Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust

Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.

What is the significance of the chloroform stabilizer C5H10 and its association with MeOH in concentration-dependent polymeric solutions?

The understanding of excitonic transitions associated with polymeric aggregates is fundamental, as such transitions have implications on coherence lengths, coherence numbers and inter- and intra-chain binding parameters. In this context, the investigation of efficient solvents and other ways to control polymer aggregate formation is key for their consolidation as materials for new technologies. In this manuscript, we use Poly(3-hexothiophene) (P3HT) as a probe to investigate the significance of amylene (C5H10) and its association with methanol (MeOH) in both pure and C5H10-stabilized chloroform (CHCl3)-based polymeric solutions. Using the intensity ratio between the first and second vibronic transitions of the P3HT H-aggregates formed, values for their exciton bandwidths and interchain interactions are obtained and correlated with the presence of C5H10 and MeOH as agents determining the CHCl3 quality.

Artificial humic acid regulates the impact of fungal community on soil macroaggregates formation

Artificial humic acid (A-HA), which is synthesized from agricultural wastes and has high similarity to a natural humic substance (HS) extracted from soil, has been proven by our group to have potential for biological carbon sequestration in black soils. However, the mechanism involves in the application of A-HA on soil aggregation processes resulting from microbial activity stimulation and modifications to microbial communities remains unclear. This study investigates the correlation between the formation and stability of soil aggregates and fungal communities with various amounts of A-HA added to the rhizosphere and non-rhizosphere soil. A-HA can increase the total organic carbon (TOC) and dissolved organic carbon (DOC) concentrations in soil, promoting macroaggregate formation and increasing the mean weight diameter (MWD). In addition, soil aggregate binding agents such as polysaccharides, protein, extracellular polymeric substances (EPS), and glomalin-related soil protein (GRSP) are significantly increased by the addition of A-HA. A-HA can drive microaggregate to assemble into macroaggregate by increasing the abundance of beneficial fungi (e.g., Trichoderma and Mortierella). The co-occurrence network supports that A-HA shifted the key species and increased interactions of fungal taxa. This study will lay a solid foundation for sustainable agricultural development of A-HA application for soil fertility restoration in the future.

Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host

Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.

In vivo Validation of Bimolecular Fluorescence Complementation (BiFC) to Investigate Aggregate Formation in Amyotrophic Lateral Sclerosis (ALS)

Amyotrophic lateral sclerosis (ALS) is a form of motor neuron disease (MND) that is characterized by the progressive loss of motor neurons within the spinal cord, brainstem, and motor cortex. Although ALS clinically manifests as a heterogeneous disease, with varying disease onset and survival, a unifying feature is the presence of ubiquitinated cytoplasmic protein inclusion aggregates containing TDP-43. However, the precise mechanisms linking protein inclusions and aggregation to neuronal loss are currently poorly understood. Bimolecular fluorescence complementation (BiFC) takes advantage of the association of fluorophore fragments (non-fluorescent on their own) that are attached to an aggregation-prone protein of interest. Interaction of the proteins of interest allows for the fluorescent reporter protein to fold into its native state and emit a fluorescent signal. Here, we combined the power of BiFC with the advantages of the zebrafish system to validate, optimize, and visualize the formation of ALS-linked aggregates in real time in a vertebrate model. We further provide in vivo validation of the selectivity of this technique and demonstrate reduced spontaneous self-assembly of the non-fluorescent fragments in vivo by introducing a fluorophore mutation. Additionally, we report preliminary findings on the dynamic aggregation of the ALS-linked hallmark proteins Fus and TDP-43 in their corresponding nuclear and cytoplasmic compartments using BiFC. Overall, our data demonstrates the suitability of this BiFC approach to study and characterize ALS-linked aggregate formation in vivo. Importantly, the same principle can be applied in the context of other neurodegenerative diseases and has therefore critical implications to advance our understanding of pathologies that underlie aberrant protein aggregation.

Gerstmann-Sträussler-Scheinker disease revisited: accumulation of covalently-linked multimers of internal prion protein fragments

Despite their phenotypic heterogeneity, most human prion diseases belong to two broadly defined groups: Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler-Scheinker disease (GSS). While the structural characteristics of the disease-related proteinase K-resistant prion protein (resPrPD) associated with the CJD group are fairly well established, many features of GSS-associated resPrPD are unclear. Electrophoretic profiles of resPrPD associated with GSS variants typically show 6-8 kDa bands corresponding to the internal PrP fragments as well as a variable number of higher molecular weight bands, the molecular nature of which has not been investigated. Here we have performed systematic studies of purified resPrPD species extracted from GSS cases with the A117V (GSSA117V) and F198S (GSSF198S) PrP gene mutations. The combined analysis based on epitope mapping, deglycosylation treatment and direct amino acid sequencing by mass spectrometry provided a conclusive evidence that high molecular weight resPrPD species seen in electrophoretic profiles represent covalently-linked multimers of the internal ~ 7 and ~ 8 kDa fragments. This finding reveals a mechanism of resPrPD aggregate formation that has not been previously established in prion diseases.

Effect of liquid flow by pipetting during medium change on deformation of hiPSC aggregates

Introduction

Maintaining the pluripotency and homogeneity of human induced pluripotent stem cells (hiPSCs) requires stable culture conditions with consistent medium change. In this study, we evaluated the performance of medium change by machine vs. medium change performed manually in terms of their impact on the aggregate shape of hiPSCs.

Methods

Aggregates of two hiPSC lines (1383D2 and Tic) were cultured, and the medium change was conducted either manually or with a machine. The populational homogeneity in aggregate shape was determined based on the projected aggregate area for size expansion as well as the circularity for spherical morphology.

Results

In the case of manually performed medium changes, the size of 1383D2 aggregates expanded homogeneously, maintaining its spherical morphology as culture duration increased, while spherical morphology was deformed in Tic aggregates, which had a heterogeneous population in terms of shape. In the case of medium change performed by a machine under a low flux of liquid flow, cultures of both aggregates showed homogeneous populations without deformation, although a high flux led to a heterogeneous population. The heterogeneous population observed in manually performed medium change was caused by the low stability of motion. In addition, time-lapse observation revealed that the Tic aggregates underwent tardive deformation with cellular protrusions from the aggregate surface after medium change with high flux. Histological analysis revealed a spatial heterogeneity of collagen type I inside 1383D2 aggregates, which had a shell structure with strong formation of collagen type I at the periphery of the aggregates, while Tic aggregates did not have a shell structure, suggesting that the shell structure prevented aggregate deformation.

Conclusion

Medium change by a machine led to a homogeneous population of aggregate shapes. Liquid flow caused tardive deformation of aggregates, but the shell structure of collagen type I in aggregates maintained its spherical shape.

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Mechanization of medium change leads to homogeneous shape of iPSC aggregates.

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Tardive change of aggregates was observed.

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Collagen type I distribution in aggregates induces shell structure formation.

Role of cell-secreted extracellular matrix formation in aggregate formation and stability of human induced pluripotent stem cells in suspension culture

Clinical and industrial applications require large quantities of human induced pluripotent stem cells (hiPSCs); however, little is known regarding the mechanisms governing aggregate formation and stability in suspension culture. To address this, we determined differences in growth processes among hiPSC lines in suspension culture. Using an hiPSC aggregate suspension culture system, hiPSCs from different lines formed multicellular aggregates classified as large compact or small loose based on their size and morphology. Time-lapse observation of the growth processes of two different hiPSC lines revealed that the balance between cell division and the extent of subsequent cell death determined the final size and morphology of aggregates. Comparison of the cell survival and death of two hiPSC lines showed that the formation of small, loose aggregates was due to continued cell death during the exponential phase of growth, with apoptotic cells extruded from growing hiPSC aggregates by the concerted contraction of their neighbors. Western blot and immunofluorescent staining revealed that aggregate morphology and proliferative ability relied to a considerable extent upon secretion of the extracellular matrix (ECM). hiPSCs forming large compact and stable aggregates showed enhanced production of collagen type I in suspension culture at 120 h. Furthermore, these aggregates exhibited higher expression of E-cadherin and proliferation marker Ki-67 as compared with levels observed in small and loose aggregates at 120 h. These findings indicated that differences in both aggregate formation and stability in suspension culture among hiPSC lines were caused by differences in ECM secretion capacity.

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil

Long-term nitrogen (N) fertilization affects soil aggregation and localizations of soil organic carbon (SOC), N and microbial parameters within aggregates. The mechanisms of these N effects are poorly understood. We studied these processes in a loamy soil from a 23-year repeated N addition field experiment under a rice-barley rotation. Nitrogen fertilization increased plant productivity and the portion of large macroaggregates (>2mm). However, SOC contents in macro- and micro-aggregates remained constant despite an N-induced increase of 27% in root C input into soil. Therefore, N fertilization accelerated SOC turnover. Nitrogen addition increased total N (TN) content in bulk soil and two macroaggregates (>2, and 1-2mm), but not in microaggregates (<0.25mm). Also, N fertilization increased the phospholipid fatty acids (PLFAs) contents of fungi in the large macroaggregates, but not in the microaggregates. In contrast, the effect of N addition on contents of bacterial and total microbial PLFAs was not apparent. Nitrogen fertilization increased N-acetyl-β-D-glucosaminidase (NAG) activities in the two larger macroaggregate size classes (>2, and 1-2mm), but not in the aggregates (<1mm). In both control and N fertilization, the large macroaggregates localized more TN, microbial PLFAs, and NAG activities than the microaggregates. In conclusion, long-term N fertilization not only directly promotes soil N resource but also indirectly improves soil structure by forming large macroaggregates, accelerates SOC turnover, and shiftes localization of microorganisms to the macroaggregates.

In Vivo Roles of a Patient-Derived Induced Pluripotent Stem Cell Line (HD72-iPSC) in the YAC128 Model of Huntington's Disease

Induced pluripotent stem cells (iPSCs) generated from somatic cells of patients can provide immense opportunities to model human diseases, which may lead to develop novel therapeutics. Huntington’s disease (HD) is a devastating neurodegenerative genetic disease, with no available therapeutic options at the moment. We recently reported the characteristics of a HD patient-derived iPSC carrying 72 CAG repeats (HD72-iPSC). In this study, we investigated the in vivo roles of HD72-iPSC in the YAC128 transgenic mice, a commonly used HD mouse model carrying 128 CAG repeats. To do this, we transplanted HD72-iPSC-derived neural precursors into the striatum of YAC128 mice bilaterally and observed a significant behavioral improvement in the grafted mice. Interestingly, the transplanted HD72-iPSC-derived neural precursors formed GABAeric neurons efficiently, but no EM48-positive protein aggregates were detected at 12 weeks after transplantation. Taken together, these results indicate no HD pathology was developed from the grafted cells, or no transmission of HD pathology from the host to the graft occurred at 12 weeks post-transplantation.