A Genetic Strategy for Probing the Functional Diversity of Magnetosome Formation

Model genetic systems are invaluable, but limit us to understanding only a few organisms in detail, missing the variations in biological processes that are performed by related organisms. One such diverse process is the formation of magnetosome organelles by magnetotactic bacteria. Studies of model magnetotactic α-proteobacteria have demonstrated that magnetosomes are cubo-octahedral magnetite crystals that are synthesized within pre-existing membrane compartments derived from the inner membrane and orchestrated by a specific set of genes encoded within a genomic island. However, this model cannot explain all magnetosome formation, which is phenotypically and genetically diverse. For example, Desulfovibrio magneticus RS-1, a δ-proteobacterium for which we lack genetic tools, produces tooth-shaped magnetite crystals that may or may not be encased by a membrane with a magnetosome gene island that diverges significantly from those of the α-proteobacteria. To probe the functional diversity of magnetosome formation, we used modern sequencing technology to identify hits in RS-1 mutated with UV or chemical mutagens. We isolated and characterized mutant alleles of 10 magnetosome genes in RS-1, 7 of which are not found in the α-proteobacterial models. These findings have implications for our understanding of magnetosome formation in general and demonstrate the feasibility of applying a modern genetic approach to an organism for which classic genetic tools are not available

Mikrokosmos

This music score was submitted for the Kaleidoscope 2020 Call for Scores, an open access collaboration with the UCLA Music Library

Chang'an

This music score was submitted for the Kaleidoscope 2020 Call for Scores, an open access collaboration with the UCLA Music Library

Genetic Adaptation of Two Enteric Bacteria to Shifting Environmental Landscapes

All organisms require the ability to respond appropriately to changes in their environment. Inhabiting diverse environments from dry deserts to deep-sea hydrothermal vents with only membrane layers separating their cytoplasm from the external world, bacteria are constantly interacting with their environment and being challenged by them to evolve. They adapt exceptionally quickly to these transitions via complex genetic, transcriptional, and post-transcriptional mechanisms (4–16). Studying the regulated and stochastic responses of bacteria to environmental pressures is significant to the advancement of our understanding of biological adaptation as well as the improvement of therapeutics for human health. In this dissertation, I discuss how two enteric model organisms adapt genetically to host-associated selective pressures and how the findings of these studies provide fundamental insights into microbial adaptation that can be used to improve clinical therapies for humans

A novel observation points‐based positive‐unlabeled learning algorithm

Abstract In this study, an observation points‐based positive‐unlabeled learning algorithm (hence called OP‐PUL) is proposed to deal with positive‐unlabeled learning (PUL) tasks by judiciously assigning highly credible labels to unlabeled samples. The proposed OP‐PUL algorithm has three components. First, an observation point classifier ensemble (OPCE) algorithm is constructed to divide unlabeled samples into two categories, which are temporary positive and permanent negative samples. Second, a temporary OPC (TOPC) is trained based on the combination of original positive samples and permanent negative samples and then the permanent positive samples that are correctly classified with TOPC are retained from the temporary positive samples. Third, a permanent OPC (POPC) is finally trained based on the combination of original positive samples, permanent positive samples and permanent negative samples. An exhaustive experimental evaluation is conducted to validate the feasibility, rationality and effectiveness of the OP‐PUL algorithm, using 30 benchmark PU data sets. Results show that (1) the OP‐PUL algorithm is stable and robust as unlabeled samples and positive samples are increased in unlabeled data sets and (2) the permanent positive samples have a consistent probability distribution with the original positive samples. Moreover, a statistical analysis reveals that POPC in the OP‐PUL algorithm can yield better PUL performances on the 30 data sets in comparison with four well‐known PUL algorithms. This demonstrates that OP‐PUL is a viable algorithm to deal with PUL tasks

Wnt/β-catenin pathway regulates cementogenic differentiation of adipose tissue-deprived stem cells in dental follicle cell-conditioned medium.

The formation and attachment of new cementum is crucial for periodontium regeneration. Tissue engineering is currently explored to achieve complete, reliable and reproducible regeneration of the periodontium. The capacity of multipotency and self-renewal makes adipose tissue-deprived stem cells (ADSCs) an excellent cell source for tissue regeneration and repair. After rat ADSCs were cultured in dental follicle cell-conditioned medium (DFC-CM) supplemented with DKK-1, an inhibitor of the Wnt pathway, followed by 7 days of induction, they exhibited several phenotypic characteristics of cementoblast lineages, as indicated by upregulated expression levels of CAP, ALP, BSP and OPN mRNA, and accelerated expression of BSP and CAP proteins. The Wnt/β-catenin signaling pathway controls differentiation of stem cells by regulating the expression of target genes. Cementoblasts share phenotypical features with osteoblasts. In this study, we demonstrated that culturing ADSCs in DFC-CM supplemented with DKK-1 results in inhibition of β-catenin nuclear translocation and down-regulates TCF-4 and LEF-1 mRNA expression levels. We also found that DKK-1 could promote cementogenic differentiation of ADSCs, which was evident by the up-regulation of CAP, ALP, BSP and OPN gene expressions. On the other hand, culturing ADSCs in DFC-CM supplemented with 100 ng/mL Wnt3a, which activates the Wnt/β-catenin pathway, abrogated this effect. Taken together, our study indicates that the Wnt/β-catenin signaling pathway plays an important role in regulating cementogenic differentiation of ADSCs cultured in DFC-CM. These results raise the possibility of using ADSCs for periodontal regeneration by modifying the Wnt/β-catenin pathway

Tailoring grain boundary stability of zinc-titanium alloy for long-lasting aqueous zinc batteries

Abstract The detrimental parasitic reactions and uncontrolled deposition behavior derived from inherently unstable interface have largely impeded the practical application of aqueous zinc batteries. So far, tremendous efforts have been devoted to tailoring interfaces, while stabilization of grain boundaries has received less attention. Here, we demonstrate that preferential distribution of intermetallic compounds at grain boundaries via an alloying strategy can substantially suppress intergranular corrosion. In-depth morphology analysis reveals their thermodynamic stability, ensuring sustainable potency. Furthermore, the hybrid nucleation and growth mode resulting from reduced Gibbs free energy contributes to the spatially uniform distribution of Zn nuclei, promoting the dense Zn deposition. These integrated merits enable a high Zn reversibility of 99.85% for over 4000 cycles, steady charge-discharge at 10 mA cm−2, and impressive cyclability for roughly 3500 cycles in Zn-Ti//NH4V4O10 full cell. Notably, the multi-layer pouch cell of 34 mAh maintains stable cycling for 500 cycles. This work highlights a fundamental understanding of microstructure and motivates the precise tuning of grain boundary characteristics to achieve highly reversible Zn anodes

DFC-CM condition effect Wnt/β-catenin signaling pathway in ADSCs.

<p>(<b>A</b>) Immunocytochemical staining showed that ADSCs cultured in basic medium or in DFC-CM condition expressed β-catenin. Scale bar represents 100 µm. (<b>B</b>) Beta-Catenin levels were examined by Western blot analysis and scanning densitometer. Beta-actin was used as internal control. (<b>C</b>). LEF-1and TCF-4 mRNA were subjected to real time-PCR analysis after cells were cultured in DFC-CM or basal medium (control) for 7 days. The expression levels were normalized to those of β-actin. The results represent mean values (SD) from three independent experiments performed in triplicates. *<i>P</i><0.05 vs. the control group.</p

Isolation and identification of ADSCs.

<p>(<b>A</b>) Representative images of colonies formed by ADSCs at low seeding density after 2 weeks in culture. (<b>B</b>). Flow cytometry analysis of the expression of cell surface markers related to mesenchymal (CD31, CD90, CD105, CD146 and STRO-1) or hematopoietic stem cells (CD34 and CD45). Cont: isotype control. (<b>C</b>) After ADSCs were cultured under osteogenic inductive conditions for 21 days, mineralized nodules were detected following alizarin red staining. ADSCs formed lipid clusters that stained positive for Oil Red O after 21 days of adipogenic induction. Scale bars represent 100 µm.</p

Regulation of cementogenic differentiation of ADSCs by Wnt/β-catenin signaling pathway.

<p>(<b>A</b>) Immunostaining of BSP and CAP in ADSCs cultured in basal medium or DFC-CM with or without Wnt3a (100 ng/mL)/DKK-1 (100 ng/mL) treatment for 7 d. Scale bar represents 100 µm. (<b>B–E</b>) Expression of CAP (<b>B</b>), ALP (<b>C</b>), BSP (<b>D</b>), and OPN (<b>E</b>) genes in ADSCs cultured in basal medium or in DFC-CM with Wnt3a (100 ng/mL)/DKK-1 (100 ng/mL) for 7 d. PBS was used as control condition. The expression levels were normalized to that of β-actin. The results represent mean values (SD) from three independent experiments performed in triplicates. *<i>P</i><0.05 vs. the PBS group.</p