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  1. Abstract The supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages that have been recalcitrant to modern phylogenetics. Deep divergences, taxonomic placement of some key taxa and character evolution in the group largely remain poorly elucidated or controversial. We surveyed available Amoebozoa genomes and transcriptomes to mine conserved putative single copy genes, which were used to enrich gene sampling and generate the largest supermatrix in the group to date; encompassing 824 genes, including gene sequences not previously analyzed. We recovered a well-resolved and supported tree of Amoebozoa, revealing novel deep level relationships and resolving placement ofmore »enigmatic lineages congruent with morphological data. In our analysis the deepest branching group is Tubulinea. A recent proposed major clade Tevosa, uniting Evosea and Tubulinea, is not supported. Based on the new phylogenetic tree, paleoecological and paleontological data as well as data on the biology of presently living amoebozoans, we hypothesize that the evolution of Amoebozoa probably was driven by adaptive responses to a changing environment, where successful survival and predation resulted from a capacity to disrupt and graze on microbial mats-a dominant ecosystem of the mid-Proterozoic period of the Earth history.« less
    Free, publicly-accessible full text available December 1, 2023
  2. Abstract To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus , an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium ’s sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial numbermore »of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11 . We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.« less
    Free, publicly-accessible full text available December 1, 2023
  3. Abstract Filtering facepiece respirators (FFRs) provide effective protection against diseases spread through airborne infectious droplets and particles. The widespread use of FFRs during the COVID-19 pandemic has not only led to supply shortages, but the disposal of single-use facemasks also threatens the environment with a new kind of plastic pollution. While limited reuse of filtering facepiece respirators has been permitted as a crisis capacity strategy, there are currently no standard test methods available for decontamination before their repeated use. The decontamination of respirators can compromise the structural and functional integrity by reducing the filtration efficiency and breathability. Digital segmentation ofmore »X-ray microcomputed tomography (microCT) scans of the meltblown nonwoven layers of a specific N95 respirator model (Venus-4400) after treatment with one and five cycles of liquid hydrogen peroxide, ultraviolet radiation, moist heat, and aqueous soap solution enabled us to perform filtration simulations of decontaminated respirators. The computed filtration efficiencies for 0.3 µm particles agreed well with experimental measurements, and the distribution of particle penetration depths was correlated with the structural changes resulting from decontamination. The combination of X-ray microCT imaging with numerical simulations thus provides a strategy for quantitative evaluation of the effectiveness of decontamination treatments for a specific respirator model.« less
    Free, publicly-accessible full text available December 1, 2023
  4. Free, publicly-accessible full text available May 1, 2023
  5. With the recent emergence of highly transmissible variants of the novel coronavirus SARS-CoV-2, the demand for N95 respirators is expected to remain high. The extensive use of N95 respirators by the public is susceptible to demand‐supply gaps and raises concern about their disposal, threatening the environment with a new kind of plastic pollution. Herein, we investigated the filtration performance of the N95 respirator by specifically analyzing the structure in the key filtration layers of meltblown nonwoven after decontamination with one and five cycles of liquid hydrogen peroxide, ultraviolet radiation, moist heat, and aqueous soap solution treatments. With the aid ofmore »X-ray microcomputed tomography (microCT) analysis, the local structural heterogeneity of the meltblown nonwoven has been unfolded and subsequently correlated with their filtration performance at a face velocity that matched with speaking conditions (∼3.89 m/s). The filtration efficiency results of the N95 respirator remain unaltered after performing one cycle of treatment modalities (except autoclave).« less
    Free, publicly-accessible full text available April 10, 2023
  6. Abstract The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate themore »association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.« less
    Free, publicly-accessible full text available December 1, 2022
  7. Free, publicly-accessible full text available August 13, 2022
  8. Wetting and spreading of liquids on fibers occurs in many natural and artificial processes. Unlike on a planar substrate, a droplet attached to one or more fibers can assume several different shapes depending on geometrical parameters such as liquid volume and fiber size and distance. This paper presents lattice Boltzmann simulations of the morphology of liquid droplets on two parallel cylindrical fibers. We investigate the final shapes resulting from spreading of an initially spherical droplet deposited on the fibers and from retraction of an initial liquid column deposited between the fibers. We observe three possible equilibrium configurations: barrel-shaped droplet, dropletmore »bridges, and liquid columns. We determine the complete morphology diagram for varying inter-fiber spacing and liquid volume and find a region of bistability that spans both the column regime and the droplet regime. We further present a simulation protocol that allows to probe the hysteresis of transitions between different shapes. The results provide insights into energies and forces associated with shape transformations of droplets on fibers that can be used to develop fiber-based materials and microfluidic systems for manipulation of liquids at small scale.« less
  9. Biopolymer composites based on silk fibroin have shown widespread potential due to their brilliant applications in tissue engineering, medicine and bioelectronics. In our present work, biocomposite nanofilms with different special topologies were obtained through blending silk fibroin with crystallizable poly(L-lactic acid) (PLLA) at various mixture rates using a stirring-reflux condensation blending method. The microstructure, phase components, and miscibility of the blended films were studied through thermal analysis in combination with Fourier-transform infrared spectroscopy and Raman analysis. X-ray diffraction and scanning electron microscope were also used for advanced structural analysis. Furthermore, their conformation transition, interaction mechanism, and thermal stability were alsomore »discussed. The results showed that the hydrogen bonds and hydrophobic interactions existed between silk fibroin (SF) and PLLA polymer chains in the blended films. The secondary structures of silk fibroin and phase components of PLLA in composites vary at different ratios of silk to PLLA. The β-sheet content increased with the increase of the silk fibroin content, while the glass transition temperature was raised mainly due to the rigid amorphous phase presence in the blended system. This results in an increase in thermal stability in blended films compared to the pure silk fibroin films. This study provided detailed insights into the influence of synthetic polymer phases (crystalline, rigid amorphous, and mobile amorphous) on protein secondary structures through blending, which has direct applications on the design and fabrication of novel protein–synthetic polymer composites for the biomedical and green chemistry fields.« less