Discovery of genes related to witches broom disease in Paulownia tomentosa × Paulownia fortunei by a De Novo assembled transcriptome

In spite of its economic importance, very little molecular genetics and genomic research has been targeted at the family Paulownia spp. The little genetic information on this plant is a big obstacle to studying the mechanisms of its ability to resist Paulownia Witches' Broom (PaWB) disease. Analysis of the Paulownia transcriptome and its expression profile data are essential to extending the genetic resources on this species, thus will greatly improves our studies on Paulownia. In the current study, we performed the de novo assembly of a transcriptome on P. tomentosa × P. fortunei using the short-read sequencing technology (Illumina). 203,664 unigenes with a mean length of 1,328 bp was obtained. Of these unigenes, 32,976 (30% of all unigenes) containing complete structures were chosen. Eukaryotic clusters of orthologous groups, gene orthology, and the Kyoto Encyclopedia of Genes and Genomes annotations were performed of these unigenes. Genes related to PaWB disease resistance were analyzed in detail. To our knowledge, this is the first study to elucidate the genetic makeup of Paulownia. This transcriptome provides a quick way to understanding Paulownia, increases the number of gene sequences available for further functional genomics studies and provides clues to the identification of potential PaWB disease resistance genes. This study has provided a comprehensive insight into gene expression profiles at different states, which facilitates the study of each gene's roles in the developmental process and in PaWB disease resistance.

Effect of temperature gradient on liquid-liquid phase separation in a polyolefin blend

We have investigated experimentally the structure formation processes during phase separation via spinodal decomposition above and below the spinodal line in a binary polymer blend system exposed to in-plane stationary thermal gradients using phase contrast optical microscopy and temperature gradient hot stage. Below the spinodal line there is a coupling of concentration fluctuations and thermal gradient imposed by the temperature gradient hot stage. Also under the thermal gradient annealing phase-separated domains grow faster compared with the system under homogeneous temperature annealing on a zero-gradient or a conventional hot stage. We suggest that the in-plane thermal gradient accelerates phase separation through the enhancement in concentration fluctuations in the early and intermediate stages of spinodal decomposition. In a thermal gradient field, the strength of concentration fluctuation close to the critical point (above the spinodal line) is strong enough to induce phase separation even in one-phase regime of the phase diagram. In the presence of a temperature gradient the equilibrium phase diagrams are no longer valid, and the systems with an upper critical solution temperature can be quenched into phase separation by applying the stationary temperature gradient. The in-plane temperature gradient drives enhanced concentration fluctuations in a binary polymer blend system above and below the spinodal line.

Decreased functional connectivity between the amygdala and the left ventral prefrontal cortex in treatment-naive patients with major depressive disorder: a resting-state functional magnetic resonance imaging study

BACKGROUND

Convergent studies provide support for abnormalities in the structure and functioning of the prefrontal cortex (PFC) and the amygdala, the key components of the neural system that subserves emotional processing in major depressive disorder (MDD). We used resting-state functional magnetic resonance imaging (fMRI) to examine potential amygdala-PFC functional connectivity abnormalities in treatment-naive subjects with MDD.

METHODS

Resting-state fMRI data were acquired from 28 individuals with MDD and 30 healthy control (HC) subjects. Amygdala-PFC functional connectivity was compared between the MDD and HC groups.

RESULTS

Decreased functional connectivity to the left ventral PFC (VPFC) from the left and right amygdala was observed in the MDD group, compared with the HC group (p < 0.05, corrected).

CONCLUSIONS

The treatment-naive subjects with MDD showed decreased functional connectivity from the amygdala to the VPFC, especially to the left VPFC. This suggests that these connections may play an important role in the neuropathophysiology of MDD at its onset.

Potential implication of activating killer cell immunoglobulin-like receptor and HLA in onset of pulmonary tuberculosis

Killer cell immunoglobulin-like receptor (KIR) and human leucocyte antigen (HLA) play crucial role in maintaining immune homoeostasis and controlling immune responses. To investigate the influence of KIR and HLA-C ligands on the risk of pulmonary tuberculosis (PTB), we studied 200 patients who were confirmed to have PTB and 200 healthy controls on the different frequencies of KIR and HLA-C ligands. Genotyping of these genes was conducted by sequence-specific primer polymerase chain reaction (SSP-PCR) method. Gene frequencies were compared between PTB group and the control group by χ(2) test, and P < 0.05 was regarded as statistically significant. As a result, the frequency of KIR genotype A/B was increased in PTB than controls but A/A was decreased. Moreover, striking differences were observed in the frequencies of HLA-Cw*08 between the two groups. Besides, the frequencies of '2DL2/3 with C1' in PTB were increased compared with control group. In addition, individuals with no KIR2DS3 and no Cw*08 were higher in controls than in PTB. KIR2DS1 was increased in PTB when HLA-C group 2 alleles were missing. In conclusion, KIR and HLA-C gene polymorphisms were related to susceptibility to PTB.

Dnmt1-dependent DNA methylation is essential for photoreceptor terminal differentiation and retinal neuron survival

Epigenetic regulation of the genome is critical for the emergence of diverse cell lineages during development. To understand the role of DNA methylation during retinal network formation, we generated a mouse retinal-specific Dnmt1 deletion mutation from the onset of neurogenesis. In the hypomethylated Dnmt1-mutant retina, neural progenitor cells continue to proliferate, however, the cell cycle progression is altered, as revealed by an increased proportion of G1 phase cells. Despite production of all major retinal neuronal cell types in the Dnmt1-mutant retina, various postmitotic neurons show defective differentiation, including ectopic cell soma and aberrant dendritic morphologies. Specifically, the commitment of Dmnt1-deficient progenitors towards the photoreceptor fate is not affected by DNA hypomethylation, yet the initiation of photoreceptor differentiation is severely hindered, resulting in reduction and mislocalization of rhodopsin-expressing cells. In addition to compromised neuronal differentiation, Dnmt1 deficiency also leads to rapid cell death of photoreceptors and other types of neurons in the postnatal retina. These results indicate that Dnmt1-dependent DNA methylation is critical for expansion of the retinal progenitor pool, as well as for maturation and survival of postmitotic neurons.

First Report of Anthracnose Caused by Colletotrichum gloeosporioides on Pistachio (Pistacia vera) in China

In the 1990s, pistachio (Pistacia vera L. 'Kerman' and 'Peters') was introduced in China. They are found in many orchards in Beijing and Gansu and Hebei provinces, northern China. In 2009, a new disease was observed on leaves, stems, and fruits in pistachio orchards in Gansu Province. Disease incidence in 8- to 12-year-old orchards was 30%. Yield losses reached 25%. Symptoms began as discrete, sunken, black spots, approximately 10 mm in diameter, followed by circular lesions that eventually coalesced with tissue death recorded and orange fructifications developed on lesions. Pieces of diseased leaves, stems, and fruits were surfaced sterilized and placed on 2% potato dextrose agar (PDA) at 25°C. A fungus was consistently isolated. After 10 days, cultures on PDA showed aerial, white mycelium that turned gray to grayish black with a salmon-to-orange conidial mass at 25°C and a 12-h photoperiod. Brown, 80 to 120 μm long setae were observed in the acervulus. Conidia were hyaline, fusiform to nearly straight, and averaged 12 to 18 × 3 to 5 μm. On the basis of morphological characteristics, the fungus was identified as Colletotrichum gloeosporioides (Penz.) Sacc. (2). On PDA, 0.5 μg/ml of benomyl was applied for the sensitivity test (3). Benomyl completely inhibited the growth of the fungus. Mycelial DNA was extracted, PCR amplified using ITS1 and ITS4 primers for the ribosomal DNA internal transcribed spacers 1 and 2, and sequenced. The DNA sequence was recorded in GenBank as No. HQ631378. The DNA sequence was blasted showing 99% identity with Accession Nos. GQ144454 and GU004376, for C. gloeosporioides. Pathogenicity tests were conducted under greenhouse conditions at 25°C. Three replicates of 2-year-old 'Kerman' plants were inoculated with mycelial PDA plugs placed on 0.5-cm² stem wounds and then wrapped with Parafilm. Controls were inoculated with PDA plugs without the fungus. After 3 weeks, stem cankers were observed on inoculated plants. Control plants remained healthy. Pathogenicity was also tested on injured leaves and fruits. A 10-μl drop of a spore suspension of 10⁴ conidia/ml was applied on 'Kerman' and 'Peters' leaves and 'Kerman' fruits and placed on plates with a wet filter paper at 25°C. Small, black lesions were observed at 2 days after inoculation. At 7 days, necrotic lesions covered the entire surface. C. gloeosporioides was reisolated from necrotic lesions. Controls did not develop symptoms. C. acutatum has been reported on pistachio in Australia (1), but to our knowledge, this is the first report of anthracnose caused by C. gloeosporioides on pistachio. References: (1) G. J. Ash and V. M. Lanoiselet. Australas. Plant Pathol. 30:365, 2001. (2) J. Y. Lu. Plant Pathogenic Mycology. China Agricultural Press, Beijing, 2001. (3) N. A. R. Peres et al. Plant Dis. 86:620, 2002.

Exercise impacts brain-derived neurotrophic factor plasticity by engaging mechanisms of epigenetic regulation

We have evaluated the possibility that the action of voluntary exercise on the regulation of brain-derived neurotrophic factor (BDNF), a molecule important for rat hippocampal learning, could involve mechanisms of epigenetic regulation. We focused the studies on the Bdnf promoter IV, as this region is highly responsive to neuronal activity. We have found that exercise stimulates DNA demethylation in Bdnf promoter IV, and elevates levels of activated methyl-CpG-binding protein 2, as well as BDNF mRNA and protein in the rat hippocampus. Chromatin immunoprecipitation assay showed that exercise increases acetylation of histone H3, and protein assessment showed that exercise elevates the ratio of acetylated :total for histone H3 but had no effects on histone H4 levels. Exercise also reduces levels of the histone deacetylase 5 mRNA and protein implicated in the regulation of the Bdnf gene [N.M. Tsankova et al. (2006)Nat. Neurosci., 9, 519-525], but did not affect histone deacetylase 9. Exercise elevated the phosphorylated forms of calcium/calmodulin-dependent protein kinase II and cAMP response element binding protein, implicated in the pathways by which neural activity influences the epigenetic regulation of gene transcription, i.e. Bdnf. These results showing the influence of exercise on the remodeling of chromatin containing the Bdnf gene emphasize the importance of exercise on the control of gene transcription in the context of brain function and plasticity. Reported information about the impact of a behavior, inherently involved in the daily human routine, on the epigenome opens exciting new directions and therapeutic opportunities in the war against neurological and psychiatric disorders.

Symptom clusters in cancer patients: a review of the literature

Cancer patients often experience multiple symptoms, and those symptoms can independently predict changes in patient function, treatment failures, and post-therapeutic outcomes. Symptom clusters are defined as two or more concurrent symptoms that are related and may or may not have a common cause. The purpose of the present study was to review, in cancer patients, common symptom clusters and their predictors.

Using medline, embase, Cochrane Central, and cinahl, we conducted a literature search on symptom clusters in cancer patients. Studies that investigated predetermined clusters were not included. We identified seven individual studies and one group of five studies validating the M.D. Anderson Symptom Inventory. These studies had been published between 1997 and 2006. Two of the seven individual studies and the group of five studies that had validated the M.D. Anderson Symptom Inventory included patients with any cancer type; three studies included breast cancer patients only; and two studies included lung cancer patients only.

A gastrointestinal cluster consisting of nausea and vomiting was the single cluster common to two of the studies. The severity of this cluster increased when patients were treated with chemotherapy. No common clusters were found in the lung and breast cancer patient populations. However, breast cancer patients experienced more symptom cluster involvement while undergoing chemotherapy. We noted methodology disparities among the papers with regard to assessment tools used, statistical analyses, and populations.

Research on symptom clusters is still in an early stage. Multiple symptoms clearly affect prognosis, quality of life, and functional status. The study of symptom clusters is important for its implications regarding patient management, and a consensus on appropriate research methodology is vital.

Determination and pharmacokinetic study of indirubin in rat plasma by high-performance liquid chromatography

A specific, simple and sensitive HPLC method with UV detection was developed and validated for the pharmacokinetic studies of indirubin in rat plasma for the first time. Indirubin, with osthole as the internal standard, was extracted from plasma samples by liquid-liquid extraction. Chromatographic separation was conducted on a reverse-phase ODS column (200 mm x 4.6 mm, i.d., 5 microm), using a mixture of methanol-water (75:25, v/v) as the mobile phase at a flow rate of 1.0 ml/min with UV detection at 289 nm. The calibration curve of indirubin was linear over the range of 6.5-1950 ng/ml in rat plasma. The lower limit of quantification (LLOQ) was found to be 6.5 ng/ml. The present method was successfully applied for estimating the pharmacokinetic parameters of indirubin following intravenous and intraperitoneal administration of indirubin to rats.

Symptom clusters in cancer patients with brain metastases

AIM

To explore the presence of symptom clusters in patients with brain metastases.

MATERIALS AND METHODS

Patients with brain metastases referred to an outpatient palliative radiotherapy clinic were asked to rate their symptom distress using the Edmonton Symptom Assessment Scale (ESAS). Baseline demographic data were obtained. To determine interrelationships between symptoms, a principal component analysis with 'varimax rotation' was carried out on the nine ESAS items. Follow-up was carried out by telephone 1, 2, 4, 8 and 12 weeks after radiation.

RESULTS

Between January 1999 and January 2002, 170 patients with brain metastases provided complete baseline data on the ESAS. The most common primary cancer sites were lung, breast and gastrointestinal. Fatigue was the highest scored symptom, followed by a poor sense of well-being, anxiety, drowsiness and poor appetite. The four most prevalent symptoms were fatigue (91.7%), a poor sense of well-being (88.1%), drowsiness (82.2%) and anxiety (82.1%). Three symptom clusters were found at baseline. Cluster 1 included fatigue, drowsiness, shortness of breath and pain. Cluster 2 included anxiety and depression. Cluster 3 included poor appetite, nausea and a poor sense of well-being. Fatigue, nausea, drowsiness and poor appetite showed an overall increase in symptom severity over time; whereas fatigue, drowsiness and poor appetite were experienced to some extent by a greater proportion of patients at week 12 compared with baseline. Symptom clusters emerged in all weeks of follow-up, but consisted of different symptoms in each week.

CONCLUSION

Symptom clusters seemed to exist in patients with brain metastases before and after whole brain radiotherapy. However, different symptoms clustered at various time points. The effectiveness of whole brain radiotherapy in providing palliative relief to patients with brain metastases needs to be explored with regards to symptom clusters.

Bfl-1/A1 functions, similar to Mcl-1, as a selective tBid and Bak antagonist

The prosurvival Bcl-2-family member Bfl-1/A1 is a transcriptional target of nuclear factor-kappaB (NF-kappaB) that is overexpressed in many human tumors and is a means by which NF-kappaB inhibits apoptosis, but its mode of action is controversial. To better understand how Bfl-1 functions, we investigated its interaction with proapoptotic multidomain proteins Bax and Bak, and the BH3-only proteins Bid and tBid. We demonstrate that in living cells Bfl-1 selectively interacts with Bak and tBid, but not with Bax or Bid. Bfl-1/Bak interaction is functional as Bfl-1 suppressed staurosporine (STS)-induced apoptosis in wild-type and Bax-deficient cells, but not in Bak-/- cells. We also show that Bfl-1 blocks tumor necrosis factor-alpha (TNFalpha)-induced activation of Bax indirectly, via association with tBid. C-terminal deletion decreased Bfl-1's interaction with Bak and tBid and reduced its ability to suppress Bak- and tBid-mediated cell death. These data indicate that Bfl-1 utilizes different mechanisms to suppress apoptosis depending on the stimulus. Bfl-1 associates with tBid to prevent activation of proapoptotic Bax and Bak, and it also interacts directly with Bak to antagonize Bak-mediated cell death, similar to Mcl-1. Thus, part of the protective function of NF-kappaB is to induce Mcl-1-like activity by upregulating Bfl-1.