A Structural Model of the Genome Packaging Process in a Membrane-Containing Double Stranded DNA Virus

Peer reviewe

Zernike Phase Contrast Cryo-Electron Microscopy and Tomography for Structure Determination at Nanometer and Subnanometer Resolutions

Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with advanced image processing methods, we achieved subnanometer resolution for two biological specimens: 2D bacteriorhodopsin crystal and epsilon15 bacteriophage. For an asymmetric reconstruction of epsilon15 bacteriophage, ZPC-cryoEM can reduce the required amount of data by a factor of ~3, compared with conventional cryoEM. The reconstruction was carried out to 13 Å resolution without the need to correct the contrast transfer function. New structural features at the portal vertex of the epsilon15 bacteriophage are revealed in this reconstruction. Using ZPC cryo-electron tomography (ZPC-cryoET), a similar level of data reduction and higher resolution structures of epsilon15 bacteriophage can be obtained relative to conventional cryoET. These results show quantitatively the benefits of ZPC-cryoEM and ZPC-cryoET for structural determinations of macromolecular machines at nanometer and subnanometer resolutions.National Institutes of Health (U.S.) (Grant P41RR002250)National Institutes of Health (U.S.) (Grant R01AI0175208)National Institutes of Health (U.S.) (Grant PN1EY016525)Robert Welch Foundation (Q1242

BolA-like protein (IbaG) promotes biofilm formation and pathogenicity of Vibrio parahaemolyticus

Vibrio parahaemolyticus is a gram-negative halophilic bacterium widespread in temperate and tropical coastal waters; it is considered to be the most frequent cause of Vibrio-associated gastroenteritis in many countries. BolA-like proteins, which reportedly affect various growth and metabolic processes including flagellar synthesis in bacteria, are widely conserved from prokaryotes to eukaryotes. However, the effects exerted by BolA-like proteins on V. parahaemolyticus remain unclear, and thus require further investigation. In this study, our purpose was to investigate the role played by BolA-like protein (IbaG) in the pathogenicity of V. parahaemolyticus. We used homologous recombination to obtain the deletion strain ΔibaG and investigated the biological role of BolA family protein IbaG in V. parahaemolyticus. Our results showed that IbaG is a bacterial transcription factor that negatively modulates swimming capacity. Furthermore, overexpressing IbaG enhanced the capabilities of V. parahaemolyticus for swarming and biofilm formation. In addition, inactivation of ibaG in V. parahaemolyticus SH112 impaired its capacity for colonizing the heart, liver, spleen, and kidneys, and reduced visceral tissue damage, thereby leading to diminished virulence, compared with the wild-type strain. Finally, RNA-sequencing revealed 53 upregulated and 71 downregulated genes in the deletion strain ΔibaG. KEGG enrichment analysis showed that the two-component system, quorum sensing, bacterial secretion system, and numerous amino acid metabolism pathways had been altered due to the inactivation of ibaG. The results of this study indicated that IbaG exerts a considerable effect on gene regulation, motility, biofilm formation, and pathogenicity of V. parahaemolyticus. To the best of our knowledge, this is the first systematic study on the role played by IbaG in V. parahaemolyticus infections. Thus, our findings may lead to a better understanding of the metabolic processes involved in bacterial infections and provide a basis for the prevention and control of such infections

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

This study uses high-resolution cryo-electron microscopy to provide a complete structural model of the VEEV alphavirus, bridging the gap between incomplete crystal structures and lower resolution electron microscopy analyses

Effect of sources of sulphur on yield and disease incidence in crops in Jiangxi Province, China

The Jiangxi Academy of Agricultural Sciences (JAAS) has conducted five experiments to compare elemental S and sulphate S containing fertilizers. The elemental S containing fertilizer used was a sulphur enhanced diammonium phosphate (SEF12) and the sulphate S was supplied from single superphosphate (SSP). A diammonium phosphate (DAP) control was used. In a cabbage experiment conducted in 2003 there was a significant response to S and a lower incidence of soft rot where SEF12 was applied (18-19% reduction compared to DAP, c.f. 5% with SSP) and leaf disease (20-31% reduction, c.f. 19% with SSP) where elemental S was applied. In two rice experiments there was a greater response to SEF12 compared to SSP and this was associated with a lower incidence of disease and insects (rice leaf roller and brown plant hopper) where SEF12 was applied. Incidences of rice leaf blight and rice blast were also observed on the DAP and SSP treatments. Two plot trials with rapeseed were established in 2006 in which the fertilizers were applied either at rates to deliver the same rate of P as applied in DAP at Maying Shishan or with the same rate of S as applied in SSP at Maying Sequ. At the Maying Shishan site there was a significant response to S in SSP and SEF12 when applied at the same P application rate. At the Maying Sequ site SEF12 out yielded SSP when applied at the same S rate. These trials are the first to report soil applied elemental S having an effect on protecting crops against insects and disease and indicate that the mechanism involved requires further investigation in both upland and flooded crops

Global 500 m seamless dataset (2000–2022) of land surface reflectance generated from MODIS products

<jats:p>Abstract. The Moderate Resolution Imaging Spectroradiometer (MODIS) is widely utilized for retrieving land surface reflectance to reflect plant conditions, detect ecosystem phenology, monitor forest fires, and constrain terrestrial energy budgets. However, the state-of-the-art MODIS surface reflectance products suffer from temporal and spatial gaps due to atmospheric conditions (e.g. clouds and aerosols), limiting their use in ecological, agricultural, and environmental studies. Therefore, there is a need for reconstructing spatiotemporally seamless (i.e. gap-filled) surface reflectance data from MODIS products, which is difficult due to the intrinsic inconsistency of observations resulting from various sun/view geometry and the prolonged missing values resulting from polar night or heavy cloud coverage, especially in monsoon season. We built a framework for generating the global 500 m daily seamless data cubes (SDC500) based on MODIS surface reflectance dataset, which contains the generation of a land-cover-based a priori database, bidirectional reflectance distribution function (BRDF) correction, outlier detection, gap filling, and smoothing. The first global spatiotemporally seamless land surface reflectance at 500 m resolution was produced, covering the period from 2000 to 2022. Preliminary evaluation of the dataset at 12 sites worldwide with different land cover demonstrated its robust performance. The quantitative assessment shows that the SDC500 gap-filling results have a root-mean-square error (RMSE) of 0.0496 and a mean absolute error (MAE) of 0.0430. The SDC500 BRDF correction results showed an RMSE of 0.056 and a bias of −0.0085 when compared with MODIS nadir BRDF-adjusted reflectance (NBAR) products, indicating the acceptable accuracy of both products. From a temporal perspective, the SDC500 eliminates abnormal fluctuations while retaining the useful localized feature of rapid disturbances. From a spatial perspective, the SDC500 shows satisfactory spatial continuity. In conclusion, the SDC500 is a well-processed global daily surface reflectance product, which can serve as the fundamental input for large-scale ecological, agricultural, and environmental applications and quantitative remote sensing studies. The SDC500 is available at http://data.starcloud.pcl.ac.cn/resource/27 (Liang et al., 2023b) or https://doi.org/10.12436/SDC500.27.20230701 (Liang et al., 2023a). </jats:p&gt

Computational Model of Primary Visual Cortex Combining Visual Attention for Action Recognition

<div><p>Humans can easily understand other people’s actions through visual systems, while computers cannot. Therefore, a new bio-inspired computational model is proposed in this paper aiming for automatic action recognition. The model focuses on dynamic properties of neurons and neural networks in the primary visual cortex (V1), and simulates the procedure of information processing in V1, which consists of visual perception, visual attention and representation of human action. In our model, a family of the three-dimensional spatial-temporal correlative Gabor filters is used to model the dynamic properties of the classical receptive field of V1 simple cell tuned to different speeds and orientations in time for detection of spatiotemporal information from video sequences. Based on the inhibitory effect of stimuli outside the classical receptive field caused by lateral connections of spiking neuron networks in V1, we propose surround suppressive operator to further process spatiotemporal information. Visual attention model based on perceptual grouping is integrated into our model to filter and group different regions. Moreover, in order to represent the human action, we consider the characteristic of the neural code: mean motion map based on analysis of spike trains generated by spiking neurons. The experimental evaluation on some publicly available action datasets and comparison with the state-of-the-art approaches demonstrate the superior performance of the proposed model.</p></div

The architecture of the proposed model of visual primary cortex combining visual attention.

<p>It is consisted of four parts: visual perception, visual attention, feature extraction and action recognition. Spatiotemporal information is detected by modeling properties of classical and nonclassical receptive field of cells in V1; motion objects are detected with attention computational model by grouping spatiotemporal information; spike trains of spiking neurons produced by stimulus-driven leaky integrate-and-fire are analyzed to extract action features; the mean motion map as feature sets is constructed for action recognition with SVM classifier.</p

Histograms representing the average recognition rates obtained by our model with 2 conditions: (1) surround inhibition and (2) no surround inhibition on Weizmann and KTH datasets.

<p><i>A</i>. Weizmann, <i>B</i>. KTH(s1), <i>C</i>. KTH(s2), <i>D</i>. KTH(s3), <i>E</i>. KTH(s4)</p

Example of operation of the attention model with a video subsequence.

<p>From the first to final column: snapshots of origin sequences, surround suppression energy (with <i>v</i> = 0.5<i>ppF</i> and <i>θ</i> = 0°), perceptual grouping feature maps (with <i>v</i> = 0.5<i>ppF</i> and <i>θ</i> = 0°), saliency maps and binary masks of moving objects, and ground truth rectangles after localization of action objects.</p