Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells.

Introduction: The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective: To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results: We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions: The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.

Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequencing. We present a deep learning framework, NanoDeep, to overcome these limitations by incorporating convolutional neural network and squeeze and excitation. We first showed that the raw squiggle derived from native DNA sequences determines the origin of microbial and human genomes. Then, we demonstrated that NanoDeep successfully classified bacterial reads from the pooled library with human sequence and showed enrichment for bacterial sequence compared with routine nanopore sequencing setting. Further, we showed that NanoDeep improves the sequencing efficiency and preserves the fidelity of bacterial genomes in the mock sample. In addition, NanoDeep performs well in the enrichment of metagenome sequences of gut samples, showing its potential applications in the enrichment of unknown microbiota. Our toolkit is available at https://github.com/lysovosyl/NanoDeep.

[Value of Serum Light Chain in Diagnosis and Evaluation of Efficacy for Multiple Myeloma].

OBJECTIVE: To explore the clinical application value of serum light chain (sLC) in the diagnosis and therapeutic efficacy evaluation for multiple myeloma. METHODS: 46 patients with newly diagnosed multiple myeloma were selected as MM group and 50 healthy persons as control group. Rate scattering immunoturbidimetry was used to detect serum light chain and immunoglobulin (Ig) in two groups, serum protein electrophoresis was used to detect M protein by agarose gel. Then, the sensitivity and specificity of the two methods in MM diagnosis were analyzed and compared, and the significance of sLC detection in MM diagnosis were discussed. In addition, 15 MM patients after received conventional therapy were tracked, sLC levels in five different therapentic times were recorded, and the effect of sLC in efficacy evaluation of MM was analyzed. RESULTS: There were 11 cases of IgA type, 15 cases of IgG type, 8 cases of light chain κ type, 8 cases of light chain λ type, 2 cases of IgD type, and 2 cases of non-secretion type. The sLC-κ, sLC-λ and their ratio (including light chain type and double clone type), IgA and IgG (except IgD type), as well as albumin, beta-globulin and gamma-globulin levels showed statistically significant differences (P＜0.05) compared with the control group. The sensitivity of serum protein electrophoresis, Ig quantification, sLC and its ratio in the diagnosis of multiple myeloma were 57%, 76% and 65%, and their specificity were 83%, 61% and 90%, respectively. After the second or third chemotherapy, the sLC-κ/λ ratio gradually approached the normal range as the disease reliefes, and the sLC-κ/λ ratio continued to be on or off the line at outliers or further away from the reference value as the disease progresses in MM patients with κ type or λ type. CONCLUSION: sLC detection shows positive significance in early diagnosis of multiple myeloma, SLC monitoring can be used for the efficacy evaluation for treatment of MM patients.

Co-overexpression of geraniol-10-hydroxylase and strictosidine synthase improves anti-cancer drug camptothecin accumulation in Ophiorrhiza pumila.

Camptothecin (CPT) belongs to a group of monoterpenoidindole alkaloids (TIAs) and its derivatives such as irinothecan and topothecan have been widely used worldwide for the treatment of cancer, giving rise to rapidly increasing market demands. Genes from Catharanthus roseus encoding strictosidine synthase (STR) and geraniol 10-hydroxylase (G10H), were separately and simultaneously introduced into Ophiorrhiza pumila hairy roots. Overexpression of individual G10H (G lines) significantly improved CPT production with respect to non-transgenic hairy root cultures (NC line) and single STR overexpressing lines (S lines), indicating that G10H plays a more important role in stimulating CPT accumulation than STR in O. pumila. Furthermore, co-overexpression of G10H and STR genes (SG Lines) caused a 56% increase on the yields of CPT compared to NC line and single gene transgenic lines, showed that simultaneous introduction of G10H and STR can produce a synergistic effect on CPT biosynthesis in O. pumila. The MTT assay results indicated that CPT extracted from different lines showed similar anti-tumor activity, suggesting that transgenic O. pumila hairy root lines could be an alternative approach to obtain CPT. To our knowledge, this is the first report on the enhancement of CPT production in O. pumila employing a metabolic engineering strategy.