Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughput sequencing approach. A total of 165 miRNAs, representing 55 conserved families, and 50 novel miRNAs, representing 19 families, were identified in three libraries. In addition, 12 miRNAs were randomly selected from a differentially expressed conserved miRNA family in three libraries with expression alterations and subjected to qRT-PCR validation. Of these, the expression level of nta-miR167d is highly enriched in the leaf tissue. In addition, the expression level of nta-miR319a is prominently enriched in the stem, while nta-miR160c is highly enriched in the root. Moreover, the target prediction showed that most of the targets coded for transcription factors that are involved in cellular and metabolic processes. GO analysis showed that most of the targets were involved in organelle function, served binding functions, and take part in cellular and metabolic processes. This study helps shed new light on understanding the role of miRNAs in different parts of the tobacco plant and adds a significant number of novel miRNAs to the tobacco miRNA transcriptome.

Visualization of the Peripheral Branches of the Mandibular Division of the Trigeminal Nerve on 3D Double-Echo Steady-State with Water Excitation Sequence

BACKGROUND AND PURPOSE

Although visualization of the extracranial branches of the cranial nerves has improved with advances in MR imaging, only limited studies have assessed the detection of extracranial branches of the mandibular nerve (V3). We investigated the detectability of the branches of V3 on a 3D double-echo steady-state with water excitation sequence.

MATERIALS AND METHODS

We retrospectively evaluated the detectability of the 6 branches of the V3, the masseteric, buccal, auriculotemporal, lingual, inferior alveolar, and mylohyoid nerves, by using a 5-point scale (4, excellent; 3, good; 2, fair; 1, poor; and 0, none) in 86 consecutive patients who underwent MR imaging with the 3D double-echo steady-state with water excitation sequence. Weighted κ analysis was used to calculate interobserver variability among the 3 readers.

RESULTS

The detection of the lingual and inferior alveolar nerves was the most successful, with excellent average scores of 3.80 and 3.99, respectively. The detection of the masseteric, the buccal, and the auriculotemporal nerves was good, with average scores of 3.31, 2.67, and 3.11, respectively. The mylohyoid nerve was difficult to detect with poor average scores of 0.62. All nerves had excellent interobserver variability across the 3 readers (average weighted κ value, 0.95-1.00).

CONCLUSIONS

The 3D double-echo steady-state with water excitation sequence demonstrated excellent visualization of the extracranial branches of V3 in most patients. The 3D double-echo steady-state with water excitation sequence has the potential for diagnosing V3 pathologies and preoperatively identifying peripheral cranial nerves to prevent surgical complications.

Evaluation of normal changes in pons metabolites due to aging using turbo spectroscopic imaging

BACKGROUND AND PURPOSE

To date, MRS study of both normal and pathologic brains have focused mainly on the supratentorial regions; few studies have investigated the infratentorial regions. However, the pons, an important structure of the brain, is associated with many neurodegenerative diseases and is often damaged by brain trauma. For MRS study of pontine disease, one must obtain MRS reference data on normal metabolite levels in the pons, including data on how these levels vary with age. The aim of this study was to analyze normal, age-related, metabolic changes in the pons by using turbo spectroscopic imaging.

MATERIALS AND METHODS

Seventy-eight healthy subjects with ages ranging from 5 days to 78 years were included in this study. NAA/Cr, Cho/Cr, and Cho/NAA ratios were measured by using turbo spectroscopic imaging. The 78 cases were divided into 4 groups by age: 0-5, 6-20, 21-50, and older than 50 years. The metabolite levels were compared with observed age-related changes among the groups.

RESULTS

The normal mean pontine metabolite ratios obtained for the combined age groups were NAA/Cr, 2.44 ± 0.45 (mean); Cho/Cr, 1.93 ± 0.25; and Cho/NAA, 0.83 ± 0.28. Statistically significant differences were found in the NAA/Cr between the 0- to 5- and 6- to 20-year-old groups, and among the 6- to 20-, 21- to 50-, and older than 50-year-old groups. A statistically significant difference was found in Cho/Cr between the 0- to 5- and 6- to 20-year-old subjects; however, no differences were found among the 6- to 20-, 21- to 50-, and older than 50-year-old groups. Statistically significant differences in Cho/NAA were also found among the 4 age groups. The NAA/Cr at birth was low, it rose rapidly at 0-5 years, reaching a peak at approximately 10-20 years, and then gradually decreased. The Cho/Cr decreased rapidly at 0-5 years, then continued to decline, and was stable after 20 years of age.

CONCLUSIONS

Turbo spectroscopic imaging is a good method for analyzing normal changes in the pons metabolites during growth, maturation, and aging.

Note: Design and initial results of a multi-pulsed intense electron beam source

A multi-pulsed intense electron beam source is introduced, including the design and the initial experimental results. The source can generate a burst of three pulses of intense electron beams with energy of 2-3 MeV and beam intensities of around 2.5 kA. An inductive adder is chosen to generate the pulsed diode voltages and a dispenser cathode is chosen to emit electron beams. The test results indicate that the design of the source is reliable. The multi-pulsed diode voltage is up to 2.5 MV and the beam intensities are more than 2 kA at the exit of the source with small variation.

Reovirus-associated meningoencephalomyelitis in baboons

Baboon orthoreovirus (BRV) is associated with meningoencephalomyelitis (MEM) among captive baboons. Sporadic cases of suspected BRV-induced MEM have been observed at Southwest National Primate Research Center (SNPRC) for the past 20 years but could not be confirmed due to lack of diagnostic assays. An immunohistochemistry (IHC)-based assay using an antibody against BRV fusion-associated small transmembrane protein p15 and a conventional polymerase chain reaction (PCR)-based assay using primers specific for BRV were developed to detect BRV in archived tissues. Sixty-eight cases of suspected BRV-induced MEM from 1989 through 2010 were tested for BRV, alphavirus, and flavivirus by IHC. Fifty-nine of 68 cases (87%) were positive for BRV by immunohistochemistry; 1 tested positive for flavivirus (but was negative for West Nile virus and St Louis encephalitis virus by real-time PCR), and 1 virus isolation (VI) positive control tested negative for BRV. Sixteen cases (9 BRV-negative and 7 BRV-positive cases, by IHC), along with VI-positive and VI-negative controls, were tested by PCR for BRV. Three (of 9) IHC-negative cases tested positive, and 3 (of 7) IHC-positive cases tested negative by PCR for BRV. Both IHC and PCR assays tested 1 VI-positive control as negative (sensitivity: 75%). This study shows that most cases of viral MEM among baboons at SNPRC are associated with BRV infection, and the BRV should be considered a differential diagnosis for nonsuppurative MEM in baboons.

Effect of vitamin E supplementation on α-tocopherol and β-carotene concentrations in tissues from pasture- and grain-fed cattle

The effects of dietary vitamin E supplementation of grain-fed cattle on lipid oxidation and meat colour have been extensively investigated, but little attention has been given to pasture-fed cattle where meat is likely to contain naturally high amounts of α-tocopherol and carotenoids. In the work described, we evaluated the effects of pasture-feeding alone and with vitamin E supplementation on tissue levels of anti-oxidants and compared the findings with those obtained for grain-fed cattle with and without supplementation. Sorghum was the major component of the grained-based ration. α-Tocopherol concentrations in plasma, muscle and fat tissues of pasture-fed cattle were not affected by vitamin E supplementation (2500 IU/head/day for 132 days prior to slaughter) while those of grain-fed cattle increased significantly. The α-tocopherol concentrations in the supplemented grain-fed cattle were similar in muscle and liver to pasture-fed animals but were lower in their fat (P<0.05). The major carotenoid present in all tissues studied from pasture-fed was β-carotene and its contents in plasma, liver, fat and muscles were decreased (P<0.05) by supplementation with vitamin E. Carotenoids were essentially absent in grain-fed cattle except for small amounts in liver. The implication of this study for the meat industry is that cattle grazed on good pasture can achieve concentrations of α-tocopherol in muscles and other tissues at least as high as those obtained by supra-nutritional supplementation of grain-fed cattle with vitamin E. However, α-tocopherol supplementation of pasture-fed cattle reduced tissue concentrations of β-carotene, which would reduce carcase fat yellowness and make pasture-fed cattle more acceptable to some Asian markets.

Lipid stability and meat colour of beef from pasture- and grain-fed cattle with or without vitamin E supplement

Meat from pasture-fed cattle can have high contents of α-tocopherol and other anti-oxidants originating from naturally occurring compounds present in grasses. However, meat from pasture-fed cattle may have an increased demand for endogenous anti-oxidants because of its high content of polyunsaturated fatty acids, which in turn, may affect its colour and lipid stability. In the work described, we evaluated the effects of pasture-feeding alone and with vitamin E supplementation and compared the findings with those obtained for grain-fed cattle (predominantly sorghum) with and without supplementation. Within each nutritional background, vitamin E supplementation did not alter meat colour or colour stability of fresh or 47-day aged muscle during 7-day aerobic storage. However, both control and supplemented grain-fed product had better meat colour (more redness) compared with meat from grass-fed cattle. These differences in redness between pasture- and grain-fed fresh beef were not apparent after ageing. The treatments did not affect the lipid stability of fresh meat during aerobic storage; however, supplementation reduced (P<0.01) lipid oxidation in grain-fed aged beef compared with pasture-fed aged beef, despite both having similar α-tocopherol contents. Pasture-fed beef had more linolenic acid, less linoleic acid and, overall, was more polyunsaturated than grain-fed beef (P<0.05). In summary, vitamin E supplementation of pasture-fed cattle did not alter muscle tocopherol contents but pasture-fed beef (both control and supplemented) was more susceptible to lipid oxidation following ageing than vitamin E supplemented grain-fed beef.

A comparison of fat composition of Japanese and long-term grain-fed Australian steers

Subcutaneous and intermuscular fat samples were collected from carcases of four major breeds of steers in Japan: Wagyu, Wagyu × Angus, Dairy and Murray Grey. For comparison, we also collected subcutaneous fat samples from carcases of long-term grain-fed (350-455 days) Angus, Jersey and Angus × Hereford steers, and short-term grain-fed (70-100 days) Murray Grey steers in Australia. Fatty acid profiles were determined on all samples and triacylglycerol composition, thermal properties, fat cell size and lipid and connective tissue contents were determined on representative samples. Compared with the Japanese samples which were soft to very soft when assessed subjectively, samples of Australian fat were generally hard and somewhat fibrous in appearance. These tactile and visual differences in the hardness of the subcutaneous fat between the Japanese and Australian beef were confirmed by the physical and chemical properties determined. Markedly different melting patterns were observed for the Australian and Japanese fat samples. The Japanese fat had considerably less saturated and more unsaturated fatty acids resulting in much higher unsaturated/saturated ratios (1.9) compared with the Australian samples (1.0). This resulted primarily from the high contents of oleic and palmitoleic acids and the low content of stearic acid of the Japanese samples. The triacylglycerols from the Japanese fat had considerably less tri-saturated and di-saturated fatty acids and more di-monounsaturated and tri-monounsaturated fatty acids in their structure. Differences were observed when the Japanese subcutaneous fat samples were grouped by their meat quality grades. From Grade 5 to Grade 2, there was a significant decrease in marbling score (9.3 to 2.5) and in the ratio of palmitoleic to stearic acid (1.7 to 1.2) and an increase in the connective tissue content (1.5 to 2.1%). Compared with subcutaneous fat, intermuscular fat had a higher content of saturated and a lower content of unsaturated fatty acids resulting in a lower ratio of unsaturated to saturated fatty acids and of palmitoleic to stearic acid. It was concluded that the fatty acid composition and the triacylglycerol structure of fat plays the predominant role in determining the lustre, texture and properties of fat desired by the Japanese market: the soft character of fat from Japanese cattle results primarily from its low content of stearic acid and consequent lower melting temperatures. Fat cell size and the lipid and connective tissue contents of fat appear to be less important.

Mapping brain networks in awake mice using combined optical neural control and fMRI

Behaviors and brain disorders involve neural circuits that are widely distributed in the brain. The ability to map the functional connectivity of distributed circuits, and to assess how this connectivity evolves over time, will be facilitated by methods for characterizing the network impact of activating a specific subcircuit, cell type, or projection pathway. We describe here an approach using high-resolution blood oxygenation level-dependent (BOLD) functional MRI (fMRI) of the awake mouse brain-to measure the distributed BOLD response evoked by optical activation of a local, defined cell class expressing the light-gated ion channel channelrhodopsin-2 (ChR2). The utility of this opto-fMRI approach was explored by identifying known cortical and subcortical targets of pyramidal cells of the primary somatosensory cortex (SI) and by analyzing how the set of regions recruited by optogenetically driven SI activity differs between the awake and anesthetized states. Results showed positive BOLD responses in a distributed network that included secondary somatosensory cortex (SII), primary motor cortex (MI), caudoputamen (CP), and contralateral SI (c-SI). Measures in awake compared with anesthetized mice (0.7% isoflurane) showed significantly increased BOLD response in the local region (SI) and indirectly stimulated regions (SII, MI, CP, and c-SI), as well as increased BOLD signal temporal correlations between pairs of regions. These collective results suggest opto-fMRI can provide a controlled means for characterizing the distributed network downstream of a defined cell class in the awake brain. Opto-fMRI may find use in examining causal links between defined circuit elements in diverse behaviors and pathologies.

Structural and functional characterization of a pollen-specific promoter NTPp13 in tobacco

A novel 407 bp nucleotide sequence NTPp13 was isolated from tobacco (Nicotiana tabacum L.) by PCR, its structure and function were characterized. The NTPp13 sequence was highly homologous with the pollen-specific expression promoter Zm13 from maize (Zea mays L.) and contained some key motifs which controlled pollen-specific expression. The NTPp13 was fused to the beta-glucuronidase (GUS) reporter gene and transferred into tobacco. Analysis of the transgenic plants revealed that this putative promoter fragment was sufficient to direct GUS expression specifically in the anther, exactly in the pollen and pollen tube, and that GUS activity reached the maximum at the stage of pollen grain began to separate. Further study showed that the expression of NTPp13 sequence at pollen was stable at the range of temperature measured. These data suggested that the NTPp13 sequence was likely the essential element of promoter region of an unknown pollen-specific gene from tobacco.

Survivin knockdown by short hairpin RNA abrogates the growth of human hepatocellular carcinoma xenografts in nude mice

Abnormal high activation of survivin is involved in carcinogenesis of various types of cancer. Survivin has been shown to promote cell proliferation in human hepatocellular carcinoma (HCC). Survivin-targeting approaches have become a promising strategy for treating HCC. Here, we used a reporter system to screen effective survivin siRNA sequences. The effect of vector-based survivin short hairpin RNA (shRNA) on the malignant phenotype of HCC cells in vitro and in vivo was determined, and an adenovirus-mediated shRNA expression vector was developed to decrease survivin expression of the established HCC tumor in nude mice. In vitro study showed that stable survivin knockdown inhibited cancer cell proliferation, enhanced apoptotic susceptibility, arrested cell cycle in the G1 phase and resulted in apparent mitotic catastrophe. Moreover, cells stably expressing survivin shRNA showed decreased tumorigenicity in nude mice. An additional in vivo study showed that intratumoral injection of adenovirus-delivered survivin shRNA suppressed tumor growth by spontaneous apoptosis of cancer cells and significantly prolonged animal survival. In conclusion, we proved the therapeutic potential of survivin shRNA for the treatment of HCC. And our results indicated that adenovirus-delivered shRNA may serve as a novel therapeutic for HCC.

Simultaneous subsecond hyperpolarization of the nuclear and electron spins of phosphorus in silicon by optical pumping of exciton transitions

We demonstrate a method which can hyperpolarize both the electron and nuclear spins of 31P donors in Si at low field, where both would be essentially unpolarized in equilibrium. It is based on the selective ionization of donors in a specific hyperfine state by optically pumping donor bound exciton hyperfine transitions, which can be spectrally resolved in 28Si. Electron and nuclear polarizations of 90% and 76%, respectively, are obtained in less than a second, providing an initialization mechanism for qubits based on these spins, and enabling further ESR and NMR studies on dilute 31P in 28Si.

[Comparative study of experimental conjugated and combined vaccines against group B streptococci]

Immunogenic properties of recombinant protein ScaAB mixed with polypeptide P6 as well as conjugate of the former with capsular polysaccharide type III (PSIII) were assessed. Protein-polysaccharide conjugate was synthesized by reductive amination method. Immunogenicity was studied on the mouse model using aluminium hydroxide as adjuvant. Antibody titers in antisera were measured by immunoenzyme assay. Functional activity of antibodies was evaluated by opsonophagocytic test. Immunization with ScaAB-PSIII conjugate resulted in increased immune response to both ScaAB and polysaccharide. Administration of ScaAB and P6 proteins mixture compared to their separated administration led to increased of antibody titer and prolonged circulation of specific antibodies. Injection of studied vaccines increased opsonizing activity of antisera compared to immunization with uncombined components.

Establishment of an enzyme-linked immunosorbent assay system for determining soluble CD96 and its application in the measurement of sCD96 in patients with viral hepatitis B and hepatic cirrhosis

CD96, previously named T cell activation increased late expression (Tactile), is a transmembrane molecule that functions as an activated receptor on natural killer cells. It is well known that many transmembrane molecules have soluble forms, which were either shed from the cell surface or spliced at mRNA level. In many cases, the levels of soluble forms in the circulation could be used as biomarkers of lymphocyte activation in bacterial or virus infection, tumour, transplantation and autoimmune disease. To investigate whether CD96 could be released into the sera and the possible biological function of soluble hCD96 (sCD96), we generated and characterized five clones of anti-hCD96 mouse monoclonal antibodies (mAb) and developed a sandwich enzyme-linked immunosorbent assay (ELISA) system based on two anti-hCD96 mAbs with different epitope specificities. Using this ELISA system, sCD96 in serum samples from 99 healthy individuals could be detected. Furthermore, we found that the level of sCD96 in serum samples from patients with chronic viral hepatitis B or classes B and C of hepatic cirrhosis classified using the Child-Pugh score was much higher (P < 0.001 versus healthy individuals; P = 0.006 versus healthy individuals respectively) than that from healthy individuals (0.98 ng/ml). Our study demonstrates for the first time that sCD96 existed in sera, and suggests that sCD96 may be used as a serous marker for some diseases such as chronic viral hepatitis B infection or hepatic cirrhosis in classes B and C. The level of sCD96 in patients' serum may have some relationship with a chronic inflammatory reaction.

Reduction of the linewidths of deep luminescence centers in 28Si reveals fingerprints of the isotope constituents

Dramatic reductions of the linewidths of well-known deep centers in 28Si reveal "isotopic fingerprints" of the constituents. The approximately 1014 meV Cu center, thought to be either a Cu pair or an isolated Cu, is shown to contain four Cu atoms, and the approximately 780 meV Ag center is shown to contain four Ag. The approximately 944 meV ;{*}Cu center, thought to be a different configuration of a Cu pair, in fact contains three Cu and one Ag, and a new two-Cu two-Ag center is found. The approximately 735 meV center, previously assigned to Fe, actually contains Au and three Cu. This suggests a family of four-atom (Cu, Ag, Au) centers.