Microscale methods to investigate and manipulate multispecies biological systems

The continuing threats from viral infectious diseases highlight the need for new tools to study viral interactions with host cells. Understanding how these viruses interact and respond to their environment can help predict outbreaks, shed insight on the most likely strains to emerge, and determine which viruses have the potential to cause significant human illness. Animal studies provide a wealth of information, but the interpretation of results is confounded by the large number of uncontrolled or unknown variables in complex living systems. In contrast, traditional tissue culture approaches have provided investigators a valuable platform with a high degree of experimental control and flexibility, but the static nature of flask-based cell culture makes it difficult to study viral evolution. Serial passaging introduces un-physiological perturbations to cell and virus populations by drastically reducing the number of species with each passage. Low copy, high fitness viral variants maybe eliminated, while in vivo these variants would be essential in determining the virus’ evolutionary fate. Bridging technologies are urgently needed to mitigate the unrealistic dynamics in static flask-based cultures, and the complexity and expense of in vivo experiments. This thesis details the development of a continuous perfusion platform capable of more closely mimicking in vivo cell-virus dynamics, while surpassing the experimental control and flexibility of standard cell culture. First, a microfluidic flow through acoustic device is optimized to enable efficient and controllable separation of cells and viruses. Repeatable isolation of cell and virus species is demonstrated with both a well-characterized virus, Dengue Virus (DENV), and the novel Golden Gate Virus. Next, a platform is built around this device to enable controllable, automated, continuous cell culture. Beads are used to assess system performance and optimize operation. Subsequently, the platform is used to culture both murine hybridoma (4G2) and human monocyte (THP-1) cell lines for over one month, and demonstrate the ability to manipulate population dynamics. Finally, we use the platform to establish a multispecies culture with THP-1 cells and Sindbis Virus (SINV). This work integrates distinct engineering feats to create a platform capable of enhancing existing cell virus studies and opening the door to a variety of high-impact investigations

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice.

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15-1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing

Deletion of the Basement Membrane Heparan Sulfate Proteoglycan Type XVIII Collagen Causes Hypertriglyceridemia in Mice and Humans

Background: Lipoprotein lipase (Lpl) acts on triglyceride-rich lipoproteins in the peripheral circulation, liberating free fatty acids for energy metabolism or storage. This essential enzyme is synthesized in parenchymal cells of adipose tissue, heart, and skeletal muscle and migrates to the luminal side of the vascular endothelium where it acts upon circulating lipoproteins. Prior studies suggested that Lpl is immobilized by way of heparan sulfate proteoglycans on the endothelium, but genetically altering endothelial cell heparan sulfate had no effect on Lpl localization or lipolysis. The objective of this study was to determine if extracellular matrix proteoglycans affect Lpl distribution and triglyceride metabolism. Methods and Findings: We examined mutant mice defective in collagen XVIII (Col18), a heparan sulfate proteoglycan present in vascular basement membranes. Loss of Col18 reduces plasma levels of Lpl enzyme and activity, which results in mild fasting hypertriglyceridemia and diet-induced hyperchylomicronemia. Humans with Knobloch Syndrome caused by a null mutation in the vascular form of Col18 also present lower than normal plasma Lpl mass and activity and exhibit fasting hypertriglyceridemia. Conclusions: This is the first report demonstrating that Lpl presentation on the lumenal side of the endothelium depends on a basement membrane proteoglycan and demonstrates a previously unrecognized phenotype in patients lacking Col18.National Institute of Health (NIH)[HL087228]National Institute of Health (NIH)[GM33063]National Institute of Health (NIH)[HL67255]CEPID/FAPESPCNPqUniversity of Colorado Denver Department of MedicineLeducq FoundationAmerican Heart Association[0735038N

Object-Space Optimization of Tomographic Reconstructions for Additive Manufacturing

Volumetric 3D printing motivated by computed axial lithography enables rapid printing of homogeneous parts but requires a high dimensionality gradient-descent optimization to calculate image sets. Here we introduce a new, simpler approach to image-computation that algebraically optimizes a model of the printed object, significantly improving print accuracy of complex parts under imperfect material and optical precision by improving optical dose contrast between the target and surrounding regions. Quality metrics for volumetric printing are defined and shown to be significantly improved by the new algorithm. The approach is extended beyond binary printing to grayscale control of conversion to enable functionally graded materials. The flexibility of the technique is digitally demonstrated with realistic projector point spread functions, printing around occluding structures, printing with restricted angular range, and incorporation of materials chemistry such as inhibition. Finally, simulations show that the method facilitates new printing modalities such as printing into flat, rather than cylindrical packages to extend the applications of volumetric printing. &nbsp;</p

Bone Marrow Mononuclear Cells Up-Regulate Toll-Like Receptor Expression and Produce Inflammatory Mediators in Response to Cigarette Smoke Extract

Several reports link cigarette smoking with leukemia. However, the effects of cigarette smoke extract (CSE) on bone marrow hematopoiesis remain unknown. The objective of this study was to elucidate the direct effects of cigarette smoke on human bone marrow hematopoiesis and characterize the inflammatory process known to result from cigarette smoking. Bone marrow mononuclear cells (BMCs) from healthy individuals when exposed to CSE had significantly diminished CFU-E, BFU-E and CFU-GM. We found increased nuclear translocation of the NF-κB p65 subunit and, independently, enhanced activation of AKT and ERK1/2. Exposure of BMCs to CSE induced IL-8 and TGF-β1 production, which was dependent on NF-κB and ERK1/2, but not on AKT. CSE treatment had no effect on the release of TNF-α, IL-10, or VEGF. Finally, CSE also had a significant induction of TLR2, TLR3 and TLR4, out of which, the up-regulation of TLR2 and TLR3 was found to be dependent on ERK1/2 and NF-κB activation, but not AKT. These results indicate that CSE profoundly inhibits the growth of erythroid and granulocyte-macrophage progenitors in the bone marrow. Further, CSE modulates NF-κB- and ERK1/2-dependent responses, suggesting that cigarette smoking may impair bone marrow hematopoiesis in vivo as well as induce inflammation, two processes that proceed malignant transformation

An Indo-Pacifc coral spawning database

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change

Genetic Enablers Underlying the Clustered Evolutionary Origins of C-4 Photosynthesis in Angiosperms

The evolutionary accessibility of novel adaptations varies among lineages, depending in part on the genetic elements present in each group. However, the factors determining the evolutionary potential of closely related genes remain largely unknown. In plants, CO2-concentrating mechanisms such as C4 and crassulacean acid metabolism (CAM) photosynthesis have evolved numerous times in distantly related groups of species, and constitute excellent systems to study constraints and enablers of evolution. It has been previously shown for multiple proteins that grasses preferentially co-opted the same gene lineage for C4 photosynthesis, when multiple copies were present. In this work, we use comparative transcriptomics to show that this bias also exists within Caryophyllales, a distantly related group with multiple C4 origins. However, the bias is not the same as in grasses and, when all angiosperms are considered jointly, the number of distinct gene lineages co-opted is not smaller than that expected by chance. These results show that most gene lineages present in the common ancestor of monocots and eudicots produced gene descendants that were recruited into C4 photosynthesis, but that C4-suitability changed during the diversification of angiosperms. When selective pressures drove C4 evolution, some copies were preferentially co-opted, probably because they already possessed C4-like expression patterns. However, the identity of these C4-suitable genes varies among clades of angiosperms, and C4 phenotypes in distant angiosperm groups thus represent genuinely independent realizations, based on different genetic precursors