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Recombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, whereas variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, although PRDM9 binding peaks are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favored loci, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity. We propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.

Biological regulatory systems, such as cell signaling networks, nervous systems and ecological webs, consist of complex dynamical interactions among many components. Network motif models focus on small sub-networks to provide quantitative insight into overall behavior. However, such models often overlook time delays either inherent to biological processes or associated with multi-step interactions. Here we systematically examine explicit-delay versions of the most common network motifs via delay differential equation (DDE) models, both analytically and numerically. We find many broadly applicable results, including parameter reduction versus canonical ordinary differential equation (ODE) models, analytical relations for converting between ODE and DDE models, criteria for when delays may be ignored, a complete phase space for autoregulation, universal behaviors of feedforward loops, a unified Hill-function logic framework, and conditions for oscillations and chaos. We conclude that explicit-delay modeling simplifies the phenomenology of many biological networks and may aid in discovering new functional motifs., Network motif models focus on small sub-networks in biological systems to quantitatively describe overall behavior but they often overlook time delays. Here, the authors systematically examine the most common network motifs via delay differential equations (DDE), often leading to more concise descriptions.

BackgroundRecombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, while variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, though PRDM9 binding sites are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity.ResultsWe apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strandbreak (DSB) and crossover formation at PRDM9 hotspots. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favoured hotspots, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity.ConclusionsWe propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.

Synthetic multicellular (MC) systems have the capacity to increase our understanding of biofilms and higher organisms, and to serve as engineering platforms for developing complex products in the areas of medicine, biosynthesis and smart materials. Here we provide an interdisciplinary perspective and review on emerging approaches to engineer and model MC systems. We lay out definitions for key terms in the field and identify toolboxes of standardized parts which can be combined into various MC algorithms to achieve specific outcomes. Many essential parts and algorithms have been demonstrated in some form. As key next milestones for the field, we foresee the improvement of these parts and their adaptation to more biological systems, the demonstration of more complex algorithms, the advancement of quantitative modeling approaches and compilers to support rational MC engineering, and implementation of MC engineering for practical applications.

Significance Bacteria live in surface-attached communities known as biofilms, where spatial structure is tightly linked to community function. We have developed a genetically encoded biofilm patterning tool (“Biofilm Lithography”) by engineering bacteria such that the expression of membrane adhesion proteins responsible for surface attachment is optically regulated. Accordingly, these bacteria only form biofilm on illuminated surface regions. With this tool, we are able to use blue light to pattern Escherichia coli biofilms with 25 μm spatial resolution. We present an accompanying biophysical model to understand the mechanism behind light-regulated biofilm formation and to provide insight on related natural biofilm processes. Overall, this biofilm patterning tool can be applied to study natural microbial communities as well as to engineer living biomaterials., Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However, our ability to control spatial structure in biofilms remains limited. Here we engineer Escherichia coli with a light-activated transcriptional promoter (pDawn) to optically regulate expression of an adhesin gene (Ag43). When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25 μm can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests that the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool—termed “Biofilm Lithography”—has distinct advantages over existing cell-depositing/patterning methods and provides the ability to grow structured biofilms, with applications toward an improved understanding of natural biofilm communities, as well as the engineering of living biomaterials and bottom–up approaches to microbial consortia design.

Wheat gluten hydrolysates (WGH) and KCl were used to examine their effects on fermentation performances and physiological characteristics of brewer's yeast during very high gravity (VHG) fermentation. Results showed that all supplementations exhibited a notable promotion in yeast growth, glucose utilization, ethanol production, and physiological characteristics. Combination supplementation of 0.3% WGH and 0.5% KCl showed the best promotion effect with 6.38%, 9.41% and 8.68% of increases in biomass, glucose utilization and ethanol production, respectively. Moreover, combination addition of WGH and KCl also enhanced significantly membrane integrity and mitochondrial functionality of brewer's yeast. Amino acid compositions of WGH and intracellular metabolites analysis indicated that active nitrogen metabolism and high levels of stress resistant substances might be responsible for the improvement of growth and fermentation performances in brewer's yeast by nutrient supplementation.

Spatial structure and patterning play an important role in bacterial biofilms. Here we demonstrate an accessible method for culturing E. coli biofilms into arbitrary spatial patterns at high spatial resolution. The technique uses a genetically encoded optogenetic construct-pDawn-Ag43-that couples biofilm formation in E. coli to optical stimulation by blue light. We detail the process for transforming E. coli with pDawn-Ag43, preparing the required optical set-up, and the protocol for culturing patterned biofilms using pDawn-Ag43 bacteria. Using this protocol, biofilms with a spatial resolution below 25 μm can be patterned on various surfaces and environments, including enclosed chambers, without requiring microfabrication, clean-room facilities, or surface pretreatment. The technique is convenient and appropriate for use in applications that investigate the effect of biofilm structure, providing tunable control over biofilm patterning. More broadly, it also has potential applications in biomaterials, education, and bio-art.

Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However our ability to control spatial structure in biofilms remains limited. Here we engineerEscherichia coliwith a light-activated transcriptional promoter to optically regulate adhesin gene expression. When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25μmcan be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending new evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool – termed ‘Biofilm Lithography’ – has distinct advantages over existing cell-depositing and patterning methods and provides the ability to grow structured biofilms, with applications towards an improved understanding natural biofilm communities, as well as the engineering of living biomaterials and bottom-up approaches to microbial consortia design.

Developmental biology is extraordinarily robust in its ability to self-organize exquisite spatio-temporal patterns despite an intrinsically noisy set of parts. Lateral inhibition is one mechanism commonly implicated in the formation of such precise emergent behavior. Models of lateral inhibition's patterning capabilities usually implicitly assume, however, that cells receive expression signals from their neighbors without delay. Here we explicitly investigate the effects of signaling delays as well as their relation to cis-interactions in lateral inhibition patterning. We find that rather than being a source of error, signaling delays counter-intuitively allow biology to ensure defect-free patterning, which together with cis-interactions can be both fast and robust to noise and parameter variation. This suggests that overlooking time delays in developmental signaling does not just ignore a potential source of error, but rather ignores a knob with which evolution may tune patterning robustness in general.

Interacting with biological systems via experiments is important for academia, industry, and education, but access barriers exist due to training, costs, safety, logistics, and spatial separation. High-throughput equipment combined with web streaming could enable interactive biology experiments online, but no such platform currently exists. We present a cloud experimentation architecture (paralleling cloud computation), which is optimized for a class of domain-specific equipments (biotic processing units - BPU) to share and execute many experiments in parallel remotely and interactively at all time. We implemented an instance of this architecture that enables chemotactic experiments with a slime mold Physarum Polycephelum. A user study in the blended teaching and research setting of a graduate-level biophysics class demonstrated that this platform lowers the access barrier for non-biologists, enables discovery, and facilitates learning analytics. This architecture is flexible for integration with various biological specimens and equipments to facilitate scalable interactive online education, collaborations, research, and citizen science.

Over the past decade, synthetic biology has developed increasingly robust gene networks within single bacterial cells, but relatively few systems have demonstrated engineered multicellular behaviour. In contrast, naturally existing terrestrial bacteria primarily live in complex surface-attached communities known as biofilms. Within these biofilms, multiple distinct microbial sub-populations form intricate spatial structures including colony co-localization and cell-cell co-aggregation. This spatial organization allows bacterial communities to achieve cooperative behaviours such as metabolic division-of-labour, and conversely, ecological interactions between different microbial subpopulations in turn influence the spatial patterning within the biofilm. Using optogenetic, metabolic, and cell-adhesion tools from synthetic biology, we are developing a biofilm culture platform that can generate optically patterned, metabolically interacting microbial communities. The platform will provide spatiotemporal control of both cell-surface and cell-cell attachment, tunable for both strength and specificity, as well as adjustable regulation of intercellular metabolic interactions. Taken together, these represent new tools to investigate how spatiotemporal patterning develops in biofilms and to engineer synthetic microbial consortia capable of complex tasks requiring biological division of labour.

Interacting with biological systems via experiments is important for academia, industry, and education, but access barriers exist due to training, costs, safety, logistics, and spatial separation. Automated high-throughput equipment combined with web streaming could enable interactive biology experiments online, but no such platform currently exists. Here we present a cloud experimentation architecture (paralleling cloud computation), that is optimized for a class of domainspecific equipment (biotic processing units) to share and execute many experiments in parallel by mapping synchronous equipment cycles to asynchronous user actions. We implemented an instance of this architecture that enables chemotactic stimulation experiments with the slime mold Physarum polycephelum. A user study in the blended teaching and research setting of a graduate-level biophysics class demonstrated that this platform lowers the access barrier for nonbiologists, enables discovery, and facilitates learning analytics. This architecture is flexible for integration with various biological specimens and equipments to facilitate scalable interactive online education, collaborations, conventional research, and citizen science.