[Comparison of QuantiFERON-TB Gold Plus and QuantiFERON-TB Gold In Tube in the diagnosis of pulmonary tuberculosis]

Objective: To compare the screening value of QuantiFERON-TB Gold Plus (QFT-Plus) and QuantiFERON®-TB Gold in tube (QFT-GIT) in the auxiliary diagnosis of pulmonary tuberculosis (TB). Methods: A screening test was performed. Patients who were hospitalized in Guangzhou Chest Hospital and underwent QFT-GIT testing from October to December 2020 were prospectively included as research subjects, QFT-Plus testing was added. And the basic information, clinical manifestations, laboratory test results, imaging examinations and other data of these patients were collected. A total of 207 patients were included and divided into tuberculosis group and non-tuberculosis group according to these data. There were 124 cases in the tuberculosis group (94 confirmed patients and 30 clinically diagnosed patients), including 90 males and 34 females, aged 18-93 years, with a median age of 57 (38, 67) years. The non-tuberculosis group included 83 patients (16 patients with non-tuberculous Mycobacteria and 67 patients with other lung diseases), including 49 males and 34 females, with a median age of 60 (51, 68) years. The confirmed patients were subdivided into three grades of low, medium and high Mycobacteriam tuberculosis (MTB) bacterial load, and three grades of mild, moderate and severe pulmonary tuberculosis. The results of QFT-Plus and QFT-GIT were compared, and the levels of IFN-γ in different antigen tubes were compared. Differences between different groups were compared using Mann-Whitney U test and Kruskal-Wallis H test. Results: The QFT-Plus showed a high degree of agreement with the QFT-GIT (κ=0.786, 95%CI: 0.740-0.832), while the main discordant result was QFT-GIT negative/QFT-Plus positive, accounting for 15/17. The sensitivity of QFT-GIT was 80.7%(95%CI: 0.706-0.880), the specificity was 76.3%(95%CI: 0.649-0.850), the positive predictive value was 79.8%(95%CI: 0.697-0.873), and the negative predictive value was 77.3%(95%CI: 0.659-0.859), repectively. QFT-Plus showed a sensitivity of 84.3%(95%CI: 0.743-0.910), a specificity of 78.8% (95%CI: 0.679-0.868), and a positive predictive value of 80.5%(95%CI: 0.703-0.879), the negative predictive value being 82.9%(95%CI: 0.721-0.902), slightly improved to that of the QFT-GIT. Also, this study found that there were significant differences in IFN-γ values between different MTB load or disease severity (P<0.05). Conclusions: There is a good consistency between the QFT-Plus test and the QFT-GIT test, both of which show good application value in the auxiliary diagnosis of pulmonary tuberculosis. Moreover, because of the addition of tuberculosis-specific CD8 cell antigen, the QFT-Plus test has higher sensitivity, lower uncertainty and more application value. This study also found that the bacterial load and disease severity of patients with pulmonary tuberculosis may have a certain correlation with the measured value of IFN-γ.

Cloning of PCS gene (TpPCS1) from Tagetes patula L. and expression analysis under cadmium stress

Phytochelatins (PCs) constitute an important mechanism for plants to resist heavy metal stress. Widely found in higher plants, they are small heavy metal binding peptides, synthesized through catalysis of phytochelatin synthase (PCS). We speculate that there may be PCS genes in Peacock grass (Tagetes patula L., Asteraceae), which is an important reason for its rich cadmium. In order to obtain the full-length cDNA sequence of the PCS gene from T. patula L. used rapid amplification of cDNA ends (RACE). Meanwhile, Relative expression of TpPCS1 under different concentrations of cadmium (Cd) stress was analysed using quantitative real-time polymerase chain reaction (qRT-PCR). Results found ORF of TpPCS1 genes with a length of 1970 bp, a gene coding area length of 1764 bp, coding for 587 amino acids. Expression of TpPCS1 under Cd stress was tissue specific. TpPCS1 in the root showed higher expression, while expression in the leaf and seed was relatively low. This research demonstrates that expression of TpPCS1 enhanced the enrichment of cadmium in T. patula L. roots and could be used to construct a plant hyperexpression carrier that would provide new avenues for plant restoration technology.

Sirt1 suppresses MCP-1 production during the intervertebral disc degeneration by inactivating AP-1 subunits c-Fos/c-Jun

OBJECTIVE

The anti-inflammatory effect of Sirtuin 1 (Sirt1) during intervertebral disc degeneration (IDD) has been widely confirmed. Monocyte chemoattractant protein-1 (MCP-1) activation is the initiating inflammatory response associated with the IDD. However, whether Sirt1 suppresses MCP-1 in the intervertebral disc is unclear.

PATIENTS AND METHODS

The MCP-1 and Sirt1 protein expression in the degenerated and non-degenerated NP tissues were compared by immunohistochemistry (IHC). We induced nucleus pulposus (NP) cell degeneration by IL-1β and mediated cellular Sirt1 expression through the Sirt1 activator resveratrol (Res) or inhibitor Nicotinamide (Nico). In addition, the inhibitors of MCP-1 and Activator protein 1 (AP-1) were also used in cell culture. The function of NP cells was determined by the type II collagen and Cell Counting Kit-8 (CCK-8) assay. We assessed the Sirt1 and MCP-1 expression by the Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR). The AP-1 activity was valued by the phosphorylation of its components c-Fos, and c-Jun.

RESULTS

Both in vivo and in vitro experimental results indicated that MCP-1 was upregulated in the degenerated condition, which was opposite to Sirt1 expression. Res suppressed AP-1, the phosphorylation of c-Fos/c-Jun, and the MCP-1 expression. On the contrary, Sirt1 downregulation by Nico aggravated the phosphorylation of c-Fos/c-Jun and MCP-1 expression. However, the MCP-1 suppression did not affect the Sirt1 and AP-1 levels. The destruction of AP-1 activation also inhibited MCP-1 expression but not Sirt1. The upregulation of Sirt1 and suppression of MCP-1 improved the type II collagen expression and cell viability, which was injured by IL-1β.

CONCLUSIONS

Sirt1 suppresses the MCP-1 production in the degenerated NP cells by suppressing the phosphorylation of the AP-1 subunits c-Fos and c-Jun.

MiRNA-206 suppresses the metastasis of osteosarcoma via targeting Notch3

To investigate the role of microRNA-206 (miRNA-206) in the malignant progression of osteosarcoma and the underlying mechanism, expression pattern of miRNA-206 in osteosarcoma tissues and cell lines was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Correlation between miRNA-206 level and prognosis of osteosarcoma patients was analyzed. Regulatory effects of miRNA-206 on the proliferation and metastasis of U2OS and MG63 cells were evaluated by cell counting kit-8 (CCK-8), Transwell and wound healing assay. Through dual-luciferase reporter gene assay, the target gene of miRNA-206 was verified. A series of rescue experiments were conducted to explore the role of miRNA-206/Notch3 in regulating the malignant progression of osteosarcoma. MiRNA-206 was downregulated in osteosarcoma tissues and cell lines, and its level was correlated to poor prognosis and distant metastasis of osteosarcoma patients. Overexpression of miRNA-206 attenuated the proliferative and metastatic abilities of osteosarcoma cells, and miRNA-206 knockdown obtained the opposite trends. Notch3 was verified to be the target gene of miRNA-206, which was upregulated in osteosarcoma and accelerated osteosarcoma cells to proliferate and metastasize. Finally, rescue experiments showed that Notch3 overexpression partially reversed the regulatory effects of miRNA-206 on cellular behaviors of osteosarcoma cells. MiRNA-206 is downregulated in osteosarcoma. Overexpression of miRNA-206 accelerates osteosarcoma cells to proliferate and metastasize by targeting Notch3, thus accelerating the malignant progression of osteosarcoma.

Caveolin-1 improves lung injury in rats with chronic obstructive pulmonary disease partially through Wnt/β-catenin signaling pathway

The aim of this study was to explore the effects of Caveolin-1 on lung injury in rats with chronic obstructive pulmonary disease (COPD). The forced expiratory volume in 0.3 s/forced vital capacity (FEV0.3/ FVC) and peak expiratory flow (PEF) were determined. The total white blood cells (WBC), neutrophil ratio (NEUT%), mononuclear macrophage ratio (MNM%), lymphocyte ratio (LY%) and protein concentration in bronchoalveolar lavage fluid (BALF) were measured. Both FEV0.3/FVC and PEF significantly declined in the COPD group compared with those in the Control group, while they significantly rose in the IWR-1 group and Daidzin group compared with those in the COPD group. HE staining showed that there were alveolar dilatation and enlargement with obviously increased intercept in the COPD group, while there were basically no changes in the alveoli in the IWR-1 group and Daidzin group. Massive apoptosis of alveolar tissues was observed in COPD group, and there was only a little apoptosis in IWR-1 group and Daidzin group. In COPD group, WBC, NEUT% and protein concentration in BALF were obviously increased, MNM% was obviously decreased, and there was no obvious difference in LY% compared with those in the Control group. In the the IWR-1 group and Daidzin group, WBC, NEUT%, protein concentration, MNM% and LY% in BALF had no obvious differences compared with those in the Control group. In the IWR-1 group and Daidzin group, WBC, NEUT% and protein concentration evidently declined, MNM% evidently rose, and there was no obvious difference in LY% compared with those in the COPD group. Caveolin-1, Wnt-1 and β-catenin in lung tissues were remarkably higher in the COPD group than those in the Control group. Caveolin-1 was remarkably higher in the IWR-1 group than that in the Control group. And Wnt-1 and β-catenin were higher in the Daidzin group than those in the Control group. In addition, Wnt-1 and β-catenin in lung tissues markedly declined in the IWR-1 group compared with those in the COPD group. Caveolin-1, Wnt-1 and β-catenin in lung tissues also markedly declined in the Daidzin group compared with those in the COPD group. Caveolin-1 can improve lung injury in COPD rats through the Wnt/β-catenin signaling pathway.

Mutational Signatures in Mandibular Ameloblastoma Correlate with Smoking

Ameloblastoma is a rare tumor of odontogenic epithelium, the low incidence rate of which precludes statistical determination of its molecular characterizations. Despite recent genomic and transcriptomic profiling, the etiology of ameloblastomas remains poorly understood. Risk factors of ameloblastoma development are also largely unknown. Whole exome sequencing was performed on 11 mandibular ameloblastoma samples. We identified 2 convergent mutational signatures in ameloblastoma: 1) a signature found in multiple types of lung cancers with probable etiology of tobacco carcinogens (COSMIC signature 4) and 2) a signature present in gingivobuccal oral squamous cell carcinoma and correlated with tobacco-chewing habits (COSMIC signature 29). These mutational signatures highlight tobacco usage or related mutagens as one possible risk factor of ameloblastoma, since the association of BRAF mutations and smoking was demonstrated in multiple studies. In addition to BRAF hotspot mutations (V600E), we observed clear inter- and intratumor heterogeneities. Interestingly, prior to BRAF mutation, important genes regulating odontogenesis mutated (e.g., corepressor BCOR), possibly playing important roles in tumorigenesis. Furthermore, recurrent mutations in the CDC73 gene, the germline mutations of which predispose patients to the development of jaw tumors, were found in 2 patients, which may lead to recurrence if not targeted by therapeutic drugs. Our unbiased profiling of coding regions of ameloblastoma genomes provides insights to the possible etiology of mandibular ameloblastoma and highlights potential disease risk factors for screening and prevention, especially for Asian patients. Because of the limited sample size and incomplete habitual, dietary, and occupational data, a causal link between tobacco usage and ameloblastoma still requires further investigations.

E2F is required for STAT3-mediated upregulation of cyclin B1 and Cdc2 expressions and contributes to G2-M phase transition

Activation of transcription factor STAT3 is involved in cell proliferation, differentiation, and cell survival. Constitutive activation of STAT3 pathway has been associated with the oncogenesis of various types of cancers. It has been reported that STAT3 plays a key role in the G1 to S phase cell cycle transition induced by the cytokine receptor subunit gp130, through the upregulation of cyclins D1, D2, D3, A, and Cdc25A and the concomitant downregulation of p21 and p27. However, its role in mediating G2-M phase transition has not been studied. The cyclin B1/Cdc2 complex is widely accepted as the trigger of mitosis in all organisms and is believed to be necessary for progression through S phase and keep active during the G2-M transition and progression. In the present study, we found that activation of STAT3 stimulates cyclin B1 and Cdc2 expressions. Deletion and site-directed mutations on cyclin B1 and Cdc2 promoters indicated that E2F element mediates the upregulation of these two promoters in a STAT3-dependent manner. The findings reported here demonstrated that STAT3 participates in modulating G2-M phase checkpoint by regulating gene expressions of cyclin B1 and Cdc2 via E2F.

The prognostic value of combination of CD90 and OCT4 for hepatocellular carcinoma after curative resection

CD90 has been identified as a candidate marker of cancer stem cells (CSCs) for HCC, whereas it also has been considered as a marker for tumor-associated fibroblasts (CAFs). OCT4, as a key transcription factor required to maintain pluripotency of human embryonic stem cell and cancer cells, has been characterized to be involved in malignant transformation and tumorigenesis of various cancers. This study aimed to examine expression patterns of CD90 in HCC and investigate whether combination of both CD90 and OCT4 could provide a more powerful predictor for prognosis of HCC than either one alone.CD90 and OCT4 were examined by immunohistochemistry. The relationship between CD90/OCT4 expression and clinicopathologic characteristics was analyzed. The correlation between CD90/OCT4 expression and overall survival and disease-free survival was determined with Kaplan-Meier analysis.CD90 was found mainly expressed in tumor-associated CAFs and OCT4 was mainly expressed in tumor cells. The expression of CD90 and OCT4 in HCC was significantly higher than in adjacent non-tumor and normal liver tissues. CD90 expression was correlated with pathological grade, satellite lesion, PVTT and recurrence. OCT4 expression was correlated with pathological grade, tumor size and recurrence. Data demonstrated no correlation between CD90 and OCT4. High expression of CD90 or OCT4 predicts a poor prognosis. Furthermore, combination of both CD90 and OCT4 provides a more sensitive predictor for prognosis of HCC than either marker alone.CD90 and OCT4 are both independent and reliable biomarker for predicting prognosis of HCC patients after hepatic resection. Our results indicated the accuracy of prediction can be enhanced by their combination.

Optimization and characterization of highly nonlinear fiber for broadband optical time lens applications

We demonstrate simple and intuitive methods, for dispersion optimization and characterization of highly nonlinear fiber (HNLF) for use in four-wave-mixing (FWM) based time lens applications. A composite dispersion-flattened HNLF is optimized for high bandwidth time lens processing, by segmentation to mitigate FWM impairments due to dispersion fluctuations. The fiber is used for FWM conversion of 32 WDM-channels with 50 GHz spacing in a time lens, with -4.6 dB total efficiency, and <1 dB per-channel efficiency difference. The novel characterization method is based on two tunable continuous-wave lasers. The method is experimentally verified to predict the spectral output profile of time lenses for broadband multicarrier input, with detailed numerical simulations for support.

Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis

In nature and agriculture, nitrate availability is a main environmental cue for plant growth, development and stress responses. Nitrate signaling and regulation are hence at the center of communications between plant intrinsic programs and the environment. It is also well known that endogenous phytohormones play numerous critical roles in integrating extrinsic cues and intrinsic responses, regulating and refining almost all aspects of plant growth, development and stress responses. Therefore, interaction between nitrate and phytohormones, such as auxins, cytokinins, abscisic acid, gibberellins, and ethylene, is prevalent. The growing evidence indicates that biosynthesis, de-conjugation, transport, and signaling of hormones are partly controlled by nitrate signaling. Recent advances with nitrate signaling and transcriptional regulation in Arabidopsis give rise to new paradigms. Given the comprehensive nitrate transport, sensing, signaling and regulations at the level of the cell and organism, nitrate itself is a local and long-distance signal molecule, conveying N status at the whole-plant level. A direct molecular link between nitrate signaling and cell cycle progression was revealed with TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) - NIN-LIKE PROTEIN 6/7 (NLP6/7) regulatory nexus. NLPs are key regulators of nitrogen responses in plants. TCPs function as the main regulators of plant morphology and architecture, with the emerging role as integrators of plant developmental responses to the environment. By analogy with auxin being proposed as a plant morphogen, nitrate may be an environmental morphogen. The morphogen-gradient-dependent and cell-autonomous mechanisms of nitrate signaling and regulation are an integral part of cell growth and cell identification. This is especially true in root meristem growth that is regulated by intertwined nitrate, phytohormones, and glucose-TOR signaling pathways. Furthermore, the nitrate transcriptional hierarchy is emerging. Nitrate regulators in primary nitrate signaling can individually and combinatorially control downstream transcriptional networks and hormonal pathways for signal propagation and amplification. Under the new paradigms, nitrate-induced hormone metabolism and signaling deserve fresh examination. The close interplay and convergent regulation of nitrate and hormonal signaling at morphological, physiological, and molecular levels have significant effects on important agronomic traits, especially nutrient-dependent adaptive root system growth and architecture.

The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators

We show that NITRATE REGULATORY GENE2 (NRG2), which we identified using forward genetics, mediates nitrate signaling in Arabidopsis thaliana. A mutation in NRG2 disrupted the induction of nitrate-responsive genes after nitrate treatment by an ammonium-independent mechanism. The nitrate content in roots was lower in the mutants than in the wild type, which may have resulted from reduced expression of NRT1.1 (also called NPF6.3, encoding a nitrate transporter/receptor) and upregulation of NRT1.8 (also called NPF7.2, encoding a xylem nitrate transporter). Genetic and molecular data suggest that NRG2 functions upstream of NRT1.1 in nitrate signaling. Furthermore, NRG2 directly interacts with the nitrate regulator NLP7 in the nucleus, but nuclear retention of NLP7 in response to nitrate is not dependent on NRG2. Transcriptomic analysis revealed that genes involved in four nitrogen-related clusters including nitrate transport and response to nitrate were differentially expressed in the nrg2 mutants. A nitrogen compound transport cluster containing some members of the NRT/PTR family was regulated by both NRG2 and NRT1.1, while no nitrogen-related clusters showed regulation by both NRG2 and NLP7. Thus, NRG2 plays a key role in nitrate regulation in part through modulating NRT1.1 expression and may function with NLP7 via their physical interaction.

All-optical OFDM demultiplexing by spectral magnification and band-pass filtering

We propose a simple OFDM receiver allowing for the use of standard WDM receivers to receive spectrally advanced OFDM signals. We propose to spectrally magnify the optical-OFDM super-channels using a spectral telescope consisting of two time-lenses, which enables reduced inter-carrier-interference in subcarrier detection by simple band-pass filtering. A demonstration on an emulated 100 Gbit/s DPSK optical-OFDM channel shows improved sensitivities after 4-times spectral magnification.

Clinical development of histone deacetylase inhibitor romidepsin

Histone deactylase inhibitors have emerged as a promising epigenetic therapy for neoplasic indications. The US Food and Drug Administration granted approval to romidepsin for treatment of cutaneous T cell lymphoma (CTCL) in 2009. Phase I/II trials of romidepsin as monotherapy or hybird therapy have demonstrated substantial efficacy profoundly in CTCL and peripheral T-cell lymphoma and marginally in other hematogological malignancies and solid tumors, with a tolerable safety and toxicity profile. The current status of the clinical evaluation of romidepsin is detailed in the present contribution.

Multiple regulatory elements in the Arabidopsis NIA1 promoter act synergistically to form a nitrate enhancer

To accommodate fluctuating nutrient levels in the soil, plants modulate their metabolism and root development via signaling mechanisms that rapidly reprogram the plant transcriptome. In the case of nitrate, over 1,000 genes are induced or repressed within minutes of nitrate exposure. To identify cis-regulatory elements that mediate these responses, an enhancer screen was performed in transgenic Arabidopsis (Arabidopsis thaliana) plants. A 1.8-kb promoter fragment from the nitrate reductase gene NIA1 was identified that acts as a nitrate enhancer when fused to a 35S minimal promoter. Enhancer activity was localized to a 180-bp fragment, and this activity could be enhanced by the addition of a 131-bp fragment from the nitrite reductase promoter. A promoter construct containing the 180- and 131-bp fragments was also induced by nitrite and repressed by ammonium, indicating that it was responsive to multiple nitrogen signals. To identify specific regulatory elements within the 180-bp NIA1 fragment, a transient expression system using agroinfiltration of Nicotiana benthamiana was developed. Deletion analysis identified three elements corresponding to predicted binding motifs for homeodomain/E-box, Myb, and Alfin1 transcription factors. A fully active promoter showing nitrate and nitrite enhancer activity equivalent to that of the wild-type 180-bp fragment could be built from these three elements if the spacing between the homeodomain/E-box and Myb-Alfin1 sites was equivalent to that of the native promoter. These findings were validated in transgenic Arabidopsis plants and identify a cis-regulatory module containing three elements that comprise a nitrate enhancer in the NIA1 promoter.

A physical map of the papaya genome with integrated genetic map and genome sequence

Background

Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly.

Results

The physical map consists of 963 contigs, representing 9.4× genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes.

Conclusion

A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics and map-based cloning of agronomically and economically important genes and for sex chromosome research.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome

Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high-quality bases. Microsatellites discovered in 5,452 BESs and flanking primer sequences are available to papaya breeding programs at http://www.genomics.hawaii.edu/papaya/BES . Sixteen percent of BESs contain plant repeat elements, the vast majority (83.3%) of which are class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the BESs have homology to Arabidopsis cDNA. Increasing numbers of completely sequenced plant genomes and BES projects enable novel approaches to comparative plant genomics. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. In general the level of microsynteny was highest between closely related organisms. However, papaya revealed a higher degree of apparent synteny with the more distantly related poplar than with the more closely related Arabidopsis. This, as well as significant colinearity observed between peach and poplar genome sequences, support recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggest that the poplar genome sequence may be more useful for elucidating the papaya and other rosid genomes. These insights will play a critical role in selecting species and sequencing strategies that will optimally represent crop genomes in sequence databases.

High-level secretion of functional green fluorescent protein from transgenic tobacco cell cultures: characterization and sensing

Green fluorescent protein (GFP) is useful for studying protein trafficking in plant cells. This utility could potentially be extended to develop an efficient secretory reporter system or to enable on-line monitoring of secretory recombinant protein production in plant cell cultures. Toward this end, the aim of the present study was to: (1) demonstrate and characterize high levels of secretion of fluorescent GFP from transgenic plant cell culture; and (2) examine the utility of GFP fluorescence for monitoring secreted recombinant protein production. In this study we expressed in tobacco cell cultures a secretory GFP construct made by splicing an Arabidopsis basic chitinase signal sequence to GFP. Typical extracellular GFP accumulation was 12 mg/L after 10 to 12 days of culture. The secreted GFP is functional and it accounts for up to 55% of the total GFP expressed. Findings from culture treatments with brefeldin A suggest that GFP is secreted by the cultured tobacco cells via the classical endoplasmic reticulum-Golgi pathway. Over the course of flask cultures, medium fluorescence increased with the secreted GFP concentrations that were determined using either Western blot or enzyme-linked immunoassay. Real-time monitoring of secreted GFP in plant cell cultures by on-line fluorescence detection was verified in bioreactor cultures in which the on-line culture fluorescence signals showed a linear dependency on the secreted GFP concentrations.

Association of HIF-1alpha expression and cell apoptosis after traumatic brain injury in the rat

OBJECTIVE

To explore the expression of hypoxia inducible factor-1alpha (HIF-1alpha) and the correlation between HIF-1alpha and apoptosis after traumatic brain injury.

METHODS

Using experimental traumatic brain injury in the rats, the expression of HIF-1alpha was studied by immunohistochemistry in cerebral tissue, apoptotic cell death was evaluated with TUNEL (transferase-mediated X-dUTP nick end labeling), and double-labeled immunohistochemistry and TUNEL methods were used to investigate the relationship between HIF-1alpha and apoptosis.

RESULTS

There was remarkable difference in the expression of H IF-1alpha between the experimental groups and the control groups (P<0.01), in the experimental groups, the expression of HIF-1alpha at 48 hours was highest; the evidence of apoptotic cell death after experimental traumatic brain injury was found by TUNEL; the apoptotic percentage increased or decreased according to the changes of the positive expression of HIF-1alpha (r=0.99).

CONCLUSIONS

The results suggest that secondary brain ischemia plays a crucial role in apoptotic cell death after traumatic brain injury; HIF-1alpha can prompt apoptotic cell death after experimental traumatic brain injury.

[Study of the mechanism of cultured neuron injury mediated by nitric oxide during hypoxia and oxidative stress]

OBJECTIVE

To study the mechanisms of cultured neurons injury mediated by nitric oxide and free oxygen radical during hypoxia and oxidative stress.

METHODS

The cultured newborn rat neurons were treated with hypoxia, H2O2 and pretreated superoxide dismutase (SOD) respectively. We examined the content of NO, malonaldehyde (MDA), lactate dehydrogenase (LDH) and SOD in cultured supernatant.

RESULTS

Comparing with that of control group, the content of NO, LDH, MDA increased and the content of SOD decreased in hypoxia group and H2O2 group. The content between NO and SOD showed the negative correlation. Administration of 200 U/ml SOD before oxidative stress could efficiently decrease the release of NO, LDH and MDA in neurons. The content of NO, LDH and MDA manifested in positive correlation in each group.

CONCLUSION

Hypoxia and oxidative stress increased NO production which strengthen neurons injury induced by free radical. SOD played an important role in elimination of free oxygen radicals and protecting neurons from injury by NO.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Indoor air pollution and pulmonary adenocarcinoma among females: a case-control study in Shenyang, China

Factors that affect the risk of lung adenocarcinoma among females were investigated in Shenyang, China, using a population-based case-control study design. A total of 72 new cases, ages 35-69, diagnosed with incident, primary pulmonary adenocarnoma, were collected between April 1991 and December 1995, and were 1:1 age-matched with healthy females randomly selected from the general population. A questionnaire covering demographics, diet/nutritional preferences and cooking habits, living conditions, family history of cancer, sources of indoor/outdoor/occupational pollution, exposure to ETS from spousal smoking, workplace exposure, and exposure during childhood, history of menstruation and pregnancy, was given to each subject in a structured in-person interview given by trained field workers. Univariate analysis was performed on the data collected. The results showed that cooking fumes, family history of lung cancer, economic status, and number of live births and intake of vitamin E were risk factors significantly associated with adenocarcinoma of the lung. In particular, exposure to different levels of cooking fumes, an indoor air pollutant, increased the odds ratio of lung adenocarcinoma by 1.33, 7.33 and 1.67, respectively (trend p=0.006). Another important risk factor was family history of lung cancer, which gave an OR of 7.65 (95% CI, 0.90-169.84). Intake of beta-carotene from vegetables and fruit offered protection against lung adenocarcinoma, giving an OR of 0.28 (95% CI, 0.12-0.69). These results were confirmed by multivariable logistic regression analysis.

[Effect of vasostomy on expression of Bcl-2 and Bax gene in rat spermatogenic cells]

The objective of this study was to explore the change of Bcl-2 and Bax gene expression in rat spermatogneic cells after vasostomy. A rat model with vasoligation and vasostomy was set up and then used for detecting the protein expression of Bcl-2 and Bax gene at 4, 8, 12, 16 weeks after vasostomy by means of immunohistochemistry. Sixty rats were randomly distributed into three groups named vasoligation group (VG), vasostomy group(VOG) and sham-operation group(SOG) respectively. The results showed that the Bcl-2 protein expression in VOG group increased gradually and came to be significantly higher than that in VG group 8 weeks after vasostomy, and it's level was the same as that in SOG group at the 12th week. The bax protein expressions in VG and VOG groups were significantly higher than that in SOG group, but there was no difference between VOG and VG groups. In conclusion, the change of Bcl-2 protein expression observed in this study is indicative of the anti-apoptosis function of Bcl-2 gene in both the status of being vasoligated and vasostomized, whereas the consistent Bax protein expression before and often the repatency of the vas suggests further researches into its effect on apoptosis of spermatogenic cells.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Comparative genomics of the eukaryotes

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

Genomic organization and biological characterization of the novel human CC chemokine DC-CK-1/PARC/MIP-4/SCYA18

The chemokines are a group of chemotactic molecules that appear to regulate the directed movement of white blood cells in vitro and in vivo and may therefore play important roles in inflammation and immunity. The genes encoding the chemokines are clustered in close physical proximity to each other. A large cluster of human CC chemokine genes resides on chromosome 17. We have used this information in a positional cloning approach to identify novel chemokine genes within this cluster. We constructed a YAC contig encompassing the MIP-1alpha (HGMW-approved symbol SCYA3) gene region and used exon trapping and sequence analysis to isolate novel chemokine genes. Using this approach, a gene encoding a chemokine named MIP-4, based on its homology with MIP-1alpha (49.5% identity at the nucleotide level and 59.6% at the predicted amino acid level), was found. The MIP-4 gene (HGMW-approved symbol SCYA18) consists of three exons spread over 7.1 kb and is separated from the MIP-1alpha gene by 16 kb. The MIP-4 gene encodes a 750-bp mRNA that is expressed in lung and macrophages but not in brain or muscle. The mRNA encodes an 89-amino-acid protein and includes a predicted signal peptide of 21 amino acids. Recombinant or synthetic MIP-4 induced calcium mobilization in naive and activated T lymphocyte subpopulations in vitro. Injection of synthetic MIP-4 into the peritoneal cavity of mice led to the accumulation of both CD4(+) and CD8(+) T lymphocytes, but not monocytes or granulocytes. These observations provide new information concerning the arrangement of the CC chemokine gene cluster on human chromosome 17 and indicate that the MIP-4 gene product is chemotactic in vivo for both CD4(+) and CD8(+) T lymphocytes and may therefore be implicated in both humoral and cell-mediated immunity.

[A study of 44 forensic autopsy cases of adrenal hemorrhage]

44 cases of adrenal hemorrhage (AH) were analyzed. The forensic autopsy showed that AH occurred mainly in male aged from 20 to 40 years old. The traumatic AH was more often seen in young men and the pathologic AH was mostly seen in elderly persons. AH were more likely found in bilateral adrenal corticomedullary junction. The pathological grade of AH was not related to the interval time of survival. The pathologic mechanism of AH was discussed as well.

A case-control study of the relationship between dietary factors and risk of lung cancer in women of Shenyang, China

A 1:1 case-control study of lung cancer incidence among women in Shenyang was conducted to explore the relationship between diet and the risk of lung cancer, with emphasis on the potential effects of a list of specific dietary constituents on modifying lung cancer risks. Dietary information on 290 cases and population-matched controls was obtained by personal interviews. Multiple logistic regression models were used for the statistical analysis and summarization of the data. A significant difference was found between cases and controls with respect to intake of beta-carotene, vitamin C and fibers, all of which reduced the risk for lung cancer in a dose-dependent manner; yielding calculated odds ratio (OR) of 0.84, 0.75, and 0.46, respectively. The apparent effects of these nutrients persisted after adjusting for cigarette smoking;suggesting that they may function as protective factors to reduce the risk for lung cancer in Chinese women.