Search

CRISPR/Cas-based transcriptional activators can be enhanced by intrinsically disordered regions (IDRs). However, the underlying mechanisms are still debatable. Here, we examine 12 well-known IDRs by fusing them to the dCas9-VP64 activator, of which only seven can augment activation, albeit independently of their phase separation capabilities. Moreover, modular domains (MDs), another class of multivalent molecules, though ineffective in enhancing dCas9-VP64 activity on their own, show substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and fusing dCas9-VP64 with different IDRs/MDs, we uncover that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs yields synergistic effects, which can be further amplified via enhancing chromatin interactions. Overall, our study develops a versatile platform for efficient gene activation and sheds important insights into CRIPSR-based transcriptional activators enhanced with multivalent molecules., (© 2024. The Author(s).)

The three-dimensional (3D) organization of chromatin within the nucleus is crucial for gene regulation. However, the 3D architectural features that coordinate the activation of an entire chromosome remain largely unknown. We introduce an omics method, RNA-associated chromatin DNA-DNA interactions, that integrates RNA polymerase II (RNAPII)-mediated regulome with stochastic optical reconstruction microscopy to investigate the landscape of noncoding RNA roX2 -associated chromatin topology for gene equalization to achieve dosage compensation. Our findings reveal that roX2 anchors to the target gene transcription end sites (TESs) and spreads in a distinctive boot-shaped configuration, promoting a more open chromatin state for hyperactivation. Furthermore, roX2 arches TES to transcription start sites to enhance transcriptional loops, potentially facilitating RNAPII convoying and connecting proximal promoter-promoter transcriptional hubs for synergistic gene regulation. These TESs cluster as roX2 compartments, surrounded by inactive domains for coactivation of multiple genes within the roX2 territory. In addition, roX2 structures gradually form and scaffold for stepwise coactivation in dosage compensation.

Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods have achieved a single-molecule resolution and can even reveal spatial localization. These emerging methods provide insights elucidating the features of genomic, epigenomic and transcriptomic heterogeneity in individual cells. However, they have given rise to new computational challenges in data processing. Here, we describe Single-cell Single-molecule multiple Omics Pipeline (ScSmOP), a universal pipeline for barcode-indexed single-cell single-molecule multiomics data analysis. Essentially, the C language is utilized in ScSmOP to set up spaced-seed hash table-based algorithms for barcode identification according to ligation-based barcoding data and synthesis-based barcoding data, followed by data mapping and deconvolution. We demonstrate high reproducibility of data processing between ScSmOP and published pipelines in comprehensive analyses of single-cell omics data (scRNA-seq, scATAC-seq, scARC-seq), single-molecule chromatin interaction data (ChIA-Drop, SPRITE, RD-SPRITE), single-cell single-molecule chromatin interaction data (scSPRITE) and spatial transcriptomic data from various cell types and species. Additionally, ScSmOP shows more rapid performance and is a versatile, efficient, easy-to-use and robust pipeline for single-cell single-molecule multiomics data analysis., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Chromatin structural domains, or topologically associated domains (TADs), are a general organizing principle in chromatin biology. RNA polymerase II (RNAPII) mediates multiple chromatin interactive loops, tethering together as RNAPII-associated chromatin interaction domains (RAIDs) to offer a framework for gene regulation. RAID and TAD alterations have been found to be associated with diseases. They can be further dissected as micro-domains (micro-TADs and micro-RAIDs) by clustering single-molecule chromatin-interactive complexes from next-generation three-dimensional (3D) genome techniques, such as ChIA-Drop. Currently, there are few tools available for micro-domain boundary identification. In this work, we developed the MCI-frcnn deep learning method to train a Faster Region-based Convolutional Neural Network (Faster R-CNN) for micro-domain boundary detection. At the training phase in MCI-frcnn, 50 images of RAIDs from Drosophila RNAPII ChIA-Drop data, containing 261 micro-RAIDs with ground truth boundaries, were trained for 7 days. Using this well-trained MCI-frcnn, we detected micro-RAID boundaries for the input new images, with a fast speed (5.26 fps), high recognition accuracy (AUROC = 0.85, mAP = 0.69), and high boundary region quantification (genomic IoU = 76%). We further applied MCI-frcnn to detect human micro-TADs boundaries using human GM12878 SPRITE data and obtained a high region quantification score (mean gIoU = 85%). In all, the MCI-frcnn deep learning method which we developed in this work is a general tool for micro-domain boundary detection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Tian, Yin, Jing, Yang, Xu, Huang, Ning, Fullwood and Zheng.)

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis., (© 2021. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

The root of Paris polyphylla var. yunnanensis , a famous and endangered traditional Chinese herb, has a significant medicinal value. The aim of this study was to analyze the composition and functional characteristics of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis . The 16S rRNA gene sequencing and functional prediction of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis were conducted. The Chao and Shannon indices of the bacteria in roots were significantly higher than those in stems and leaves. The dominant endophyte phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The main genera detected in roots were unclassified Cyanobacteria, Rhizobium, Flavobacterium , and Sphingobium ; the main genera in stems were norank&#95;c&#95;&#95;Cyanobacteria, Bacillus , and Pseudomonas ; the main genera in leaves were norank&#95;c&#95;&#95;Cyanobacteria and Rhizobium . The microbiota in roots was particularly enriched in functional categories "extracellular structures" and "cytoskeleton" compared with stems and leaves ( p < 0.05). Our study reveals the structural and functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis , which aids in the scientific understanding of this plant., The root of Paris polyphylla var. yunnanensis , a famous and endangered traditional Chinese herb, has a significant medicinal value. The aim of this study was to analyze the composition and functional characteristics of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis . The 16S rRNA gene sequencing and functional prediction of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis were conducted. The Chao and Shannon indices of the bacteria in roots were significantly higher than those in stems and leaves. The dominant endophyte phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The main genera detected in roots were unclassified Cyanobacteria, Rhizobium, Flavobacterium , and Sphingobium ; the main genera in stems were norank&#95;c&#95;&#95;Cyanobacteria, Bacillus , and Pseudomonas ; the main genera in leaves were norank&#95;c&#95;&#95;Cyanobacteria and Rhizobium . The microbiota in roots was particularly enriched in functional categories “extracellular structures” and “cytoskeleton” compared with stems and leaves ( p < 0.05). Our study reveals the structural and functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis , which aids in the scientific understanding of this plant.

Background: Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis remain largely unknown., Results: Using an inducible system, we comprehensively analyze the 3D genome organization in myeloid cells and its reorganization after PML-RARα induction and perform additional analyses in patient-derived APL cells with native PML-RARα. We discover that PML-RARα mediates extensive chromatin interactions genome-wide. Globally, it redefines the chromatin topology of the myeloid genome toward a more condensed configuration in APL cells; locally, it intrudes RNAPII-associated interaction domains, interrupts myeloid-specific transcription factors binding at enhancers and super-enhancers, and leads to transcriptional repression of genes critical for myeloid differentiation and maturation., Conclusions: Our results not only provide novel topological insights for the roles of PML-RARα in transforming myeloid cells into leukemia cells, but further uncover a topological framework of a molecular mechanism for oncogenic fusion proteins in cancers.

Endophytic microorganisms absorb nutrients and prevent pathogen damage, supporting healthy plant growth. However, the relationship between endophytic bacteria and berberine synthesis in the medicinal plant Coptis teeta Wall. remains unclear. Herein, we explored the community composition of endophytic bacteria related to berberine in roots, stems, and leaves of wild-type and cultivated C. teeta . Endophytic bacterial communities were analyzed by 16S rRNA sequencing, and berberine content in roots was analyzed by high-performance liquid chromatography. Proteobacteria, Actinobacteria, and Bacteroidetes were the major phyla, and Mycobacterium , Salmonella , Nocardioides , Burkholderia-Paraburkholderia , and Rhizobium were the dominant genera in root, stem, and leaf tissues. Root berberine content was positively correlated with total N, total P, total K, and available K in rhizosphere soil. In addition, root berberine content was positively correlated with Microbacterium and norank&#95;f&#95;7B-8 , whereas soil total K was positively correlated with Microbacterium and Burkholderia-Paraburkholderia in roots. Our results demonstrated a clear correlation between dominant endophytic bacteria and berberine synthesis in C. teeta . The findings are useful for the promotion of berberine production in C. teeta via manipulation of endophytic bacteria., Competing Interests: Conflict of interestAll authors declared that there are no conflicts of interest., (© King Abdulaziz City for Science and Technology 2020.)

The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and identify topological domains and frequent inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains. Together, MIA-Sig represents a novel algorithmic framework for multiplex chromatin interaction analysis.

Pulmonary fibrosis (PF) is a crippling disease characterized by progressive dyspnea and associated with a high mortality rate, but its origin is unknown and there is no effective treatment. Yifei Sanjie formula (YFSJF) is a Chinese medicine that is widely used for treatment of respiratory systems disease. However, the molecular basis for the function of YFSJF has not been determined. Here we investigate the contribution of YFSJF in BLM-induced PF mice. Administration with YFSJF significantly alleviated the degree of BLM-induced collagen I and III deposition and the inflammatory injuring in the lungs and suppressed hydroxyproline release in PF animals. The active components of YFSJF are comprised with flavonoid, amino acids, saponins, oligosaccharide, organic acid, vitamin, esters, purine nucleosides. Additionally, there was a significant increase in autophagosomes, after treatment with YFSJF in PF animals. Interestingly, autophagy dysfunction by the blocker chloroquine (CQ) resulted in collagen deposition and inducing the expression of fibrosis-related genes. In addition, YFSJF-induced autophagy is mediated by the PI3K-AKT-mTOR pathway, and knockdown of PI3K by siRNA up-regulated the expression of autophagy-related genes and down-regulated the expression of collagen in human lung fibroblasts (HLF). Our findings provide a detailed understanding that YFSJF-antifibrotic effects are mainly mediated by triggering autophagy, and suppressing phosphorylation of the PI3K-AKT-mTOR pathway is required for YFSJF-curative effect., (Copyright © 2019 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Numerous well-known processes of complex systems such as spreading and cascading are mainly affected by a small number of critical nodes. Identifying influential nodes that lead to broad spreading in complex networks is of great theoretical and practical importance. Since the identification of vital nodes is closely related to propagation dynamics, a novel method DynamicRank that employs the probability model to measure the ranking scores of nodes is suggested. The influence of a node can be denoted by the sum of probability scores of its i order neighboring nodes. This simple yet effective method provides a new idea to understand the identification of vital nodes in propagation dynamics. Experimental studies on both Susceptible-Infected-Recovered and Susceptible-Infected-Susceptible models in real networks demonstrate that it outperforms existing methods such as Coreness, H-index, LocalRank, Betweenness, and Spreading Probability in terms of the Kendall τ coefficient. The linear time complexity enables it to be applied to real large-scale networks with tens of thousands of nodes and edges in a short time.

The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus 1 . Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C) 2 , and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET) 3 , have revealed topologically associating domains 4 with frequent chromatin contacts, and have identified chromatin loops mediated by specific protein factors for insulation and regulation of transcription 5-7 . However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C 8 potentially overcomes this issue, this method may be limited by the sparsity of data that is inherent to current single-cell assays. Recent advances in microfluidics have opened opportunities for droplet-based genomic analysis 9 but this approach has not yet been adapted for chromatin interaction analysis. Here we describe a strategy for multiplex chromatin-interaction analysis via droplet-based and barcode-linked sequencing, which we name ChIA-Drop. We demonstrate the robustness of ChIA-Drop in capturing complex chromatin interactions with single-molecule precision, which has not been possible using methods based on population-level pairwise contacts. By applying ChIA-Drop to Drosophila cells, we show that chromatin topological structures predominantly consist of multiplex chromatin interactions with high heterogeneity; ChIA-Drop also reveals promoter-centred multivalent interactions, which provide topological insights into transcription.

Bidirectional reflectance distribution functions (BRDFs) are of importance for their wide applications. In this study, we presented a simple and fast approach to measure the spectral BRDF of both solid and liquid samples. Based on this approach, we fabricated a prototype and measured the BRDF value of some liquid samples such as water and NaCl solution at different wavelengths. According to the experimental data, we discussed the trend of the BRDF value of the NaCl solution of different concentrations. Then, the experimental data of the different NaCl solution at 637 nm were used to invert the parameters of a five-parameter model. Additionally, we fitted the parameters as a polynomial.

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for interactions mediated by specific target proteins. This unique feature allows ChIA-PET to provide the functional specificity and higher resolution needed to detect chromatin interactions, which chromosome conformation capture (3C)/Hi-C approaches have not achieved. The original ChIA-PET protocol generates short paired-end tags (2 × 20 base pairs (bp)) to detect two genomic loci that are far apart on linear chromosomes but are in spatial proximity in the folded genome. We have improved the original approach by developing long-read ChIA-PET, in which the length of the paired-end tags is increased (up to 2 × 250 bp). The longer PET reads not only improve the tag-mapping efficiency but also increase the probability of covering phased single-nucleotide polymorphisms (SNPs), which allows haplotype-specific chromatin interactions to be identified. Here, we provide the detailed protocol for long-read ChIA-PET that includes cell fixation and lysis, chromatin fragmentation by sonication, ChIP, proximity ligation with a bridge linker, Tn5 tagmentation, PCR amplification and high-throughput sequencing. For a well-trained molecular biologist, it typically takes 6 d from cell harvesting to the completion of library construction, up to a further 36 h for DNA sequencing and <20 h for processing of raw sequencing reads.

Objective: To investigate the differences of volume of pharyngeal cavity between normal healthy subjects and patients with severe obstructive sleep apnea hypopnea syndrome(OSAHS)before and after surgery and its application value in assessment of surgical curative effect. Method: Forty-four healthy male adults were included in normal group.Thirty-eight patients with severe OSAHS diagnosed by polysomnography were included in experimental group(OSAHS group). Volume of pharyngeal cavity, oropharynx and laryngopharynx measured by acoustic pharyngealmetry and AHI, obstructive apnea frequency and the lowest oxygen saturation recorded by PSG monitor were all obtained in normal groups and experimental groups before and 3 months after the surgery. All the data are statistically analyzed. Result: Volume of pharyngeal cavity,AHI,obstructive apnea frequency and lowest oxygen saturation of patients in experimental group were all improved after surgery compared with pre-operation( P <0.01). Conclusion: The measurement of pharyngeal cavity volume is helpful to the quantitative analysis of upper airway structure and determine the stenosis location, it is also useful to guide surgery and evaluate the curative effect of the surgery., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.)

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases., (Copyright © 2015 Elsevier Inc. All rights reserved.)

By using static chamber-TGC method, an in situ observation was conducted in a 10-year conservation tillage winter wheat field to study the effects of different maize straw-returning modes on the soil respiration. The soil respiration had a significant positive correlation with the stubble height of maize straw, and two peaks were observed in wheat growth period. Under no tillage and no straw-returning, the soil respiration was 72.5% of that under no tillage with all straw-returning, and the soil respiration under conventional tillage and no straw- returning was 76.5% of that under conventional tillage with all straw-returning. The soil respiration was significantly positively correlated with the soil temperature and soil organic carbon at 20 cm depth, but no significant correlation with the soil organic carbon at 40 cm depth. A correlation was also observed between the soil respiration and soil moisture. The diurnal soil respiration in the treatments of all straw-returning presented a single-peak curve, with the peak at 18:00. There was a similar variation trend of soil temperature and soil respiration at the depth of 20 cm. Among the treatments of different straw-returning amounts, straw-returning with the stubble of 1 m height could reduce the soil respiration significantly, being a reasonable straw-returning mode.

A new p-terphenyl 1 and a novel p-terphenyl derivative 3 bearing a benzothiazole moiety were isolated from halophilic actinomycete Nocardiopsis gilva YIM 90087, along with known p-terphenyl 2, antibiotic novobiocin 4, cyclodipeptides 5-13, and aromatic acids 14 and 15. Their structures were elucidated on the basis of the interpretation of spectral data and by comparison of the corresponding data with those reported previously. The p-terphenyl 1 showed antifungal activity against the three pathogenic fungi, including Fusarium avenaceum, Fusarium graminearum, and Fusarium culmorum, that caused Fusarium head blight with minimal inhibitory concentrations (MICs) of 8, 16, and 128 μg/mL, respectively. Compound 1 showed antifungal activity against Candida albicans with a MIC of 32 μg/mL and antibacterial activity against Bacillus subtilis with a MIC of 64 μg/mL. Novobiocin 4 showed antifungal activity against Pyricularia oryzae with a MIC of 16 μg/mL and antibacterial activity against B. subtilis with a MIC of 16 μg/mL and Staphylococcus aureus with a MIC of 64 μg/mL. The 1,1-diphenyl-2-picryl-hydrazyl assay suggested that 1, 3, and 4 exhibited 54.9% (2 mg/mL), 14.3% (4 mg/mL), and 47.7% (2 mg/mL) free radical scavenging activity, respectively. The positively charged 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical (ABTS(+•)) scavenging assay indicated that 1, 3, 4, and 8 exhibited 68.6% (1 mg/mL), 28.4% (2 mg/mL), 78.2% (0.5 mg/mL), and 54.6% (2 mg/mL) ABTS(+•) scavenging capacity, respectively. The superoxide anion radical scavenging assay suggested that 4 exhibited 77.9% superoxide anion radical scavenging capacity at 2 mg/mL. N. gilva YIM 90087 is a new resource for novobiocin 4.

A Gram-positive, non-motile actinobacterium, designated YIM 65754T, was isolated from the stem of Artemisia annua L., collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 65754T comprised an evolutionary lineage within the genus Rhodococcus. The isolate clustered with Rhodococcus pyridinivorans PDB9T, Rhodococcus gordoniae W 4937T and Rhodococcus rhodochrous DSM 43241T, with which it shared 98.4, 97.9 and 97.8 % 16S rRNA gene sequence similarities, respectively. However, DNA-DNA relatedness demonstrated that strain YIM 65754T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan contained meso-diaminopimelic acid, arabinose, galactose, mannose and glucose (cell-wall chemotype IV). The major menaquinone was MK-8(H2) and the predominant fatty acids were C16:0 (27.83 %), iso-C15:0 2-OH and/or C16:1ω7c (20.21 %) and 10-methyl C18:0 (17.50 %). The DNA G+C content was 66.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate represents a novel species of the genus Rhodococcus, for which the name Rhodococcus artemisiae sp. nov. is proposed; the type strain is YIM 65754T (=CCTCC AA 209042T=DSM 45380T).

During the course of our research on new actinobacterial sources, a novel actinomycete strain YIM 63101(T) was isolated from the surface-sterilized roots of Artemisia annua L. collected from Xishuangbanna, Yunnan province, south-west China and characterized by using a polyphasic approach. The strain formed well-differentiated aerial and substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63101(T) belongs to the genus Pseudonocardia, with highest similarity to "Pseudonocardia artemisiae YIM 63587(T)" (99.4%). Sequence similarities between strain YIM 63101(T) and the other Pseudonocardia species ranged from 97.0 (Pseudonocardia saturnea IMSNU 20052(T)) to 94.0% (Pseudonocardia compacta IMSNU 20111(T)). The chemotaxonomic characteristics, such as cell wall diaminopimelic acid, whole-cell sugars, fatty acid components and the major menaquinones suggested that the organism belonged to the genus Pseudonocardia. The G + C content of the genomic DNA was 69.4 mol%. Based on comparative analysis of physiological, biochemical and chemotaxonomic data, including low DNA-DNA hybridization results, it is proposed that strain YIM 63101(T) represents a novel species of the genus Pseudonocardia, named Pseudonocardia bannaensis sp. nov. The type strain is YIM 63101(T) (= CCTCC AA 208077 (T) = DSM 45300(T)).

Taking a long-term (since 2004) straw-returning winter wheat field as the object, an investigation was made in the wheat growth seasons of 2008-2009 and 2009-2010 to study the effects of different tillage methods (rotary tillage, harrow tillage, no-tillage, subsoil tillage, and conventional tillage) and weed management on the soil water and organic carbon contents. No matter retaining or removing weeds, the weed density under subsoil tillage and no-tillage was much higher than that under rotary tillage, harrow tillage, and conventional tillage. From the jointing to the milking stage of winter wheat, retaining definite amounts of weeds, no matter which tillage method was adopted, could significantly increase the 0-20 cm soil water content, suggesting the soil water conservation effect of retaining weeds. Retaining weeds only increased the soil organic carbon content in 0-20 cm layer at jointing stage. At heading and milking stages, the soil organic carbon contents in 0-20, 20-40, and 40-60 cm layers were lower under weed retaining than under weed removal. Under the conditions of weed removal, the grain yield under subsoil tillage increased significantly, compared with that under the other four tillage methods. Under the conditions of weed retaining, the grain yield was the highest under rotary tillage, and the lowest under conventional tillage.

A two growth seasons experiment was conducted to study the effects of different tillage methods, straw-returning, and their interaction on the dynamic change of organic carbon content in 0-20 cm soil layer during the whole growth period of winter wheat. An obvious change was observed in the soil organic carbon content. Treatments with straw-returning had higher soil organic carbon content than treatments with no straw-returning, and conservation tillage induced higher soil organic carbon content than conventional tillage. In all treatments except conventional tillage, the organic carbon content in 0-10 cm soil layer was higher than that in 10-20 cm soil layer. In treatments with straw-returning, the organic carbon content in 0-10 cm soil layer decreased in order of deep soiling (PS) > rotary tillage (PR) > no tillage (PZ) > normal ploughing (PH) > conventional tillage (PC), while that in 10-20 cm soil layer was PC > PS > PR > PH > PZ, suggesting that conservation tillage could improve the organic carbon content in 0-10 cm soil layer. Multi factor variance analysis showed that tillage method, straw-returning, and their interaction had significant effects on the organic carbon content in 0-20 cm soil layer at various growth stages of winter wheat.

Objective: To investigate the treatment model and the factors that influence survival of the patients with anaplastic thyroid carcinoma (ATC)., Methods: The clinical data of all patients with ATC in our hospital from May. 1970 to May. 2005 were analyzed retrospectively with regard to mortality and survival rate (Kaplan-Meier). Multivariate analysis was performed by the Cox proportional hazard model., Results: Fifty cases together were analyzed. The overall 1-year, 3-year, 5-year survival rate were 39.4%, 29.6% and 20.7% respectively. The median survival time was 6 months. Univariate analysis showed the patients with their age < 55 years old, without distant metastasis, white blood cell count < 10.0 x 10(9)/L at presentation, without receiving chemotherapy, receiving radiotherapy with the dose no less than 40 Gy, receiving multiple modality therapy had a better prognosis. White blood cell count at presentation, the model of therapy were the risk factors independently influencing prognosis by multivariate analysis., Conclusions: White blood cell count at presentation, receiving surgery and postoperative radiotherapy or not were the risk factors independently influencing prognosis. The prognosis of anaplastic thyroid carcinoma was worse; the patients with ATC maybe get a better prognosis by receiving surgery and postoperative radiotherapy.

Objective: To explore the clinical characteristics and the survival status of the patients with laryngeal squamous cell carcinoma in the multiple primary cancers (MPC)., Methods: Follow-up and clinical data were analyzed retrospectively in 81 laryngeal squamous cell cancer patients with MPC among 1101 patients with laryngeal carcinoma. Survival analysis and every influencing factor on survival rate were performed by Kaplan-Meier method., Results: The occurrence rate of MPC in the patients with laryngeal squamous cell cancer was 7.4% (81/1101) in this report. Oral cavity carcinoma and nasopharyngeal carcinoma were the most common MPC in 29 cases (35.8%) in head and neck regions. MPC in head and neck regions were more often seen among patients who had treated with radiotherapy (chi2 = 5.7, P = 0.017). Lung carcinoma (25.9%, 21/81) and esophageal carcinoma (22.2%, 18/81) were the most common MPC in remote organs in 52 cases (64.2%). Thirty seven MPC cases (45.7%) were occurred in aerodigestive tract and 32 cases(39.5%) in respiratory tract in this series. Fourteen cases (17.3%) were synchronous MPC, the median time interval was 2 months. Other 67 cases (82.7%) were metachronous MPC, the median time interval was 28 months. The squamous cell carcinoma (66.7%) was the most common pathologic type among all MPC in 81 cases, which was more often seen among patients who had smoked and drunk (P = 0.007). The MPC of esophageal carcinoma and oropharyngeal carcinoma were more often seen among patients of supraglottic index cancer presentation (P = 0.04). The MPC of oral cavity cancers and nasopharyngeal carcinoma and lung carcinoma were more often seen among patients of glottic index cancer presentation (P = 0.006). The total three-and five-year survival rates were 45.2% and 29.7% respectively of all MPC patients, the five-year survival rate for patients (53 cases) who received actively different therapies for their MPC was 45.5%, obviously higher than that of untreated patients (28 cases) whose three-year survival rate was zero (P = 0.000)., Conclusions: Lung carcinoma and esophageal carcinoma were the most common multiple primary cancers among MPC of the laryngeal cancer. MPC of the laryngeal cancer in head and neck regions were more often seen among patients who had treated with radiotherapy. The pathologic type of squamous carcinomas of MPC was more often seen among patients who had smoked and drunk. MPC affected the prognosis of patients in laryngeal cancer largely. Treating effectively and in time could help to improve the survival rate of patients with MPC in laryngeal squamous cell carcinomas.

The morphological features of blood and milk neutrophils from peak lactating goats were compared using light microscopy, scanning electron microscopy and flow cytometry in order to investigate the cytological changes of neutrophils after migration into the mammary gland. The kinetics of reactive oxygen intermediates (ROI) generation and gelatinase release of blood and milk neutrophils, with or without stimulation of phorbol 12-myristate, 13-acetate ester (PMA), were used to characterize their responses to inflammatory stimuli. Neutrophils isolated from goat milk were highly segmented and contained multi-lobed nuclei. Ultrastructurally, milk neutrophils were more ruffled on the surface compared to blood neutrophils. Approximately 30% of milk neutrophils were undergoing cell death, either necrosis or apoptosis, in contrast to 8% of blood neutrophils. The ROI production of activated milk neutrophils peaked earlier than blood neutrophils, but the duration and the intensity were much less. Neutrophils from both sources augmented the release of gelatinase in response to PMA (1 ng/mL). However, the amount of gelatinase released from milk neutrophils was lower (P < 0.05) than that of blood neutrophils. In summary, more neutrophils become apoptotic and necrotic in the mammary gland, presumably due to spontaneous aging, the process of diapedesis, and the interaction with milk components. Milk neutrophils have impaired functionalities in comparison with blood neutrophils. The information is relevant when studying mammary gland immunity and related diseases, such as mastitis.

Background & Objective: There are few ideal predictors used to evaluate the prognosis of laryngeal squamous cell carcinoma (LSCC). This study was designed to investigate the expression of p73 and PTEN (phosphates and tension homolog deleted on chromosome ten) and their association with clinical, histologic characteristics and prognosis in LSCC., Methods: p73 protein and PTEN protein were examined by using immunochistochemical SABC staining method in 65 cases of LSCC and in 23 cases of para-tumor tissues., Results: p73 protein and PTEN protein in LSCC showed positive expression of about 58.5% (38/65) and 49.2% (32/65), compared to para-tumor tissues of about 17.4% (4/23) and 95.7% (22/23) with statistical significance (P< 0.05). p73 protein positive expression showed stronger in stage III-IV of LSCC than that in stage I-II (P< 0.05); it more often appeared in recurrent cases than in primary cases (P< 0.05). And p73 protein positive expression with distant metastasis was stronger than that in LSCC without distant metastasis (P< 0.05). PTEN protein positive expression was stronger in stage I-II of LSCC than that in stage III-IV (P< 0.05); PTEN protein positive expression appears less frequently in poor differentiation of LSCC, compared to well/moderate differentiation (P< 0.05); PTEN positive expression in cases with cervical lymph node metastasis and distant metastasis was lower than that in those without metastasis (P< 0.05). PTEN expression showed significantly stronger in the patients whose survival time over 5 years (66.7%) than in the patients whose survival time was less than 5 years (27.3%) (P< 0.05)., Conclusion: PTEN positive expression may be useful for predicting the prognosis of LSCC.