18.1% with respect to the error-prone clinical thermodilution measurements. This study promotes thorough future testing of the technique in humans.