Biology subjects

Yu, C.

Publications and source records attributed to Yu, C..

8 recordsLinked to original sources

bioRxiv2018

Changes in Microorganisms in the Rhizosphere of Mulberry Genotypes with Differing Resistance to Bacterial Wilt

A close relationship between soil-borne diseases, soil microbial community structure, and functional diversity has been described in the mulberry plant. In the present study, microbial abundance, community structure, and functional diversity in the soil rhizosphere were compared in resistant (Kangqing10) and susceptible (Guisang12) mulberry genotypes using the dilution plate method, micro-ecology technology, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The goal of this study was to develop better management methods for mulberry cultivation and preventing and controlling bacterial wilt. Rhizosphere soil microorganisms were more abundant in the resistant normal mulberry genotype than in the susceptible normal mulberry genotype. Carbon source utilization was better in the susceptible normal mulberry genotype. These properties were lower in the resistant sickly mulberry genotype than in the susceptible sickly mulberry genotype. PCR-DGGE indicated that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Correlation regression analysis implicated mulberry bacterial wilt in the loss of soil nutrients, particularly organic matter and nitrogen, which can disrupt the balance of the soil microbial community. Loss of soil organic matter and nitrogen had a lower impact on resistant genotype plants than on susceptible genotype plants. Therefore, resistant genotype plants displayed some resistance to bacterial wilt. Further insights into the soil rhizosphere microbial diversities of resistant and susceptible genotypes will help in the control and prevention of mulberry bacterial wilt.

microbiology↗

bioRxiv2018

Bclaf1 critically regulates the type I interferon response and is degraded by alphaherpesvirus US3

Type I interferon response plays a prominent role against viral infection, which is frequently disrupted by viruses. Here, we report Bcl-2 associated transcription factor 1 (Bclaf1) is degraded during the alphaherpesvirus Pseudorabies virus (PRV) and Herpes simplex virus type 1 (HSV-1) infections through the viral protein US3. We further reveal that Bclaf1 functions critically in type I interferon signaling. Knockdown or knockout of Bclaf1 in cells significantly impairs interferon- (IFN)-mediated gene transcription and viral inhibition against US3 deficient PRV and HSV-1. Mechanistically, Bclaf1 maintains a mechanism allowing STAT1 and STAT2 to be efficiently phosphorylated in response to IFN, and more importantly, facilitates IFN-stimulated gene factor 3 (ISGF3) binding with IFN-stimulated response elements (ISRE) for efficient gene transcription by directly interacting with ISRE and STAT2. Our studies establish the importance of Bclaf1 in IFN-induced antiviral immunity and in the control of viral infections.

immunology↗

bioRxiv2018

S100A4 inhibits cell proliferation by interfering with the RAGE V domain-S100A1

The Ca2+-dependent human S100A4 (Mts1) protein is part of the S100 family, and the S100A1 protein is the target of S100A4. Here, we studied the interactions of S100A1 with S100A4 using nuclear magnetic resonance (NMR; 700 MHz) spectroscopy. We used HADDOCK software to model S100A4 and S100A1, and we observed that S100A1 and the RAGE V domain have an analogous binding area in S100A4. We discovered that S100A4 acts as an antagonist among the RAGE V domain and S100A1, which inhibits tumorigenesis and cell proliferation. We used a WST-1 assay to examine the bioactivity of S100A1 and S100A4. This study could possibly be beneficial for evaluating new proteins for the treatment of cancer.

biochemistry↗

bioRxiv2018

Characterization and identification of long non-coding RNAs based on feature relationship

The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

bioinformatics↗

bioRxiv2018

Intrinsic functional reorganization of the attention network in the blind

Attention can bias visual perception by modulating the neuronal activity of visual areas. However, little is known if blindness can reshape the intrinsic functional organisation within the attention networks and between the attention and visual networks. A voxel-wise network-based functional connectivity strengthen mapping analysis was proposed to thirty congenitally, thirty early and thirty late blind subjects, and thirty sighted controls. Both the blind and sighted subjects exhibited similar spatial distributions of the intrinsic dorsal (DAN) and ventral (VAN) attention networks. Moreover, compared to the sighted controls, the blind subjects showed increased functional coupling within the DAN, and between the DAN and VAN, and between the attention sub-networks and visual areas, suggesting an increased information communication by visual deprivation. However, the onset age of blindness had little impact on the functional coupling of the attention network, indicating that non-visual sensory experience is enough for driving the development of intrinsic functional organization of the attention network. Finally, a positive correlation was identified between the duration of blindness and the functional coupling of the posterior inferior frontal gyrus with the visual network, representing an experience-dependent reorganisation after visual deprivation.

neuroscience↗

bioRxiv2017

Theta Oscillations Organize Spiking Activity in Higher-Order Visual Thalamus during Sustained Attention

Higher-order visual thalamus plays a fundamental but poorly understood role in attention-demanding tasks. To investigate how neuronal dynamics in higher-order visual thalamus are modulated by sustained attention, we performed multichannel electrophysiological recordings in the lateral posterior-pulvinar complex (LP/pulvinar) in the ferret (Mustela putorius furo). We recorded single unit activity and local field potential during the performance of the 5-choice serial reaction time task (5-CSRTT) that is used in both humans and animals as an assay of sustained attention. We found that half of the units exhibited an increasing firing rate during the delay period before stimulus onset (attention-modulated units). In contrast, the non-attention-modulated units responded to the stimulus, but not during the delay period. Spike-field coherence of only the attention-modulated neurons significantly increased from the start of the delay period until screen touch, predominantly in the theta frequency band. In addition, theta power and theta-gamma phase-amplitude coupling were elevated throughout the delay period. Our findings suggest that the theta oscillation plays a central role in orchestrating thalamic signaling during sustained attention.\n\nSignificanceImpaired sustained attention can be deadly, as illustrated by the number of motor vehicle accidents that are caused by drivers not reacting quickly enough to unexpected events on the road. Understanding how electrical signaling in higher-order visual nuclei, such as the LP/pulvinar, is modulated during tasks that require sustained attention is an important step in achieving a mechanistic understanding of sustained attention, which will eventually lead to new strategies to prevent and treat impairment in sustained attention.

neuroscience↗

bioRxiv2017

The Anatomical Tracings of Lesions After Stroke (ATLAS) Dataset - Release 1.1

Stroke is the leading cause of adult disability worldwide, with up to two-thirds of individuals experiencing long-term disabilities. Large-scale neuroimaging studies have shown promise in identifying robust biomarkers (e.g., measures of brain structure) of long-term stroke recovery following rehabilitation. However, analyzing large rehabilitation-related datasets is problematic due to barriers in accurate stroke lesion segmentation. Manually-traced lesions are currently the gold standard for lesion segmentation on T1-weighted MRIs, but are labor intensive and require anatomical expertise. While algorithms have been developed to automate this process, the results often lack accuracy. Newer algorithms that employ machine-learning techniques are promising, yet these require large training datasets to optimize performance. Here we present ATLAS (Anatomical Tracings of Lesions After Stroke), an open-source dataset of 304 T1-weighted MRIs with manually segmented lesions and metadata. This large, diverse dataset can be used to train and test lesion segmentation algorithms and provides a standardized dataset for comparing the performance of different segmentation methods. We hope ATLAS release 1.1 will be a useful resource to assess and improve the accuracy of current lesion segmentation methods.

neuroscience↗

bioRxiv2017

Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

Three DNA polymerases (Pol , Pol {delta}, and Pol {varepsilon}) are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has distinct patterns of association with active and stalled replication forks. Pol is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol {delta} contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol {varepsilon} has a greater contact with the nascent ssDNA of leading strand on active forks compared with stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitate resumption of DNA synthesis after stress removal.

molecular biology↗