Biology subjects

Tang, J. X.

Publications and source records attributed to Tang, J. X..

6 recordsLinked to original sources

bioRxiv2024

Integrated Isoform-Resolved Transcriptomic Analysis of Gossypium barbadense and Gossypium hirsutum Fibers

A comprehensive understanding of RNA expression and splicing during cotton fiber development plays a crucial role in explaining the differences in fiber quality between two different cotton species. To date, most cotton transcriptomic studies have utilized short-read sequencing data, which limits the ability to capture full-length mRNAs. In this study, we compiled long-read RNA sequencing data from the PacBio platform, as well as short-read RNA sequencing data from 10 fiber developmental stages, for both Gossypium barbadense and Gossypium hirsutum. We identified 183,767 and 178,994 isoforms in Gossypium barbadense and Gossypium hirsutum, respectively, generating the most comprehensive transcriptomic atlas of cotton to date. Alternative splicing events exhibited stage-specific variations during fiber development, and co-expression network analysis, combined with LASSO regression, identified isoforms highly correlated with each developmental stage. These findings reveal previously uncharacterized aspects of isoform regulation during fiber development and provide valuable resources for further research into the molecular mechanisms underlying fiber quality differences between cotton species.

bioinformatics↗

bioRxiv2023

Enterobacter Sp. SM3 Exhibits Run-and-Tumble Motility

The recent discovery of the peritrichous, swarm-competent bacterium Enterobacter sp. SM3 has offered a new opportunity to elucidate the role of swarming motility in the gut microbiome. Here we present first findings of the run-and-tumble behavior of SM3 in both a control solution of motility buffer and upon bulk exposure to the chemoattractants serine and aspartate, drawing a comparison with the well-studied behavior of E. coli. It was found that SM3 runs with an average speed of approximately 30 {micro}m/s for an average duration of 0.77 s. Tumble events occur for an average duration of 0.11 s with a 69{whitebullet} average tumble angle. Both values are similar to that of E. coli. When exposed to serine, SM3 suppresses the frequency of tumble events, which in turn increases the average run duration. In addition, the average tumble angle was found to decrease in response to serine. However, when exposed to up to a millimolar concentration of aspartate, SM3 does not demonstrate a notable change in run-and-tumble parameters. These results suggest that run-and-tumble is the characteristic swimming behavior of SM3 in its planktonic state. These findings serve as a benchmark in a quest to determine the connection among swimming, swarming, and the complex dynamics of the gut microbiome. IMPORTANCEBacteria form the largest domain of living creatures on this planet. Our interactions with bacteria influence us in many ways, not the least of which being in regards to human health. A recently identified species of gut bacteria, Enterobacter sp. SM3, has been shown to reduce intestinal inflammation, suggesting that swarming could play a physiologically beneficial role. In this report, we study the motility of individual SM3 bacteria This study is an essential step towards an overarching goal to understand the influence of bacterial motility on human health.

microbiology↗

bioRxiv2020

Confinement Discerns Swarmers from Planktonic Bacteria

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper flagellation have been shown to accompany the swarming phenotype. However, less noticeable, are the contrasts of collective motion between the swarming cells and the planktonic cells of comparable cell density. Here, we show that confining bacterial movement in designed dimensions allows distinguishing bacterial swarming from collective swimming. We found that on a soft agar plate, a novel bacterial strain Enterobacter sp. SM3 exhibited different motion patterns in swarming and planktonic states when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 m and 90 m, swarming SM3 formed a single swirl motion pattern in the microwells whereas planktonic SM3 showed multiple swirls. Similar differential behavior is observed across a range of randomly selected gram-negative bacteria. We hypothesize that the "rafting behavior" of the swarming bacteria upon dilution might account for the motion pattern difference. We verified our conjectures via numerical simulations where swarming cells are modeled with lower repulsion and more substantial alignment force. The novel technical approach enabled us to observe swarming on a non-agar tissue surface for the first time. Our work provides the basis for characterizing bacterial swarming under more sophisticated environments, such as polymicrobial swarmer detection, and in vivo swarming exploration.

biophysics↗

bioRxiv2020

An expanding bacterial colony forms a depletion zone with growing droplets

Many species of bacteria have developed means to spread on solid surfaces. This study focuses on the expansion of Pseudomonas aeruginosa on an agar gel surface. We report the occurrence and spread of a depletion zone, where the layer of bacteria on the agar becoming thinner. The depletion zone occurs within an expanded colony under conditions of minimal water evaporation. It is colocalized with a higher concentration of rhamnolipids, the biosurfactants that are produced by the bacteria and accumulate in the older region of the colony. With continued growth in bacterial population, dense droplets occur and coalesce in the depletion zone, displaying remarkable fluid dynamic behavior. Whereas expansion of a central depletion zone requires activities of live bacteria, new zones can be seeded by adding rhamnolipids. These depletion zones due to the added surfactants expand quickly, even on plates covered by bacteria that have been killed by ultraviolet light. We propose a model to account for the observed properties, taking into consideration bacterial growth and secretion, osmotic swelling, fluid volume expansion, cell-cell interaction, and interfacial fluid dynamics involving Marangoni flow. SignificanceBacterial growth and pattern formation have strong bearing on their biological functions, such as their spread and accumulation, biofilm growth & its effects on infection and antibiotic resistance. The bacterial species of this study, Pseudomonas aeruginosa, is a human pathogen responsible for frequent infections in wounds, airways, and urinary tract, particularly when involving the use of catheters. The findings of this study and the mechanisms we propose offer new insights on the important behaviors of bacterial collective motility, pattern dynamics, and biofilm growth.

biophysics↗

bioRxiv2020

Assessment of a weak mode of bacterial adhesion by applying an electric field

Microbial attachment to surfaces is ubiquitous in nature. Most species of bacteria attach and adhere to surfaces via special appendages such as pili and fimbriae, the roles of which have been extensively studied. Here we report an experiment on pilus-less mutants of Caulobacter crescentus weakly attached to a plastic surface and subjected to an electric field parallel to the surface. We find that some individual cells transiently but repeatedly adhere to the surface in a stick-slip fashion in the presence of an electric field. Even while transiently detached, these bacteria move significantly slower than the unattached ones in the same field of view undergoing electrophoretic motion. We refer this behavior of repeated and transient attachment as "quasi-attachment". The speed of the quasi-attached bacteria exhibits large variations, frequently dropping close to zero for short intervals of time. This study suggests applying electric field as a useful method to investigate bacteria-surface interaction, which is significant in broader contexts such as infection and environmental control. SignificanceInteraction between bacteria and surfaces occur widely in nature, including those in industrial, environmental, and medical settings. It is therefore important to understand various mechanisms and factors that affect numerous forms of bacterium-surface interaction, particularly those resulting in adhesion or attachment, be they strong or weak, permanent or transient. This work takes a unique approach to identify a transient and reversible mode of bacterial attachment to a solid surface, by applying an electric field to exert a force for detachment. The force thus exerted proves to reach the amplitude required to detach bacteria of a pilus-less strain that weakly attach to a plastic surface. The method may be applied broadly to investigate bacteria-surface interaction.

microbiology↗

bioRxiv2019

Bacterial Hyperswarming as a Protective Response to Intestinal Stress

Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. Here, we report for the first time that bacterial swarmers are associated with protection against intestinal inflammation. We show that bacterial swarmers are highly predictive of intestinal stress in mice and humans. We isolated a novel Enterobacter swarming strain, SM3, from mouse feces. SM3 and other known commensal swarmers contrast to their respective swarming-deficient, but swimming-competent isogenic strains abrogated intestinal inflammation in mice. Treatment of colitic mice with SM3, but not its mutants, enriched beneficial fecal anaerobes belonging to the family, Bacteroidales S24-7. We observed SM3 swarming associated pathways in the in vivo fecal metatranscriptomes. In vitro growth of S24-7 was enriched in presence of SM3 or its mutants conjecturing that bacterial swarming in vivo might influence SM3s access to S24-7 in the intestines. Overall, our work identifies a new paradigm in which intestinal stress allows for the emergence of swarming bacteria, which can counterintuitively heal intestinal inflammation.

microbiology↗