Biology subjects

Han, H.

Publications and source records attributed to Han, H..

121 records · Page 7Linked to original sources

bioRxiv2018

Makorin1 controls embryonic patterning by alleviating Bruno-mediated repression of oskar translation

Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning and germ cell specification. Here, we show that Mkrn1 is required for translational activation of oskar, whose product is critical for axis specification and germ plasm assembly. We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds osk 3 UTR in a region adjacent to A-rich sequences. This binding site also overlaps with Bruno (Bru) responsive elements (BREs), which regulate osk translation. We observe increased association of the translational repressor Bru with osk mRNA upon depletion of Mkrn1, implying that the two proteins compete for osk binding. Consistently, reducing Bru dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation via displacing Bru from its 3 UTR.

developmental biology↗

bioRxiv2018

Enhanced nitrous oxide production in denitrifying Dechloromonas aromatica strain RCB under salt and alkaline conditions

Salinity and pH are important environmental parameters with direct and indirect impacts on the viability and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N2O accumulated transiently only in insignificant amounts at low salinity ([≤]0.5% NaCl) and circumneutral pH (7.0 and 7.5). Incubation at 0.7% salinity resulted in substantially longer lag phase and slower growth rate, along with the increase in the amounts of transiently accumulated N2O (15.8{+/-}2.8 moles N2O-N/vessel). Incubation at pH 8.0 severely inhibited growth and resulted in permanent accumulation of 29.9{+/-}1.3 moles N2O-N/vessel from reduction of 151{+/-}20 moles NO3-. The transcription analyses observed decreased nosZ/(nirS1+nirS2) ratios coinciding with N2O accumulation. The N2O consumption rates of resting D. aromatica cells subjected to the salt and alkaline stress conditions were significantly lower than the rates of N2O production from NO2- reduction at N2O / NO2- concentration of 0.1 mM, but not at a higher concentration (1.0 mM). These results indicate that alteration in N2O consumption kinetics was another cause of enhanced N2O production observed under the stress conditions. The findings in this study suggest that canonical denitrifiers may become a significant N2O source when faced with abrupt environmental changes.

microbiology↗

bioRxiv2018

Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and phosphate release

Plasmodium actins form very short filaments and have a non-canonical link between ATP hydrolysis and polymerization. Long filaments are detrimental to the parasites, but the structural factors constraining Plasmodium microfilament lengths are currently unknown. Using high-resolution crystallography, we show that magnesium binding activates the Plasmodium actin I monomer before polymerization by a slight flattening, which is reversed upon phosphate release. A coordinated potassium ion resides in the active site during hydrolysis and leaves together with the phosphate, a process governed by the position of the Arg178/Asp180-containing A-loop. Asp180 interacts with either Lys270 or His74, depending on protonation, while Arg178 links the inner and outer domains. Hence, the A-loop is a switch between stable and non-stable filament conformations. Our data provide a comprehensive model for polymerization, phosphate release, and the inherent instability of parasite microfilaments.

biochemistry↗

bioRxiv2018

SuperCT: A supervised-learning-framework to enhance the characterization of single-cell transcriptomic profiles

Characterization of individual cell types is fundamental to the study of multicellular samples such as tumor tissues. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task. Currently, most of the scRNA-seq data analyses are commenced with unsupervised clustering of cells followed by visualization of clusters in a low-dimensional space. Clusters are often assigned to different cell types based on canonical markers. However, the efficiency of characterizing the known cell types in this way is low and limited by the investigator[s] knowledge. In this study, we present a technical framework of training the expandable supervised-classifier in order to reveal the single-cell identities based on their RNA expression profiles. Using multiple scRNA-seq datasets we demonstrate the superior accuracy, robustness, compatibility and expandability of this new solution compared to the traditional methods. We use two examples of model upgrade to demonstrate how the projected evolution of the cell-type classifier is realized.

bioinformatics↗

bioRxiv2018

Molecular structure and function of myelin protein P0 in membrane stacking

Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in fluidity changes of the bilayers themselves, but also potentially involves the rearrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.

biochemistry↗

bioRxiv2018

Transcriptional regulation of voltage-gated sodium channels contributes to GM-CSF induced pain

Granolocyte-macrophage colony stimulating factor (GM-CSF) induces production of granulocyte and macrophage populations from the hematopoietic progenitor cells; it is one of the most common growth factors in the blood. GM-CSF is also involved in bone cancer pain development by regulating tumor-nerve interactions, remodeling of peripheral nerves and sensitization of damage-sensing (nociceptive) nerves. However, the precise mechanism for GM-CSF-dependent pain is unclear. In this study, we found that GM-CSF is highly expressed in human malignant osteosarcoma. Rats implanted with bone cancer cells develop mechanical and thermal hyperalgesia but antagonizing GM-CSF in these animals significantly reduced such hypersensitivity. Nociceptor-specific voltage gated Na+ channels Nav1.7, Nav1.8 and Nav1.9 were found to be selectively up-regulated in rat DRG neurons treated with GM-CSF, which resulted in enhanced excitability. GM-CSF activated the Jak2 and Stat3 signaling pathway which promoted the transcription of Nav1.7-1.9 in DRG neurons. Accordingly targeted knocking down either Nav1.7-1.9 or Jak2/Stat3 in DRG neurons alleviated the hyperalgesia in rats. Our findings describe a new bone cancer pain mechanism and provide a new insight into the physiological and pathological functions of GM-CSF.

neuroscience↗

bioRxiv2018

High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have several technical limitations such as low process throughput from laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire. TrueRepertoire provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire was demonstrated by a phage-displayed single-chain variable fragment (scFv) library targeting human hepatocyte growth factor (hHGF) protein.

bioengineering↗

bioRxiv2018

Dectin-3 recognizes cryptococcal glucuronoxylomannan to initiate host defense against cryptococcosis

Cryptococcus neoformans and Cryptococcus gattii cause life-threatening meningoencephalitis and pneumonia in immunosuppressed and immunocompetent individuals. Given the structural differences of major polysaccharide glucuronoxylomannan (GXM) between C. neoformans and C. gattii, it remains unclear that how innate immune system recognizes GXM. Here, we report that C-type lectin receptor Dectin-3 (MCL encoded by Clec4d) is a direct receptor for GXMs from C. neoformans serotype AD (C.n-AD) and C. gattii serotype B (C.g-B). GXMs from C.n-AD and C.g-B activated both NF-{kappa}B and ERK pathways to induce the pro-inflammatory cytokine production, whereas it was completely abolished due to deficiency of Dectin-3 or its downstream adaptor protein CARD9. Upon pulmonary C.n-AD and C.g-B infection, Dectin-3- and CARD9-deficient mice were highly susceptible and showed augmented lung injury due to impairment of alveolar macrophage accumulation and killing activities. These results demonstrate that Dectin-3 contributes to host immunity against Cryptococcus infection through selectively recognizingGXM.

immunology↗

bioRxiv2018

Xist Intron 1 Repression by TALE Transcriptional Factor Improves Somatic Cell Reprogamming in Mice

Xist is the master regulator of X chromosome inactivation (XCI). In order to further understand the Xist locus in reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) and in somatic cell nuclear transfer (SCNT), we tested transcription-factor-like effectors (TALE)-based designer transcriptional factors (dTFs), which were specific to numerous regions at the Xist locus. We report that the selected dTF repressor 6 (R6) binding the intron 1 of Xist, which did not affect Xist expression in mouse embryonic fibroblasts (MEFs), substantially improved the iPSC generation and the SCNT preimplantation embryo development. Conversely, the dTF activator targeting the same genomic region of R6 decreased iPSC formation, and blocked SCNT-embryo development. These results thus uncover the critical requirement for the Xist locus in epigenetic resetting, which is not directly related to Xist transcription. This may provide a unique route to improving the reprogramming.

developmental biology↗

bioRxiv2017

Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

We describe a new light-sheet microscopy method for fast, large-scale volumetric imaging. Combining synchronized scanning illumination and oblique imaging over cleared, thick tissue sections in smooth motion, our approach achieves high-speed 3D image acquisition of an entire mouse brain within 2 hours, at a resolution capable of resolving synaptic spines. It is compatible with immunofluorescence labeling, enabling flexible cell-type specific brain mapping, and is readily scalable for large biological samples such as primate brain.

neuroscience↗

bioRxiv2017

A novel feature selection for RNA-seq analysis

RNA-seq data are challenging existing omics data analytics for its volume and complexity. Although quite a few computational models were proposed from different standing points to conduct differential expression (D.E.) analysis, almost all these methods do not provide a rigorous feature selection for high-dimensional RNA-seq count data. Instead, most or even all genes are invited into differential calls no matter they have real contributions to data variations or not. Thus, it would inevitably affect the robustness of D.E. analysis and lead to the increase of false positive ratios.\n\nIn this study, we presented a novel feature selection method: nonnegative singular value approximation (NSVA) to enhance RNA-seq differential expression analysis by taking advantage of RNA-seq count datas non-negativity. As a variance-based feature selection method, it selects genes according to its contribution to the first singular value direction of input data in a data-driven approach. It demonstrates robustness to depth bias and gene length bias in feature selection in comparison with its five peer methods. Combining with state-of-the-art RNA-seq differential expression analysis, it contributes to enhancing differential expression analysis by lowering false discovery rates caused by the biases. Furthermore, we demonstrated the effectiveness of the proposed feature selection by proposing a data-driven differential expression analysis: NSVA-seq, besides conducting network marker discovery.

bioinformatics↗

bioRxiv2017

Evaluating Methods of Correcting for Multiple Comparisons Implemented in SPM12 in Social Neuroscience fMRI Studies: An Example from Moral Psychology

In fMRI research, the goal of correcting for multiple comparisons is to identify areas of activity that reflect true effects, and thus would be expected to replicate in future studies. Finding an appropriate balance between trying to minimize false positives (Type I error) while not being too stringent and omitting true effects (Type II error) can be challenging. Furthermore, the advantages and disadvantages of these types of errors may differ for different areas of study. In many areas of social neuroscience that involve complex processes and considerable individual differences, such as the study of moral judgment, effects are typically smaller and statistical power weaker, leading to the suggestion that less stringent corrections that allow for more sensitivity may be beneficial, but also result in more false positives. Using moral judgment fMRI data, we evaluated four commonly used methods for multiple comparison correction implemented in SPM12 by examining which method produced the most precise overlap with results from a meta-analysis of relevant studies and with results from nonparametric permutation analyses. We found that voxel-wise thresholding with family-wise error correction based on Random Field Theory provides a more precise overlap (i.e., without omitting too few regions or encompassing too many additional regions) than either clusterwise thresholding, Bonferroni correction, or false discovery rate correction methods.

neuroscience↗

bioRxiv2017

Application of t-SNE to Human Genetic Data

The t-SNE (t-distributed stochastic neighbor embedding) is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.

genetics↗