A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

SAP90 binds and clusters kainate receptors causing incomplete desensitization

The mechanism of kainate receptor targeting and clustering is still unresolved. Here, we demonstrate that members of the SAP90/PSD-95 family colocalize and associate with kainate receptors. SAP90 and SAP102 coimmunoprecipitate with both KA2 and GluR6, but only SAP97 coimmunoprecipitates with GluR6. Similar to NMDA receptors, GluR6 clustering is mediated by the interaction of its C-terminal amino acid sequence, ETMA, with the PDZ1 domain of SAP90. In contrast, the KA2 C-terminal region binds to, and is clustered by, the SH3 and GK domains of SAP90. Finally, we show that SAP90 coexpressed with GluR6 or GluR6/KA2 receptors alters receptor function by reducing desensitization. These studies suggest that the organization and electrophysiological properties of synaptic kainate receptors are modified by association with members of the SAP90/PSD-95 family.

[Analysis of clinical features of 29 patients with 2019 novel coronavirus pneumonia]

Objective: To analyze the clinical characteristics of 2019 novel coronavirus (2019-nCoV) pneumonia and to investigate the correlation between serum inflammatory cytokines and severity of the disease. Methods: 29 patients with 2019-ncov admitted to the isolation ward of Tongji hospital affiliated to Tongji medical college of Huazhong University of Science and Technology in January 2020 were selected as the study subjects. Clinical data were collected and the general information, clinical symptoms, blood test and CT imaging characteristics were analyzed. According to the relevant diagnostic criteria, the patients were divided into three groups: mild (15 cases), severe (9 cases) and critical (5 cases). The expression levels of inflammatory cytokines and other markers in the serum of each group were detected, and the changes of these indicators of the three groups were compared and analyzed, as well as their relationship with the clinical classification of the disease. Results: (1) The main symptoms of 2019-nCoV pneumonia was fever (28/29) with or without respiratory and other systemic symptoms. Two patients died with underlying disease and co-bacterial infection, respectively. (2) The blood test of the patients showed normal or decreased white blood cell count (23/29), decreased lymphocyte count (20/29), increased hypersensitive C reactive protein (hs-CRP) (27/29), and normal procalcitonin. In most patients,serum lactate dehydrogenase (LDH) was significantly increased (20/29), while albumin was decreased(15/29). Alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (Tbil), serum creatinine (Scr) and other items showed no significant changes. (3) CT findings of typical cases were single or multiple patchy ground glass shadows accompanied by septal thickening. When the disease progresses, the lesion increases and the scope expands, and the ground glass shadow coexists with the solid shadow or the stripe shadow. (4) There were statistically significant differences in the expression levels of interleukin-2 receptor (IL-2R) and IL-6 in the serum of the three groups (P<0.05), among which the critical group was higher than the severe group and the severe group was higher than the mildgroup. However, there were no statistically significant differences in serum levels of tumor necrosis factor-alpha (TNF-α), IL-1, IL-8, IL-10, hs-CRP, lymphocyte count and LDH among the three groups (P>0.05). Conclusion: The clinical characteristics of 2019-nCoV pneumonia are similar to those of common viral pneumonia. High resolution CT is of great value in the differential diagnosis of this disease. The increased expression of IL-2R and IL-6 in serum is expected to predict the severity of the 2019-nCoV pneumonia and the prognosis of patients.

A retinitis pigmentosa GTPase regulator (RPGR)- deficient mouse model for X-linked retinitis pigmentosa (RP3)

The X-linked RP3 locus codes for retinitis pigmentosa GTPase regulator (RPGR), a protein of unknown function with sequence homology to the guanine nucleotide exchange factor for Ran GTPase. We created an RPGR-deficient murine model by gene knockout. In the mutant mice, cone photoreceptors exhibit ectopic localization of cone opsins in the cell body and synapses and rod photoreceptors have a reduced level of rhodopsin. Subsequently, both cone and rod photoreceptors degenerate. RPGR was found normally localized to the connecting cilia of rod and cone photoreceptors. These data point to a role for RPGR in maintaining the polarized protein distribution across the connecting cilium by facilitating directional transport or restricting redistribution. The function of RPGR is essential for the long-term maintenance of photoreceptor viability.

[Analysis of clinical features of 29 patients with 2019 novel coronavirus pneumonia]

Objective: To analyze the clinical characteristics of 2019 novel coronavirus (2019-nCoV) pneumonia and to investigate the correlation between serum inflammatory cytokines and severity of the disease. Methods: 29 patients with 2019-ncov admitted to the isolation ward of Tongji hospital affiliated to Tongji medical college of Huazhong University of Science and Technology in January 2020 were selected as the study subjects. Clinical data were collected and the general information, clinical symptoms, blood test and CT imaging characteristics were analyzed. According to the relevant diagnostic criteria, the patients were divided into three groups: mild (15 cases), severe (9 cases) and critical (5 cases). The expression levels of inflammatory cytokines and other markers in the serum of each group were detected, and the changes of these indicators of the three groups were compared and analyzed, as well as their relationship with the clinical classification of the disease. Results: (1) The main symptoms of 2019-nCoV pneumonia was fever (28/29) with or without respiratory and other systemic symptoms. Two patients died with underlying disease and co-bacterial infection, respectively. (2) The blood test of the patients showed normal or decreased white blood cell count (23/29), decreased lymphocyte count (20/29), increased hypersensitive C reactive protein (hs-CRP) (27/29), and normal procalcitonin. In most patients,serum lactate dehydrogenase (LDH) was significantly increased (20/29), while albumin was decreased(15/29). Alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (Tbil), serum creatinine (Scr) and other items showed no significant changes. (3) CT findings of typical cases were single or multiple patchy ground glass shadows accompanied by septal thickening. When the disease progresses, the lesion increases and the scope expands, and the ground glass shadow coexists with the solid shadow or the stripe shadow. (4) There were statistically significant differences in the expression levels of interleukin-2 receptor (IL-2R) and IL-6 in the serum of the three groups (P<0.05), among which the critical group was higher than the severe group and the severe group was higher than the mildgroup. However, there were no statistically significant differences in serum levels of tumor necrosis factor-alpha (TNF-α), IL-1, IL-8, IL-10, hs-CRP, lymphocyte count and LDH among the three groups (P>0.05). Conclusion: The clinical characteristics of 2019-nCoV pneumonia are similar to those of common viral pneumonia. High resolution CT is of great value in the differential diagnosis of this disease. The increased expression of IL-2R and IL-6 in serum is expected to predict the severity of the 2019-nCoV pneumonia and the prognosis of patients.

Activation of utrophin promoter by heregulin via the ets-related transcription factor complex GA-binding protein alpha/beta

Utrophin/dystrophin-related protein is the autosomal homologue of the chromosome X-encoded dystrophin protein. In adult skeletal muscle, utrophin is highly enriched at the neuromuscular junction. However, the molecular mechanisms underlying regulation of utrophin gene expression are yet to be defined. Here we demonstrate that the growth factor heregulin increases de novo utrophin transcription in muscle cell cultures. Using mutant reporter constructs of the utrophin promoter, we define the N-box region of the promoter as critical for heregulin-mediated activation. Using this region of the utrophin promoter for DNA affinity purification, immunoblots, in vitro kinase assays, electrophoretic mobility shift assays, and in vitro expression in cultured muscle cells, we demonstrate that ets-related GA-binding protein alpha/beta transcription factors are activators of the utrophin promoter. Taken together, these results suggest that the GA-binding protein alpha/beta complex of transcription factors binds and activates the utrophin promoter in response to heregulin-activated extracellular signal-regulated kinase in muscle cell cultures. These findings suggest methods for achieving utrophin up-regulation in Duchenne's muscular dystrophy as well as mechanisms by which neurite-derived growth factors such as heregulin may influence the regulation of utrophin gene expression and subsequent enrichment at the neuromuscular junction of skeletal muscle.

Sp1 cooperates with the ets transcription factor, GABP, to activate the CD18 (beta2 leukocyte integrin) promoter

CD18, the beta chain of the leukocyte integrins, plays a crucial role in immune and inflammatory responses. CD18 is expressed exclusively by leukocytes, and it is transcriptionally regulated during the differentiation of myeloid cells. The ets factors, PU.1 and GABP, bind to three ets sites in the CD18 promoter, which are essential for high level myeloid expression of CD18. We now identify two binding sites for the transcription factor, Sp1, that flank these ets sites. Sp1 is the only factor from myeloid cells that binds to these sites in a sequence-specific manner. Mutagenesis of these sites abrogates Sp1 binding and significantly reduces the activity of the transfected CD18 promoter in myeloid cells. Transfection of Sp1 into Drosophila Schneider cells, which otherwise lack Sp1, activates the CD18 promoter dramatically. GABP also activates the CD18 promoter in Schneider cells. Co-transfection of Sp1 and GABP activates CD18 more than the sum of their individual effects, indicating that these factors cooperate to transcriptionally activate myeloid expression of CD18. These studies support a model of high level, lineage-restricted gene expression mediated by cooperative interactions between widely expressed transcription factors.

Performance analysis of novel methods for detecting epistasis

Background

Epistasis is recognized fundamentally important for understanding the mechanism of disease-causing genetic variation. Though many novel methods for detecting epistasis have been proposed, few studies focus on their comparison. Undertaking a comprehensive comparison study is an urgent task and a pathway of the methods to real applications.

Results

This paper aims at a comparison study of epistasis detection methods through applying related software packages on datasets. For this purpose, we categorize methods according to their search strategies, and select five representative methods (TEAM, BOOST, SNPRuler, AntEpiSeeker and epiMODE) originating from different underlying techniques for comparison. The methods are tested on simulated datasets with different size, various epistasis models, and with/without noise. The types of noise include missing data, genotyping error and phenocopy. Performance is evaluated by detection power (three forms are introduced), robustness, sensitivity and computational complexity.

Conclusions

None of selected methods is perfect in all scenarios and each has its own merits and limitations. In terms of detection power, AntEpiSeeker performs best on detecting epistasis displaying marginal effects (eME) and BOOST performs best on identifying epistasis displaying no marginal effects (eNME). In terms of robustness, AntEpiSeeker is robust to all types of noise on eME models, BOOST is robust to genotyping error and phenocopy on eNME models, and SNPRuler is robust to phenocopy on eME models and missing data on eNME models. In terms of sensitivity, AntEpiSeeker is the winner on eME models and both SNPRuler and BOOST perform well on eNME models. In terms of computational complexity, BOOST is the fastest among the methods. In terms of overall performance, AntEpiSeeker and BOOST are recommended as the efficient and effective methods. This comparison study may provide guidelines for applying the methods and further clues for epistasis detection.

Backfoot is a novel homeobox gene expressed in the mesenchyme of developing hind limb

Homeobox genes play important roles in pattern formation during development. Here, we report the cloning and temporal and spatial expression patterns of a novel homeobox gene Backfoot (BFT for the human gene, and Bft for the mouse gene), whose expression reveals an early molecular distinction between forelimb and hind limb. BFT was identified as a sequence-specific DNA-binding protein. In addition to the homeodomain, it shares a carboxyl-terminal peptide motif with other paired-like homeodomain proteins. Northern hybridization analysis of RNAs from human tissues revealed that human BFT is highly expressed in adult skeletal muscle and bladder. During midgestation embryogenesis, mouse Bft is expressed in the developing hind limb buds, mandibular arches, and Rathke's pouch. The expression of Bft begins prior to the appearance of hind limb buds in mesenchyme but is never observed in forelimbs. At later stages of limb development, the expression is progressively restricted to perichondrial regions, most likely in tendons and ligaments. The timing and pattern of expression suggest that Bft plays multiple roles in hind limb patterning, branchial arch development, and pituitary development. Bft is likely identical to a mouse gene, Ptx1, that was recently isolated by Lamonerie et al. ([1996] Genes Dev. 10:1284-1295) and that has been suggested to play a role in pituitary development.

Effectiveness of contact precautions against multidrug-resistant organism transmission in acute care: a systematic review of the literature

Contact precautions are widely recommended to prevent multidrug-resistant organism (MDRO) transmission. However, conflicting data exist regarding their effectiveness. Prior systematic reviews examined contact precautions as part of a larger bundled approach, limiting ability to understand their effectiveness. The aim of this review was to characterize the effectiveness of contact precautions alone against transmission of any MDRO among adult acute care patients. Directed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement, comprehensive searches of four electronic scientific literature databases were conducted for studies published in English from January 2004 to June 2014. Studies were included if interventional, original research, evaluating contact isolation precautions against MDRO transmission among inpatients. Searches returned 284 studies, six of which were included in the review. These studies measured four different MDROs with one study showing a reduction in transmission. Whereas studies were of high quality regarding outcome operationalization and statistical analyses, overall quality was moderate to low due to poor intervention description, population characterization and potential biases. Where compliance was measured (N = 4), it presented a threat to validity because it included select parts of the intervention, ranged from 21% to 87%, and was significantly different across study phases (N = 2). The poor quality of evidence on this topic continues to limit interpretation of these data. Hence, this conflicting body of literature does not constitute evidence for or against contact precautions. We recommend that researchers consider power calculation, compliance monitoring, non-equivalent concurrent controls when designing future studies on this topic.

The mammalian retinal degeneration B2 gene is not required for photoreceptor function and survival

The retinal degeneration B (rdgB) gene in Drosophila is essential for photoreceptor function and survival. The rdgB mutant fly exhibits an abnormal electroretinogram and a light-dependent photoreceptor degeneration. The function of RdgB is not fully understood, but the presence of a phosphatidylinositol transfer protein domain suggests a possible role in phosphatidylinositol metabolism and signaling. Two mammalian homologs, M-RdgB1 and M-RdgB2, are known. While M-RdgB1 is widely expressed, M-RdgB2 is found primarily in the retina and the dentate gyrus. Functional conservation between the Drosophila and mammalian RdgBs was demonstrated by the ability of both M-RdgBs to rescue the photoreceptor phenotype in rdgB mutant flies through transgenic expression. To investigate the role of M-RdgB2 in the mammalian retina, we disrupted the m-rdgB2 gene in mice by gene targeting. The homozygous knockout mice are fertile and apparently healthy. By light microscopy, immunocytochemistry and electroretinograms, mice up to 18 months of age showed normal photoreceptor function and survival. The inner retinal neurons were also examined by immunolabeling with a number of cell-specific markers and no apparent defects were found in the major cell populations. We conclude that M-rdgB2 is not essential for phototransduction and photoreceptor survival. Thus, m-rdgB2 is not a candidate gene for human retinal degenerations. Whether M-rdgB2 has a role in visual processing in the inner retina, or whether it is required for hippocampal function, remains to be determined.

New spectroscopic data, spin-orbit functions, and global analysis of data on the AΣu+1 and bΠu3 states of Na2

The lowest electronically excited states of Na2 are of interest as intermediaries in the excitation of higher states and in the development of methods for producing cold molecules. We have compiled previously obtained spectroscopic data on the A 1Sigmau+ and b 3Piu states of Na2 from about 20 sources, both published and unpublished, together with new sub-Doppler linewidth measurements of about 15,000 A<--X transitions using polarization spectroscopy. We also present new ab initio results for the diagonal and off-diagonal spin-orbit functions. The discrete variable representation is used in conjunction with Hund's case a potentials plus spin-orbit effects to model data extending from v=0 to very close to the 3 2S+3 2P12 limit. Empirical estimates of the spin-orbit functions agree well with the ab initio functions for the accessible values of R. The potential function for the A state includes an exchange potential for S+P atoms, with a fitted coefficient somewhat larger than the predicted value. Observed and calculated term values are presented in an auxiliary (EPAPS) file as a database for future studies on Na2.

An enhancer located between the neutrophil elastase and proteinase 3 promoters is activated by Sp1 and an Ets factor

The adjacent neutrophil elastase, proteinase 3, and azurocidin genes encode serine proteases expressed specifically in immature myeloid cells. Subclones of a 17-kilobase (kb) murine neutrophil elastase genomic clone were assessed for their ability to stimulate the neutrophil elastase promoter in 32D cl3 myeloid cells. Region -9.3 to -7.3 kb stimulated transcription 7-fold, whereas other genomic segments were inactive. This enhancer is located in the second intron of the proteinase-3 gene and so may regulate more than one gene in the myeloid protease cluster. Deletional analysis of the enhancer identified several segments which activated the neutrophil elastase and thymidine kinase promoters 3-6-fold. The most active segment was a 220-base pair region centered at -8.6 kb, which activated transcription 31-fold. This segment contains an Sp1 consensus site, which bound Sp1, flanked by two Ets family consensus sequences, which bound PU.1, GABP, and an Ets factor present in myeloid cell extracts. Mutation of the Sp1-binding site reduced enhancer activity 8-fold in 32D cl3 cells, and mutation of either or both Ets-binding sites reduced activity 3-4-fold. Sp1 activated the distal enhancer 5-fold, GABP 3-fold, and the combination 8-fold in Schneider cells.

epiACO - a method for identifying epistasis based on ant Colony optimization algorithm

Background

Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Though many works have been done for identifying epistatic interactions, due to their methodological and computational challenges, the algorithmic development is still ongoing.

Results

In this study, a method epiACO is proposed to identify epistatic interactions, which based on ant colony optimization algorithm. Highlights of epiACO are the introduced fitness function Svalue, path selection strategies, and a memory based strategy. The Svalue leverages the advantages of both mutual information and Bayesian network to effectively and efficiently measure associations between SNP combinations and the phenotype. Two path selection strategies, i.e., probabilistic path selection strategy and stochastic path selection strategy, are provided to adaptively guide ant behaviors of exploration and exploitation. The memory based strategy is designed to retain candidate solutions found in the previous iterations, and compare them to solutions of the current iteration to generate new candidate solutions, yielding a more accurate way for identifying epistasis.

Conclusions

Experiments of epiACO and its comparison with other recent methods epiMODE, TEAM, BOOST, SNPRuler, AntEpiSeeker, AntMiner, MACOED, and IACO are performed on both simulation data sets and a real data set of age-related macular degeneration. Results show that epiACO is promising in identifying epistasis and might be an alternative to existing methods.

CNV_IFTV: An Isolation Forest and Total Variation-Based Detection of CNVs from Short-Read Sequencing Data

Accurate detection of copy number variations (CNVs) from short-read sequencing data is challenging due to the uneven distribution of reads and the unbalanced amplitudes of gains and losses. The direct use of read depths to measure CNVs tends to limit performance. Thus, robust computational approaches equipped with appropriate statistics are required to detect CNV regions and boundaries. This study proposes a new method called CNV_IFTV to address this need. CNV_IFTV assigns an anomaly score to each genome bin through a collection of isolation trees. The trees are trained based on isolation forest algorithm through conducting subsampling from measured read depths. With the anomaly scores, CNV_IFTV uses a total variation model to smooth adjacent bins, leading to a denoised score profile. Finally, a statistical model is established to test the denoised scores for calling CNVs. CNV_IFTV is tested on both simulated and real data in comparison to several peer methods. The results indicate that the proposed method outperforms the peer methods. CNV_IFTV is a reliable tool for detecting CNVs from short-read sequencing data even for low-level coverage and tumor purity. The detection results on tumor samples can aid to evaluate known cancer genes and to predict target drugs for disease diagnosis.

LncRNA DANCR accelerates the development of multidrug resistance of gastric cancer

OBJECTIVE

The development of multidrug resistance (MDR) is a key issue for tumor recurrence and metastasis, leading to treatment failure of gastric cancer (GC). Long non-coding RNA (lncRNA) DANCR has been shown to be highly expressed in GC patients, which accelerates growth and metastasis of GC cells. This study aims to elucidate the role of DANCR in regulating MDR of GC.

PATIENTS AND METHODS

The mRNA level of DANCR in GC patients with or without DDP-resistance was determined by quantitative Real-time polymerase chain reaction (qRT-PCR). DANCR expression in GC cell lines (SGC7901, BGC823) and cisplatin (DDP)-resistant cell lines (SGC7901/DDP, BGC823/DDP) was determined as well. Knockdown or overexpression of DANCR in GC cells with or without DDP-resistance was achieved by siRNA interference technology or stable transfection of lentivirus, respectively. The regulatory effects of DANCR on cytotoxicity and apoptosis were examined by cytotoxicity assay and flow cytometry method (FCM), respectively. In addition, we detected the expressions of MDR1, MRP1, mechanistic target of rapamycin (mTOR) and hypoxia inducible factor-1α (HIF-1α) in GC cells overexpressing DANCR by qRT-PCR and Western blot.

RESULTS

DANCR expression remained high in DDP-resistant GC tissues or cells. SGC7901/DDP and BGC823/DDP cells transfected with si-DANCR presented decreased survival and increased apoptosis. On the contrary, SGC7901/DDP and BGC823/DDP cells overexpressing DANCR showed increased survival and decreased apoptosis. In addition, DANCR overexpression could upregulate expressions of MDR1 and MRP1 in DDP-induced SGC901 and BGC823 cells.

CONCLUSIONS

Upregulation of DANCR can accelerate the MDR development of GC, which may become a potential target for treating GC with MDR.

Macrophage infiltrates with high levels of Toll-like receptor 4 expression in white adipose tissues of male Chinese

BACKGROUND AND AIMS

Macrophages and Toll-like receptor 4 (TLR4) are involved in the inflammatory process of adipogenesis. This study aimed to characterize macrophage infiltrates and the associated TLR4 expression in different locations of white adipose tissues (WAT) of male Chinese and determine their correlations to adipocyte hypertrophy and hyperplasia.

METHODS AND RESULTS

A total of 30 men, who were lean, overweight or with type 2 diabetes (T2D), were recruited. Their abdominal omental WAT (oWAT) and subcutaneous WAT (scWAT) were obtained. The contents of macrophages in oWAT and scWAT were quantified using anti-CD68 staining. The levels of TLR4 expression were analyzed by western blot assays and the adipocyte size was quantified, followed by linear regression analysis. Significantly higher numbers of macrophages (24.4+/-3.2 vs 6.1+/-2.9, p<0.001), associated with higher levels of TLR4 expression (0.59+/-0.19 vs 0.20+/-0.03, p<0.001), were observed in oWAT, as compared with that in scWAT. Furthermore, the levels of macrophage infiltrates and TLR4 expression in oWAT of subjects who were overweight or/and have T2D were significantly higher than that in the lean group. The average adipocyte diameters and cross-sectional areas in oWAT of subjects who were overweight were significantly greater than those in the lean group (p=0.003 and p=0.04, respectively). Importantly, the numbers of macrophage infiltrates were positively correlated to the levels of TLR4 expression, the sizes of adipocytes, the levels of body mass index and C-reactive protein, respectively.

CONCLUSION

Our data suggest that macrophage-related TLR4 expression and inflammation contribute to the development of adipocyte hypertrophy in male Chinese.

The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method

BACKGROUND

Predicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new DDIs. The existing methods mostly use the construction of heterogeneous networks to predict new DDIs. However, the number of known interacting drug-disease pairs is small, so there will be many errors in this heterogeneous network that will interfere with the final results.

RESULTS

A novel method, known as the dual-network L2,1-collaborative matrix factorization, is proposed to predict novel DDIs. The Gaussian interaction profile kernels and L2,1-norm are introduced in our method to achieve better results than other advanced methods. The network similarities of drugs and diseases with their chemical and semantic similarities are combined in this method.

CONCLUSIONS

Cross validation is used to evaluate our method, and simulation experiments are used to predict new interactions using two different datasets. Finally, our prediction accuracy is better than other existing methods. This proves that our method is feasible and effective.

Co-differential Gene Selection and Clustering Based on Graph Regularized Multi-View NMF in Cancer Genomic Data

Cancer genomic data contain views from different sources that provide complementary information about genetic activity. This provides a new way for cancer research. Feature selection and multi-view clustering are hot topics in bioinformatics, and they can make full use of complementary information to improve the effect. In this paper, a novel integrated model called Multi-view Non-negative Matrix Factorization (MvNMF) is proposed for the selection of common differential genes (co-differential genes) and multi-view clustering. In order to encode the geometric information in the multi-view genomic data, graph regularized MvNMF (GMvNMF) is further proposed by applying the graph regularization constraint in the objective function. GMvNMF can not only obtain the potential shared feature structure and shared cluster group structure, but also capture the manifold structure of multi-view data. The validity of the proposed GMvNMF method was tested in four multi-view genomic data. Experimental results showed that the GMvNMF method has better performance than other representative methods.

miR-33a expression sensitizes Lgr5+ HCC-CSCs to doxorubicin via ABCA1

Cancer stem cells (CSCs) are responsible for the unrestrained cell growth and chemo-resistance of malignant tumors. Reports about miR-33a in different type of cancer are limited, and it remains elusive whether there is a link between miR-33a and chemo-resistance of CSCs. Here we report that Lgr5+ hepatocellular carcinoma (HCC) cells from primary tissues and cell lines behave similarly to CSCs and are chemo-resistant to doxorubicin. Significantly, reduced miR-33a expression is associated with the chemo-resistance of Lgr5+ HCC-CSCs, accompanied by an overexpression of ABCA1 which is identified as target of miR-33a by mainly using miRNA luciferase assay and western-blotting. We demonstrate that down-regulation of miR-33a expression directly contributes to chemo-resistance of Lgr5+ HCC-CSCs, and restoring miR-33a expression sensitizes them to doxorubicin via apoptosis by mainly using TUNEL assay, soft agar colony formation assay and xenograft assay. Additionally, reduced miR-33a expression in HCC tissues is associated with chemo-response and poor patient survival, which suggests the therapeutic potential of miR-33a. In conclusion, our work indicates that ectopic miR-33a expression sensitizes Lgr5+ HCC-CSCs to doxorubicin via direct targeting ABCA1, which sheds new light on understanding the mechanism of chemo-resistance in HCC-CSCs and contributes to development of potential therapeutics against HCC.

LncRNA SNHG5 promotes cisplatin resistance in gastric cancer via inhibiting cell apoptosis

OBJECTIVE

To elucidate the function of long non-coding RNA (lncRNA) SNHG5 in cisplatin-resistant gastric cancer (GC), and its potential mechanism.

PATIENTS AND METHODS

We detected the expressions of SNHG5, apoptosis-specific genes (Bax and Bcl-2) and drug resistance-specific genes (MDR1 and MRP1) in cisplatin-sensitive and cisplatin-resistant GC patients. The expression levels were also detected in cisplatin-resistant GC cell lines (BGC823/DDP, SGC7901/DDP) and GC cell lines (BGC823 and SGC7901). Through the liposome transfection, the regulatory effects of SNHG5 on proliferative potential and apoptosis were examined by cytotoxicity assay and flow cytometry assay, respectively. The protein levels of apoptosis-related genes and drug resistance-related genes influenced by SNHG5 were detected by Western blot.

RESULTS

Compared with cisplatin-sensitive GC patients, SNHG5 expression was remarkably higher in cisplatin-resistant GC patients. Besides, higher SNHG5 expression was observed in BGC823/DDP and SGC7901/DDP cells relative to that of their parental cells. Proliferative rate (OD450) and IC50 decreased, but the apoptotic rate increased in BGC823/DDP and SGC7901/DDP cells with SNHG5 knockdown. It is found that SNHG5 overexpression reduced cisplatin sensitivity in BGC823 and SGC7901 cells. Decreased cisplatin cytotoxicity, elevated IC50 and inhibited apoptotic rate were observed in GC cells overexpressing SNHG5. Moreover, the expression levels of Bax, MDR1 and MRP1 were upregulated, while Bcl-2 downregulated in BGC823 and SGC7901 cells overexpressing SNHG5.

CONCLUSIONS

SNHG5 is highly expressed in cisplatin-resistant GC. SNHG5 promotes cisplatin resistance in GC by regulating apoptosis-related genes and drug resistance-related genes.

Application of a microbial consortium improves the growth of Camellia sinensis and influences the indigenous rhizosphere bacterial communities

AIMS

To investigate the role of a microbial consortium in influencing of Camellia sinensis growth and rhizosphere bacteria microbial community structure.

METHODS AND RESULTS

Based on glasshouse trials, the microbial consortium TCM was selected for a field trial. TCM significantly increased bud density (67·53%), leaf area (31·15%) and hundred-bud weight (22·5%) compared with the control treatment (P < 0·01) during 180 days. Furthermore, TCM-treated soil showed a significant increase (P < 0·05) in organic matter (60·89%), total nitrogen (66·22%), total phosphorus (3·34%), available phosphorus (3·82%), available potassium (9·24%) and 2-3 mm water-stable aggregates (77·93%). Molecular ecological network analysis of the rhizobacteria indicated an increase in modularity and the number of community, connection and nodes after TCM application. Several plant growth-promoting bacteria were categorized as hubs or indicators, such as Haliangium, Catenulispora and Gemmatimonas, and showed intensive connections with other bacteria.

CONCLUSIONS

The TCM consortium enhances the effectiveness of soil mineral nutrition, influences the indigenous rhizobacterial community, alters the rhizobacterial network structure in the rhizosphere and promotes the growth of C. sinensis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The TCM growth-promoting mechanism was closely related to rhizosphere bacterial diversity; therefore, strengthening rhizobacterial interactions may help promote C. sinensis growth, which could be a sustainable approach for improving C. sinensis growth and health in tea plantations.

Backfoot, a novel homeobox gene, maps to human chromosome 5 (BFT) and mouse chromosome 13 (Bft)

Homeobox genes play important roles in limb development. Backfoot is a recently identified mammalian homeobox gene whose temporal and spatial expression pattern during limb development suggests that it is a key component for specifying the identify and structure of the hindlimb. Here we report the chromosomal mapping of the Backfoot locus in human (BFT) and mouse (Bft). Using single-strand conformation analysis of PCR products amplified from a panel of somatic cell hybrid lines and two radiation hybrid (RH) panels, we have physically mapped BFT to human chromosome 5, closely linked to STS markers D5S2543, D5S458, D5S1947, and D5S1995 on the Stanford G3 RH map and to AFMA057VG5 and AFM350YB1 on the Gene-Bridge 4 RH map. Linkage analysis of a mouse inter-specific backcross panel (C57BL/6J x Mus musculus spretus) has localized Bft to the central part of mouse chromosome 13. The map position of Bft is near two mouse limb mutant loci defined as dumpy and mdac.