Biology subjects

Rao, Y.

Publications and source records attributed to Rao, Y..

5 recordsLinked to original sources

bioRxiv2018

Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature

The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which antibiotic binding induces ribosomal dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more biologically relevant investigation of how local antibiotic binding site interactions trigger global subunit rearrangements that perturb protein synthesis. Here, the structural effects of 2-deoxystreptamine (paromomycin and sisomicin), a novel sisomicin derivative, N1-methyl sulfonyl sisomicin (N1MS) and the non-deoxystreptamine (streptomycin) aminoglycosides on the ribosome at ambient and cryogenic temperatures were examined. Comparative studies led to three main observations. First, individual aminoglycoside-ribosome interactions in the decoding center were similar for cryogenic vs ambient temperature structures. Second, analysis of a highly conserved GGAA tetraloop of h45 revealed aminoglycoside-specific conformational changes, which are affected by temperature only for N1MS. We report the h44/h45 interface in varying states, that is, engaged, disengaged and in equilibrium. Thirdly, we observe aminoglycoside-induced effects on 30S domain closure, including a novel intermediary closure state, which is also sensitive to temperature. Analysis of three ambient and five cryogenic crystallography datasets reveal a correlation between h44/h45 engagement and domain closure. These observations illustrate the role of ambient temperature crystallography in identifying dynamic mechanisms of ribosomal dysfunction induced by local drug-binding site interactions. Together these data identify tertiary ribosomal structural changes induced by aminoglycoside binding that provides functional insight and targets for drug design.

biophysics↗

bioRxiv2018

β-lactam Antibiotics Stimulate the Pathogenicity of Methicillin-resistant Staphylococcus aureus Via SarA-controlled Tandem Lipoprotein Expression

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of nosocomial infections worldwide. MRSA resists nearly all {beta}-lactam antibiotics that have a bactericidal activity and a signal inducer effect. However, studies have yet to clarify whether the inducer effect of empirically used {beta}-lactams stimulates MRSA pathogenicity in vivo. Here, we showed that a new cluster of tandem lipoprotein genes (tlpps) was upregulated in MRSA in response to the subinhibitory concentrations of {beta}-lactam induction. The increased Tlpps significantly altered immune responses by macrophages with high IL-6 and TNF levels. The deletion of the tlpps mutant (N315{Delta}tlpps) significantly decreased the proinflammatory cytokine levels in vitro and in vivo. The bacterial loads of N315{Delta}tlpps in the mouse kidney were also reduced compared with those of the wild type N315. The {beta}-lactam-treated MRSA exacerbated cutaneous infections with increased lesion size, extended illness, and flake-like abscess-formation compared with those of the nontreatment. The {beta}-lactam antibiotics that promoted the MRSA pathogenicity were SarA dependent, and the increasing expression of tlpps after {beta}-lactam treatment was directly controlled by the global regulator SarA. Overall, our findings suggested that {beta}-lactams should be used carefully because it might lead to a worse outcome of MRSA infection than inaction in the treatment.\n\nAuthor summary{beta}-lactams are widely used in practice to treat infectious diseases, however, {beta}-lactams worsening the outcome of a certain disease is poorly understood. In this study, we have identified a new cluster of tandem lipoprotein genes (tlpps) that is upregulated in the major clinically prevalent MRSA clones in response to the subinhibitory concentrations of {beta}-lactams induction. The major highlight in this work is that {beta}-lactams induce SarA expression, and then SarA directly binds to the tlpp cluster promoter region and upregulates the tlpp expression in MRSA. Moreover, the {beta}-lactam stimulated Tlpps are important virulence factors that enhance MRSA pathogenicity. The deletion of the tlpps mutant significantly decreases the proinflammatory cytokine levels in vitro and in vivo. The {beta}-lactam induced Tlpps enhance the host inflammatory responses by triggering the expression of IL-6 and TNF, thereby promoting bacterial colonization and abscess formation. These data elucidate that {beta}-lactams can worsen the outcome of MRSA infection through the induction of tlpps that are controlled by the global regulator SarA.

pathology↗

bioRxiv2018

Post-reactivation new learning impairs and updates human episodic memory through dissociable processes

Learning of competing information after reactivation has the potential to disrupt memory reconsolidation and thus impair a consolidated memory. Yet this effect has rarely been detected in episodic memory. By introducing an additional retrieving cue to the target memory, the current study detected significant impairment on the reactivated episodic memory, in addition to an integration of new information to the old memory. However, while the integration effect followed the time window of reconsolidation disruption, the impairment effect did not. MEG measurements further revealed alpha power change during reactivation and post-reactivation learning which showed different correlation patterns with the integration and impairment effects, confirming that the two effects relied on different processes. Therefore, post-reactivation new learning disrupts episodic memory but not through reconsolidation disruption. Further findings that the impairment effect was correlated with participants voluntary inhibition ability suggest an inhibition-based memory updating process underlying post-reactivation new learning.

neuroscience↗

bioRxiv2018

A Convenient Non-harm Cervical Spondylosis Intelligent Identity method based on Machine Learning

Cervical spondylosis(CS), a most common orthopedic diseases, is mainly identified by the doctors judgment from the clinical symptoms and cervical change provided by expensive instruments in hospital. Owing to the development of the surface electromyography(sEMG) technique and artificial intelligence, we proposed a convenient non-harm CS intelligent identify method EasiCNCSII, including the sEMG data acquisition and the CS identification. For the convenience and efficiency of data acquisition with the limited testable muscles provided by the sEMG technology, we proposed a data acquisition method based on the relationship between muscle activity pattern, the tendons theory and CS etiology. It is easily performed in less than 20 minutes, even outside the hospital. Faced with the challenge of high-dimension and the weak availability, the 3-tier model EasiAI is developed to intelligently identify CS. The common features and new features are extracted from raw sEMG data in first tier. The EasiRF is proposed in second tier to further reduce the data dimension and improve the performance. With the limited and weakly available data, the gradient boosted regression tree is developed in third tier to effectively identify CS. The EasiAI achieve the best performance with 91.02% in accuracy, 97.14% in sensitivity, and 81.43% in specificity compared with 4 common machine learning classification model, validating the EasiCNCSII effectiveness.

bioinformatics↗

bioRxiv2018

Structure of the 30S ribosomal decoding complex at ambient temperature

The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 [A] resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation.

biophysics↗