Preferential Switching Research Articles

Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro.

The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding to blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput optogenetics platform, and machine learning tools to enable multiplexed control over blue light-sensitive optogenetic systems. Specifically, we identify light induction conditions for sequential activation as well as preferential activation and switching between pairs of light-sensitive split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use the high-throughput data generated from Lustro to build a Bayesian optimization framework that incorporates data-driven learning, uncertainty quantification, and experimental design to enable the prediction of system behavior and the identification of optimal conditions for multiplexed control. This work lays the foundation for designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled using designer light induction programs, with broad implications for biotechnology and bioengineering.

Assessing Loss of Regulatory Divergence, Genome-Transcriptome Incongruence, and Preferential Expression Switching in Abaca × Banana Backcrosses.

The Musa textilis var. Abuab has high fiber quality (FQ) but is susceptible to abaca bunchy top virus (AbBTV); the Musa balbisiana var. Pacol has low FQ but is resistant against AbBTV. Their backcrosses (BC2 and BC3) possess both desirable traits. Analysis using RNA-seq showed that the regulatory divergence of Abuab and Pacol is largely explained by cis differences with 27.4% and 22.3% if we are to assess it using BC2 and BC3, respectively. Cis differences between the two genotypes are significantly reduced from BC2 to BC3 due to changes in genomic constitution. Trans, on the other hand, is robust to changes in allelic composition. All these are attributed to the loss of heterozygosity in BC3 relative to BC2. Further analysis showed that both backcrosses exhibited genome-wide preferential expression of Pacol- over Abuab-specific alleles, despite the wider genetic presence of the latter in the hybrids. The ratio of the two genotype-specific expressed transcripts and the ratio of their corresponding genetic make-up are significantly disproportionate, a phenomenon that we refer to here as “genome–transcriptome incongruence”. We also observed preferential expression switching in which several genes prefer the Abuab- (or Pacol-) specific allele in BC2 but switched to the Pacol- (or Abuab-) specific allele in the BC3 genome.

Dynamics of a predator-prey model with Beddington-DeAngelis functional response, omnivory and predator switching

In this paper, a predator-prey model has been developed by considering Beddington-DeAngelis functional response among the interaction of three species prey, middle predator and top predator. It is assumed that middle predator consumes only prey, but top predator consumes prey as well as middle predator. The concept of omnivory has been introduced in this model. Also, it is assumed that due to omnivory property, the top predator has a chance to prefer the food (prey) to consume. Here two types of predator switching behavior such as preferential switching and density dependent switching have been introduced. Different possible equilibrium points are evaluated and the stability of the system has been investigated around these points. Theoretical analysis of for the existence condition of Hopf bifurcation of the system has been studied with respect to $w_4$. It is found that the increase of death rate of middle and top predator may be responsible for the extinction of both the species or that particular species. It is observed that omnivory may lead the system towards stability. It is also observed that the predator switching behaviour may strengthen the stability and persistence of all populations. Finally, some numerical simulation results have been presented to validate the analytical findings.

The dynamics of preferential host switching: Host phylogeny as a key predictor of parasite distribution.

Parasites often jump to and become established in a new host species. There is much evidence that the probability of such host shifts decreases with increasing phylogenetic distance between donor and recipient hosts, but the consequences of such preferential host switching remain little explored. We develop a computational model to investigate the dynamics of parasite host shifts in the presence of this phylogenetic distance effect. In this model, a clade of parasites evolves on an evolving clade of host species where parasites can cospeciate with their hosts, switch to new hosts, speciate within hosts or become extinct. Our model predicts that host phylogenies are major determinants of parasite distributions across trees. In particular, we predict that trees consisting of few large clades of host species and those with fast species turnover should harbor more parasites than trees with many small clades and those that diversify more slowly. Within trees, large clades are predicted to exhibit a higher fraction of infected species than small clades. We discuss our results in the light of recent cophylogenetic studies in a wide range of host-parasite systems.

A Computational Framework for Preferential Switching of Competing Aβ Aggregation Pathways Based on Game Theory Approach

Polymorphism among amyloid-β (Aβ) aggregates are emerging as the main contributors to the observed phenotypic diversity in sporadic Alzheimer's disease (sAD). Aggregation of Aβ is susceptible to several heterotypic factors, and lipids (LDs) are the most important physiological agents to interact with, and modulate Aβ aggregation. Therefore, understanding the mechanism of how LDs modulate Aβ aggregation to generate polymorphic strains along competing pathways is crucial for understanding AD pathogenesis. Here, we demonstrate that steady-state switching dynamics between the competing aggregation pathways thar arise due to heterotypic Aβ-LD interactions can be modeled by a novel game theory approach. The game theory model abstracts the mass-action based non-linear, coupled dynamical system of competing pathways of aggregation and the corresponding Nash equilibrium points can predict the preferred pathways as a function of LD parameters and the level of dilution of the medium. While higher LD concentration leads to the generation of more micelle-bound oligomers (promoting the off-pathway of aggregation), higher levels of dilution of the medium result in dissociating micelle bound oligomers enabling higher conversion to fibrils (promoting the traditional on-pathway of aggregation). These models were subsequently validated by our previously developed ensemble kinetics simulations (EKS) that use ordinary differential equations based models of the competing pathways to estimate the rate constants of converting oligomers between on- and off-pathway aggregates; the combined computational framework accurately predicts the temporal rates and stability of oligomers formed under conditions predicted by controlled in vitro biophysical experiments. Hence, our results demonstrate the possibility of switching oligomeric strains between different competing pathways of Aβ aggregation besides providing a novel computational framework to model its dynamics.

Au Nanoparticles as Template for Defect Formation in Memristive SrTiO₃ Thin Films.

We investigated the possibility of tuning the local switching properties of memristive crystalline SrTiO thin films by inserting nanoscale defect nucleation centers. For that purpose, we employed chemically-synthesized Au nanoparticles deposited on 0.5 wt%-Nb-doped SrTiO single crystal substrates as a defect formation template for the subsequent growth of SrTiO. We studied in detail the resulting microstructure and the local conducting and switching properties of the SrTiO thin films. We revealed that the Au nanoparticles floated to the SrTiO surface during growth, leaving behind a distorted thin film region in their vicinity. By employing conductive-tip atomic force microscopy, these distorted SrTiO regions are identified as sites of preferential resistive switching. These findings can be attributed to the enhanced oxygen exchange reaction at the surface in these defective regions.

Aerosol assisted chemical vapor deposition (AACVD) synthesis of nanostructured cauliflower patterning in MWCNT doped tungsten oxide

We report nanostructured tungsten oxide (WO) cauliflowers for the first time that are fabricated onto silica glass substrate at 400 °C by aerosol assisted chemical vapor deposition using tungsten hexacarbonyl and multiwalled CNTs in toluene. The deposited films are characterized by Scanning electron microscopy, Energy dispersive x-ray spectroscopy, X-ray diffractometry, Fourier transform infrared and UV–VIS spectroscopy and four-point probe for microstructural, optical and electrical properties. Surface morphology exhibits the growth of nanocauliflowers followed by the aggregation of spherical nanoparticles with high angle grain boundaries. Structural information reveals the transformation of triclinic to tetragonal phase with preferential switching from (0 2 0) to (0 0 1) plane having signatures of W-O-W symmetric vibration between (700cm-1 and 900 cm−1, somewhat perturbed by the addition of doping. In additions, films show inconsistent variation in electrical resistivity (15–109) Ω-cm due to agglomeration of MWCNTs at grain boundaries and appearance of “nanocracks” due to ionic radii mismatch of tungsten and CNTs at higher doping ratios. Black color films present decrease in optical transmittance for range of 300–400 nm attributed to trapping sites and defects generated due to incorporation of multiwalled CNTs. The splitting of Fermi level as a result of incorporation of MWCNTs caused the increase of band gap energy in range of 3.18 eV, useful in tungsten oxide based new material system which can act as the light harvesting material and energy storage simultaneously.

Shift or stick? Untangling the signatures of biased host switching, and host-parasite co-speciation

A recommendation of: Jan Engelstaedter & Nicole Fortuna The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distribution https://doi.org/10.1101/209254

B Cell-Intrinsic MyD88 Signaling Promotes Initial Cell Proliferation and Differentiation To Enhance the Germinal Center Response to a Virus-like Particle.

Although TLR signaling in B cells has been implicated in the germinal center (GC) responses during viral infections and autoimmune diseases, the underlying mechanism is unclear. Bacterial phage Qβ-derived virus-like particle (Qβ-VLP) contains TLR ligands, which can enhance Qβ-VLP-induced Ab response, including GC response, through TLR/MyD88 signaling in B cells. In this study, by examining Ag-specific B cell response to Qβ-VLP, we found that lack of B cell MyD88 from the beginning of the immune response led to a more severe defect in the GC scale than abolishing MyD88 at later time points of the immune response. Consistently, B cell-intrinsic MyD88 signaling significantly enhanced the initial proliferation of Ag-specific B cells, which was accompanied with a dramatic increase of plasma cell generation and induction of Bcl-6+ GC B cell precursors. In addition, B cell-intrinsic MyD88 signaling promoted strong T-bet expression independent of IFN-γ and led to the preferential isotype switching to IgG2a/c. Thus, by promoting the initial Ag-specific B cell proliferation and differentiation, B cell-intrinsic MyD88 signaling enhanced both T-independent and T-dependent Ab responses elicited by Qβ-VLP. This finding will provide additional insight into the role of TLR signaling in antiviral immunity, autoimmune diseases, and vaccine design.

Spatially resolved investigation of all optical magnetization switching in TbFe alloys

Optical control of magnetization using femtosecond laser without applying any external magnetic field offers the advantage of switching magnetic states at ultrashort time scales. Recently, all-optical helicity-dependent switching (AO-HDS) has drawn a significant attention for potential information and data storage device applications. In this work, we employ element and magnetization sensitive photoemission electron microscopy (PEEM) to investigate the role of heating in AO-HDS for thin films of the rare-earth transition-metal alloy TbFe. Spatially resolved measurements in a 3–5 μm sized stationary laser spot demonstrate that AO-HDS is a local phenomenon in the vicinity of thermal demagnetization in a ‘ring’ shaped region. The efficiency of AO-HDS further depends on a local temperature profile around the demagnetized region and thermally activated domain wall motion. We also demonstrate that the thickness of the film determines the preferential switching direction for a particular helicity.

Preferential host switching and its relation with Hantavirus diversification in South America.

In recent years, the notion of co-speciation between Hantavirus species and their hosts was discarded in favour of a more likely explanation: preferential host switching. However, the relative importance of this last process in shaping the evolutionary history of hantaviruses remains uncertain, given the present limited knowledge not only of virus-host relationships but also of the pathogen and reservoir phylogenies. In South America, more than 25 hantavirus genotypes were detected; several of them act as aetiological agents of hantavirus pulmonary syndrome (HPS). An understanding of the diversity of hantaviruses and of the processes underlying host switching is critical since human cases of HPS are almost exclusively the result of human-host interactions. In this study, we tested if preferential host switching is the main process driving hantavirus diversification in South America, by performing a co-phylogenetic analysis of the viruses and their primary hosts. We also suggest a new level of amino acid divergence to define virus species in the group. Our results indicate that preferential host switching would not be the main process driving virus diversification. The historical geographical proximity among rodent hosts emerges as an alternative hypothesis to be tested.

Hantaviruses: Rediscovery and new beginnings

Virus and host gene phylogenies, indicating that antigenically distinct hantaviruses (family Bunyaviridae, genus Hantavirus) segregate into clades, which parallel the molecular evolution of rodents belonging to the Murinae, Arvicolinae, Neotominae and Sigmodontinae subfamilies, suggested co-divergence of hantaviruses and their rodent reservoirs. Lately, this concept has been vigorously contested in favor of preferential host switching and local host-specific adaptation. To gain insights into the host range, spatial and temporal distribution, genetic diversity and evolutionary origins of hantaviruses, we employed reverse transcription-polymerase chain reaction to analyze frozen, RNAlater®-preserved and ethanol-fixed tissues from 1546 shrews (9 genera and 47 species), 281 moles (8 genera and 10 species) and 520 bats (26 genera and 53 species), collected in Europe, Asia, Africa and North America during 1980–2012. Thus far, we have identified 24 novel hantaviruses in shrews, moles and bats. That these newfound hantaviruses are geographically widespread and genetically more diverse than those harbored by rodents suggests that the evolutionary history of hantaviruses is far more complex than previously conjectured. Phylogenetic analyses indicate four distinct clades, with the most divergent comprising hantaviruses harbored by the European mole and insectivorous bats, with evidence for both co-divergence and host switching. Future studies will provide new knowledge about the transmission dynamics and pathogenic potential of these newly discovered, still-orphan, non-rodent-borne hantaviruses.

A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES

A growing number of studies support a tendency toward preferential host switching, by parasites and pathogens, over relatively short phylogenetic distances. This suggests that a host switch is more probable if a potential host is closely related to the original host than if it is a more distant relative. However, despite its importance for the health of humans, livestock, and wildlife, the detailed dynamics of preferential host switching have, so far, been little studied. We present an empirical test of two theoretical models of preferential host switching, using observed phylogenetic distributions of host species for RNA viruses of three mammal orders (primates, carnivores, and ungulates). The analysis focuses on multihost RNA virus species, because their presence on multiple hosts and their estimated ages of origin indicate recent host switching. Approximate Bayesian computation was used to compare observed phylogenetic distances between hosts with those simulated under the theoretical models. The results support a decreasing sigmoidal model of preferential host switching, with a strong effect from increasing phylogenetic distance, on all three studied host phylogenies. This suggests that the dynamics of host switching are fundamentally similar for RNA viruses of different mammal orders and, potentially, a wider range of coevolutionary systems.

New species of Cacatuocotyle (Monogenoidea, Dactylogyridae) parasitizing the anus and the gill lamellae of Astyanax aeneus (Pisces, Ostariophysi: Characidae) from the Rio Lacantún basin in the Biosphere Reserve of Montes Azules, Chiapas, Mexico

As part of a biological inventory of the Rio Lacantún basin in the Biosphere Reserve of Montes Azules from Chiapas State (southeastern, Mexico), the following monogenoid ectoparasites infecting the external surface of the anal opening and the gill lamellae of the freshwater fish Astyanax aeneus (Characidae) in ten streams were found: Cacatuocotyle chajuli sp. nov. (anus), Cacatuocotyle exiguum sp. nov., and Cacatuocotyle sp. (gill lamellae). C. chajuli is differentiated from its single congener, Cacatuocotyle paranaensis (Boeger et al. Syst Parasitol 36:75-78, 1997), from the gills of Characidium lanei (Characidae) from Paraná Brazil, in having a noticeably V-shaped haptoral bar and larger hooks and anchors. C. exiguum differs from these two latter species in the size of its anchors. Illustrations and data on morphological and biometric variability of individual specimens of C. chajuli and C. exiguum from different streams are provided. The present data support the statement about three species of Astyanax, which harbor the richest monogenoidean diversity in the Neotropics with a total of 18 species reported up to now. Occurrences of species of Cacatuocotyle on different sites of infection on three distant host species [including a Neotropical cichlid (Cichlidae) species] suggest that these monogenoideans switching to new hosts can result in the availability of potential hosts within the same habitat instead of showing signs of preferential switching between closely related hosts or on their respective microhabitats.

Stability of Medical Student Career Interest

To examine the stability and switching patterns of student career interests over the course of medical school. From 2001 through 2004, during the first two weeks of classes, a survey on career interest was distributed to first-year students in 15 classes at eight Canadian medical schools. Students indicated interest in eight broad career paths (emergency medicine, family medicine, internal medicine, obstetrics-gynecology, pediatrics, psychiatry, surgery, and "other") and ranked their top three. Following these students' residency match three to four years later, student residency career choice was linked to their career interest at medical school entry. For students whose career interests switched be-tween medical school entry and exit, switching patterns were examined in terms of careers' matching difficulty scores (MDSs). Of 1,941 eligible students, 1,542 contributed to the final analysis. Family medicine, internal medicine, and surgery had the greatest student interest at both the beginning and end of medical school. Family medicine, surgery, obstetrics-gynecology, psychiatry, and "other" careers showed a net gain of student interest during medical school with the remaining careers showing a loss of interest. The most stable careers were family medicine, surgery, and internal medicine. The least stable were pediatrics and obstetrics-gynecology. Students tended to switch between careers with similar MDSs. Student career choice is relatively stable with a number of careers showing approximately 50% of stability from the entrance to the exit of medical school. Students tend to switch to careers with similar MDS, but some specific switching patterns exist.

Follicular Dendritic Cell Makes Environmental Sense

Follicular dendritic cells (FDCs) are key organizers of B cell follicles and germinal centers. In this issue of Immunity, Suzuki et al. (2010) and Garin et al. (2010) identify the roles of Toll-like receptors in the responses of FDCs, providing a unique link between innate and adaptive immunity.

Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence

Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, approximately 100 million years ago. We tested this hypothesis of host-virus codivergence in two ways: 1) we used cophylogenetic reconciliation analysis to assess the fit of the virus tree onto that of the host and 2) we estimated the evolutionary rates and divergence times for the Hantavirus genus using a Bayesian Markov Chain Monte Carlo method and similarly compared these with those of their hosts. Our reconciliation analysis provided no evidence for a history of codivergence between hantaviruses and their hosts. Further, the divergence times for the Hantavirus genus were many orders of magnitude too recent to correspond with the timescale of their hosts' speciation. We therefore propose that apparent similarities between the phylogenies of hantaviruses and their mammalian hosts are the result of a more recent history of preferential host switching and local adaptation. Based on the presence of clade-defining amino acids in all genomic segments, we propose that the patterns of amino acid replacement in these viruses are also compatible with a history of host-specific adaptation.

Asymmetrical Increase of Memory Window in MFIS Devices After Avalanche Hole Injection

We have investigated the effects of charge trapping on the asymmetrical increase of the memory window in metal-ferroelectric-insulator-semiconductor (MFIS) devices. We suggest that defect centers located at the ferroelectric-insulator interface play important roles for generating the asymmetrical increase of the memory window. For example, hole trapping at/near the SBN-Y 2 O 3 /SiO 2 interface via avalanche hole injection from the Si substrate results in the preferential domain switching, causing the asymmetrical increase of the memory window.

Opportunistic pollinator shifts among sexually deceptive orchids indicated by a phylogeny of pollinating and non-pollinating thynnine wasps (Tiphiidae)

The thynnine wasp genus Neozeleboria Rohwer is the main pollinating group of the sexually deceptive Australian orchid genus, Chiloglottis R.Br. In a highly specialized interaction, Chiloglottis species attract males from a single or very few Neozeleboria species through the chemical mimicry of the female wasp's sex pheromone. An earlier study examining the historical association among Chiloglottis and Neozeleboria using DNA sequence data found matching phylogenetic patterns suggestive of cospeciation between orchids and pollinators. However, patterns of constraint in Neozeleboria emergence phenology and sex pheromones suggested that the close association among orchid and wasp clades may be due to pollinator switching among closely related wasp taxa that have similar traits. In this study, we further examine the association by incorporating a morphological phylogenetic analysis of non-pollinating as well as pollinating Neozeleboria. The morphological analysis is then compared with DNA sequence data from one nuclear and one mitochondrial gene for an increased sample of outgroup genera. The combined molecular data set finds a monophyletic Neozeleboria, although support for this was not strong in the individual data sets. A high congruence between molecular and morphological analyses was found among higher groupings of Neozeleboria. Neozeleboria species that pollinate Chiloglottis species are not found as a monophyletic group but, rather, are scattered throughout a phylogeny comprising pollinators and non-pollinators. Under the cospeciation model, the presence of related Neozeleboria non-pollinators carries the unlikely implication that the association between plant and pollinator has been repeatedly lost. Instead, we favour the alternative ‘preferential pollinator switching’ model that accounts for the specialization among orchid and wasp lineages in terms of similarities in traits among related Neozeleboria. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86, 381–395.

Asymmetrical increase of memory window in MFIS devices after avalanche electron injection

We investigated the effects of charge trapping on the asymmetrical increase in the memory window of metal–ferroelectric–insulator–semiconductor (MFIS) devices. We suggest that defect centers located at the ferroelectric–insulator interface play important roles in generating the asymmetrical increase in the memory window: Electron trapping at/near the SBN (or SBT)–Y2O3 interface via avalanche electron injection from the Si substrate results in the preferential domain switching, causing the asymmetrical increase in the memory window.