Biocontrol of Large Patch Disease in Zoysiagrass (Zoysia japonica) by Bacillus subtilis SA-15: Identification of Active Compounds and Synergism with a Fungicide

Bacillus subtilis SA-15 is a plant growth-promoting bacterium isolated from non-farming soil. We aimed to identify lipopeptides produced by B. subtilis SA-15 and evaluate the control efficacy of B. subtilis SA-15 against large patch disease caused by Rhizoctonia solani AG 2-2 (IV) in zoysiagrass (Zoysia japonica). Bacillus subtilis SA-15 inhibited mycelial growth of R. solani AG 2-2 (IV) in vitro and produced fengycin A and dehydroxyfengycin A, which are antifungal compounds. Fengycin A and deghydroxyfengycin A inhibited R. solani mycelial growth by 30.4 and 63.2%, respectively. We formulated B. subtilis SA-15 into a wettable powder and determined its control efficiency against large patch in a field trial. The control efficacy was 51.2–92.0%. Moreover, when B. subtilis SA-15 powder was applied together with half the regular dose of the fungicide pecycuron, the control efficacy was 88.5–100.0%. These results indicate that B. subtilis SA-15 can be used to control soil-borne diseases, including large patch caused by R. solani, because of lipopeptide production. The use of this bacterium can also reduce the amount of fungicide needed, providing an eco-friendly management option for turfgrass.

WRITER IDENTIFICATION: THE EFFECT OF IMAGE RESIZING ON CNN PERFORMANCE

Introducing Deep Learning has been successful in improving the performance of automated writer identification systems. However, using very large patch sizes as input to CNN consumes a lot of machine resources and requires a lot of training time. To overcome this problem, many researchers use resized images.In this paper, we will try to make a comparative study between several patches sizes which were then resized to a normalized size of 32 × 32. Our aim is to elaborate the best recommendations for choosing the image resizing in order to increase the CNN performance. Thus, we will carry our tests on three databases. The first is CVL, a Latin dataset with 310 writers, the second is CERUG-CH a Chinese dataset with 105 writers and the last is KHATT that contains the Arabic writings of 1000 writers. To see if the type of CNN model impacts the results conducted on resized images, we deploy two models: ResNet-18 and MobileNet. The main finding is that the best results correspond to the resizing values of the images which makes it possible to have the average line height of the writings closer to the height of the CNN patches.

Earthworms Modulate Impacts of Soil Heterogeneity on Plant Growth at Different Spatial Scales

Soil heterogeneity (uneven distribution of soil nutrients and/or other properties) is ubiquitous in nature and can greatly affect plant growth. As earthworm activity can influence nutrient redistribution in the soil, we hypothesize that earthworms may alter the effect of soil heterogeneity on plant growth and this effect may depend on the scale of soil heterogeneity. To test these hypotheses, we grew the clonal grass Leymus chinensis in three soil treatments (heterogeneous large vs. heterogeneous small patch vs. homogeneous soil treatment) with or without earthworms [i.e., Eisenia fetida Savigny (Lumbricidae, epigeic redworm)]. In the heterogeneous treatments, the soil consisted of patches with and without 15N-labeled litter (referred to as high- and low-quality patches, respectively), and in the homogeneous treatment, the soil was an even mixture of the two types of soil patches. Biomass of L. chinensis was significantly higher in the high- than in the low-quality patches, showing the foraging response; this foraging response occurred at both scales and under both earthworm treatments. Compared to the homogeneous treatment, the heterogeneous large patch treatment increased biomass of L. chinensis without earthworms, but decreased it with earthworms. In contrast, biomass of L. chinensis in the heterogeneous small patch treatment did not differ from that in the homogeneous treatment, irrespective of earthworms. Belowground biomass was much greater in the heterogeneous small than in the heterogeneous large patch treatment without earthworms, but it did not differ between these two scale treatments with earthworms. In the heterogeneous treatments, soil 15N was greater in the high- than in the low-quality patches, but this effect became much weaker with than without earthworms, suggesting that earthworm activity homogenized the soil. We conclude that earthworms can change the impact of soil heterogeneity on plant growth via homogenizing the soil, and that this effect of earthworms varies with patch scale. Such scale-dependent interactive effects of soil heterogeneity and earthworms could be a potential mechanism modulating plant community structure and productivity.

Overexpression of the microtubule-binding protein CLIP-170 induces a +TIP network superstructure consistent with a biomolecular condensate

Proper regulation of microtubule (MT) dynamics is critical for cellular processes including cell division and intracellular transport. Plus-end tracking proteins (+TIPs) dynamically track growing MTs and play a key role in MT regulation. +TIPs participate in a complex web of intra- and inter- molecular interactions known as the +TIP network. Hypotheses addressing the purpose of +TIP:+TIP interactions include relieving +TIP autoinhibition and localizing MT regulators to growing MT ends. In addition, we have proposed that the web of +TIP:+TIP interactions has a physical purpose: creating a dynamic scaffold that constrains the structural fluctuations of the fragile MT tip and thus acts as a polymerization chaperone. Here we examine the possibility that this proposed scaffold is a biomolecular condensate (i.e., liquid droplet). Many animal +TIP network proteins are multivalent and have intrinsically disordered regions, features commonly found in biomolecular condensates. Moreover, previous studies have shown that overexpression of the +TIP CLIP-170 induces large “patch” structures containing CLIP-170 and other +TIPs; we hypothesized that these structures might be biomolecular condensates. To test this hypothesis, we used video microscopy, immunofluorescence staining, and Fluorescence Recovery After Photobleaching (FRAP). Our data show that the CLIP-170-induced patches have hallmarks indicative of a biomolecular condensate, one that contains +TIP proteins and excludes other known condensate markers. Moreover, bioinformatic studies demonstrate that the presence of intrinsically disordered regions is conserved in key +TIPs, implying that these regions are functionally significant. Together, these results indicate that the CLIP-170 induced patches in cells are phase-separated liquid condensates and raise the possibility that the endogenous +TIP network might form a liquid droplet at MT ends or other +TIP locations.

Patch size does not always indicate bird species diversity: case in peri-urban tropical habitat in Riau, Indonesia

Larger patches generally are inhabited by higher species richness, including birds, as predicted by the island biogeography theory. The objective of this research was to reveal the response of bird species richness in different patch sizes in peri-urban habitat. The study site area was five patches (2 large patches near human activities, remote large patch with a small lake, small patch, corridor patch) of disturbed secondary shrub-forest in Riau University, Sumatra. Birds were observed using the standard point-counts in early morning and late afternoon (8 points/patch, 3 replicates, total 40 observation-hour) in March-April 2021. Species richness (S), Shannon-Wiener diversity indices (H’), Chao species prediction, and Bray-Curtis similarity indices (B) were calculated. Total of 979 individual birds were observed, consisted of 68 species from 28 families with B ranged from 0.573 to 0.846. Large patch with lake in remote area had the highest species richness (S:39 species, Chao:54) and H’ (3.097). However, two large patches closed to human activities had the lowest number of species (S:27, Chao:30, H’:2.908, and S:23, Chao:32, H’:2.938, respectively), even lower than small patch (S:30, Chao:40, H’:2.925) or corridor patch (S:34; Chao:51, H’:2.724). Clearly human disturbance and micro-habitat diversity affect species richness in a local scale.

A vision transformer for emphysema classification using CT images

Objective: Emphysema is characterized by the destruction and permanent enlargement of the alveoli in the lung. According to visual CT appearance, emphysema can be divided into three subtypes: centrilobular emphysema (CLE), panlobular emphysema (PLE), and paraseptal emphysema (PSE). Automating emphysema classification can help precisely determine the patterns of lung destruction and provide a quantitative evaluation. Approach: We propose a vision transformer (ViT) model to classify the emphysema subtypes via CT images. First, large patches (61×61) are cropped from CT images which contain the area of normal lung parenchyma (NLP), CLE, PLE, and PSE. After resizing, the large patch is divided into small patches and these small patches are converted to a sequence of patch embeddings by flattening and linear embedding. A class embedding is concatenated to the patch embedding, and the positional embedding is added to the resulting embeddings described above. Then, the obtained embedding is fed into the transformer encoder blocks to generate the final representation. Finally, the learnable class embedding is fed to a softmax layer to classify the emphysema. Main results: To overcome the lack of massive data, the transformer encoder blocks (pre-trained on ImageNet) are transferred and fine-tuned in our ViT model. The average accuracy of the pre-trained ViT model achieves 95.95% in our lab’s own dataset which is higher than that of AlexNet, Inception-V3, MobileNet-V2, ResNet34, and ResNet50. Meanwhile, the pre-trained ViT model outperforms the ViT model without the pre-training. The accuracy of our pre-trained ViT model is higher than or comparable to that by available methods for the public dataset. Significance: The results demonstrated that the proposed ViT model can accurately classify the subtypes of emphysema using CT images. The ViT model can help make an effective computer-aided diagnosis of emphysema, and the ViT method can be extended to other medical applications.

Landscape configuration affects probability of apex predator presence and community structure in experimental metacommunities

Biodiversity is declining at an unprecedented rate, highlighting the urgent requirement for well-designed protected areas. Design tactics previously proposed to promote biodiversity include enhancing the number, connectivity, and heterogeneity of reserve patches. However, how the importance of these features changes depending on what the conservation objective is remains poorly understood. Here we use experimental landscapes containing ciliate protozoa to investigate how the number and heterogeneity in size of habitat patches, rates of dispersal between neighbouring patches, and mortality risk of dispersal across the nonhabitat ‘matrix’ interact to affect a number of diversity measures. We show that increasing the number of patches significantly increases γ diversity and reduces the overall number of extinctions, whilst landscapes with heterogeneous patch sizes have significantly higher γ diversity than those with homogeneous patch sizes. Furthermore, the responses of predators depended on their feeding specialism, with generalist predator presence being highest in a single large patch, whilst specialist predator presence was highest in several-small patches with matrix dispersal. Our evidence emphasises the importance of considering how top-down effects can drive community responses to patch configuration.

High-Gain Millimeter-Wave Patch Array Antenna for Unmanned Aerial Vehicle Application

A high-gain millimeter-wave patch array antenna is presented for unmanned aerial vehicles (UAVs). For the large-scale patch array antenna, microstrip lines and higher-mode surface wave radiations contribute enormously to the antenna loss, especially at the millimeter-wave band. Here, the element of a large patch array antenna is implemented with a substrate integrated waveguide (SIW) cavity-backed patch fed by the aperture-coupled feeding (ACF) structure. However, in this case, a large coupling aperture is used to create strongly bound waves, which maximizes the coupling level between the patch and the feedline. This approach helps to improve antenna gain, but at the same time leads to a significant level of back radiation due to the microstrip feedline and unwanted surface-wave radiation, especially for the large patch arrays. Using the SIW cavity-backed patch and stripline feedline of the ACF in the element design, therefore, provides a solution to this problem. Thus, a full-corporate feed 32 × 32 array antenna achieves realized gain of 30.71–32.8 dBi with radiation efficiency above 52% within the operational band of 25.43–26.91 GHz. The fabricated antenna also retains being lightweight, which is desirable for UAVs, because it has no metal plate at the backside to support the antenna.

Changes in Bacterial Community Structure and Enriched Functional Bacteria Associated With Turfgrass Monoculture

There is increasing attention being paid to utilizing microbial communities to improve plant health while reducing management inputs. Thus, the objectives of this research were to assess changes in the rhizosphere bacterial community structure associated with long-term turfgrass monoculture and to demonstrate the feasibility of using functional bacteria as beneficial biocontrol agents. Large patch disease, caused by the fungal pathogen Rhizoctonia solani AG2-2, is a significant threat to turfgrass cultivation. Rhizosphere samples were collected from 2-, 13- and 25-year turfgrass (Zoysia japonica) monocultures. The 13-year monoculture field had a higher pathogen population density than both the 2- and 25-year monoculture fields. Analyses of the rhizosphere bacterial communities revealed that Streptomyces was dominant in the 2-year field and Burkholderia was enriched in the 25-year field. Based on the culturable rhizosphere bacteria, Streptomyces neyagawaensis J6 and Burkholderia vietnamiensis J10 were obtained from the 2- and 25-year fields, respectively. Application of S. neyagawaensis J6 and B. vietnamiensis J10 led to excellent inhibition of large patch disease as well as enhanced tolerance against drought and temperature stresses. The results showed that the selected bacteria could be developed as biocontrol and abiotic stress tolerance agents for turfgrass cultivation.

Overexpression of the microtubule-binding protein CLIP-170 induces a +TIP network superstructure consistent with a biomolecular condensate

Proper regulation of microtubule (MT) dynamics is critical for cellular processes including cell division and intracellular transport. Plus-end tracking proteins (+TIPs) dynamically track growing MTs and play a key role in MT regulation. +TIPs participate in a complex web of intra- and inter-molecular interactions known as the +TIP network. Hypotheses addressing the purpose of +TIP:+TIP interactions include relieving +TIP autoinhibition and localizing MT regulators to growing MT ends. In addition, we have proposed that the web of +TIP:+TIP interactions has a physical purpose, creating a superstructure that constrains the structural fluctuations of the fragile MT tip and thus acts as a polymerization chaperone. Many animal +TIP network proteins are multivalent and have intrinsically disordered regions, features commonly found in biomolecular condensates. This observation suggests that the +TIP network might under some conditions form a biomolecular condensate. Previous studies have shown that overexpression of the +TIP CLIP-170 induces large “patch” structures containing CLIP-170 and other +TIPs. To test the hypothesis that these patches might be biomolecular condensates, we used video microscopy, immunofluorescence staining, and Fluorescence Recovery After Photobleaching (FRAP). Our data show that the CLIP-170-induced patches have hallmarks indicative of a biomolecular condensate, one that contains +TIP proteins and excludes other known condensate markers. Moreover, bioinformatic studies demonstrate that the presence of intrinsically disordered regions is conserved in key +TIPs, implying that these regions are functionally significant. Together, these results indicate that the CLIP-170 induced patches in cells are phase-separated liquid condensates and raise the possibility that the endogenous +TIP network might form a liquid droplet at MT ends or other +TIP locations.