Surviving high temperatures: a case study of the spotted munia (Lonchura punctulata).

Every year, a combination of summer with extreme weather events such as "heatwaves" affects the life of organisms on earth. Previous studies on humans, rodents, and some birds signify the impact of heat stress on their survival and existence. Over the past four decades, the frequency of heatwaves has increased because of global warming. Therefore, we performed a longitudinal study on a resident bird species, the spotted munia (Lonchura punctulata) by simulating a heatwave-like condition. We were interested in understanding how a Passeriformes native to a sub-tropical country deals with heatwave-like conditions. Initially, the birds were subjected to room temperature (25 ± 2 °C; T1) for 10 days, followed by a simulated heatwave-like condition (42 ± 1 °C; T2) for 7 days and again back to room temperature (25 ± 2 °C; RT1) for the next 7 days. To elucidate how birds cope with simulated heatwave conditions, we examined different behavioral and physiological parameters. We found that although heat stress significantly reduced total activity counts and food intake but, the body mass, blood glucose, and hemoglobin levels remained unaffected by any of the temperature conditions. Furthermore, HSP70 and biochemical markers of liver injuries such as ALP, AST, ALT, bilirubin direct, and bilirubin total were found elevated in response to the simulated heatwave-like condition, whereas uric acid and triglyceride were reduced. Creatinine and total protein levels were unaffected by the heatwave. The post heatwave treatment resulted in a rebound of the behavioral and physiological responses, but the recovered responses were not equivalent to the pre-heatwave levels (T1 conditions). Thus, the present study demonstrates heatwave-associated behavioral and physiological changes in a resident passerine finch which has tremendous physiological flexibility.

Role of genetic architecture in phenotypic plasticity.

Phenotypic plasticity, the ability of an organism to display different phenotypes across environments, is widespread in nature. Plasticity aids survival in novel environments. Herein, we review studies from yeast that allow us to start uncovering the genetic architecture of phenotypic plasticity. Genetic variants and their interactions impact the phenotype in different environments, and distinct environments modulate the impact of genetic variants and their interactions on the phenotype. Because of this, certain hidden genetic variation is expressed in specific genetic and environmental backgrounds. A better understanding of the genetic mechanisms of phenotypic plasticity will help to determine short- and long-term responses to selection and how wide variation in disease manifestation occurs in human populations.

Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting.

The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca2+/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca2+ signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.

Effect of artificial light at night on sleep and metabolism in weaver birds.

Artificial light at night is constantly minimizing the span of dark nights from the natural light-dark cycle of earth. Over the past century, the "lightscape" of earth has completely changed owing to technological advancements which subsequently changed the lifestyle of human as well as the nearby animal species. This motivated the present study, wherein we investigated the impact of light at night (LAN) on behavior and physiology of a diurnal passerine finch, baya weaver (Ploceus philippinus). A group of bird (N=10) exposed to 12L:12D photoperiod was initially subjected to dark nights (0 lux) for a period of 1.5 weeks followed by 5 lux, night light for a span of 4 weeks. The first week in LAN served as acute treatment with respect to the fourth week (chronic). The results reveal significant increase in nighttime activity and sleep loss with respect to acute LAN, while significant inclusion of drowsiness behavior during the day in response to chronic LAN. Besides these behavioral alterations, changes in physiological parameters such as reduction in body mass, loss of gradient between pre- and post- prandial blood glucose levels, and elevation in plasma corticosterone levels were more prominent during acute exposure of LAN. Plasma metabolites such as triglycerides, total protein, serum glutamic-oxaloacetic transaminase (SGOT), and creatinine concentrations also hiked in response to acute LAN treatment. Thus, acute exposure of LAN seems to serve as a novel environment for the bird leading to more pronounced impacts on behavioral and physiological observations during the experiment. In chronic exposure, the birds sort of adapted themselves to the prevailing circumstances as evident by decreased nighttime activity, rebound of sleep and corticosterone levels, etc. Thus, the study clearly demonstrates the differential impact of acute and chronic exposure of LAN on behavior and physiology of birds.

A Composite Microfiber for Biodegradable Stretchable Electronics.

Biodegradable stretchable electronics have demonstrated great potential for future applications in stretchable electronics and can be resorbed, dissolved, and disintegrated in the environment. Most biodegradable electronic devices have used flexible biodegradable materials, which have limited conformality in wearable and implantable devices. Here, we report a biodegradable, biocompatible, and stretchable composite microfiber of poly(glycerol sebacate) (PGS) and polyvinyl alcohol (PVA) for transient stretchable device applications. Compositing high-strength PVA with stretchable and biodegradable PGS with poor processability, formability, and mechanical strength overcomes the limits of pure PGS. As an application, the stretchable microfiber-based strain sensor developed by the incorporation of Au nanoparticles (AuNPs) into a composite microfiber showed stable current response under cyclic and dynamic stretching at 30% strain. The sensor also showed the ability to monitor the strain produced by tapping, bending, and stretching of the finger, knee, and esophagus. The biodegradable and stretchable composite materials of PGS with additive PVA have great potential for use in transient and environmentally friendly stretchable electronics with reduced environmental footprint.

Concurrent changes in photoperiod-induced seasonal phenotypes and hypothalamic CART peptide-containing systems in night-migratory redheaded buntings.

This study tested the hypothesis whether hypothalamic cocaine-and amphetamine-regulated transcript (CART)-containing systems were involved in photoperiod-induced responses associated with spring migration (hyperphagia and weight gain) and reproduction (gonadal maturation) in migratory songbirds. We specifically chose CART to examine neural mechanism(s) underlying photoperiod-induced responses, since it is a potent anorectic neuropeptide and involved in the regulation of changes in the body mass and reproduction in mammals. We first studied the distribution of CART-immunoreactivity in the hypothalamus of migratory redheaded buntings (Emberiza bruniceps). CART-immunoreactive neurons were found extensively distributed in the preoptic, lateral hypothalamic (LHN), anterior hypothalamic (AN), suprachiasmatic (SCN), paraventricular (PVN), dorsomedialis hypothalami (DMN), inferior hypothalamic (IH), and infundibular (IN) nuclei. Then, we correlated hypothalamic CART-immunoreactivity in buntings with photostimulated seasonal states, particularly winter non-migratory/non-breeding (NMB) state under short days, and spring premigratory/pre-breeding (PMB) and migratory/breeding (MB) states under long days. There were significantly increased CART-immunoreactive cells, and percent fluorescent area of CART-immunoreactivity was significantly increased in all mapped hypothalamic areas, except the SCN, PVN, AN, and DMN in photostimulated PMB and MB states, as compared to the non-stimulated NMB state. In particular, CART was richly expressed in the medial preoptic nucleus, LHN, IH and IN during MB state in which buntings showed reduced food intake and increased night-time activity. These results suggest that changes in the activity of the CART-containing system in different brain regions were associated with heightened energy needs of the photoperiod-induced seasonal responses during spring migration and reproduction in migratory songbirds.

Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples.

We give results from a detailed analysis of human Ribosomal Protein (RP) levels in normal and cancer samples and cell lines from large mRNA, copy number variation and ribosome profiling datasets. After normalizing total RP mRNA levels per sample, we find highly consistent tissue specific RP mRNA signatures in normal and tumor samples. Multiple RP mRNA-subtypes exist in several cancers, with significant survival and genomic differences. Some RP mRNA variations among subtypes correlate with copy number loss of RP genes. In kidney cancer, RP subtypes map to molecular subtypes related to cell-of-origin. Pan-cancer analysis of TCGA data showed widespread single/double copy loss of RP genes, without significantly affecting survival. In several cancer cell lines, CRISPR-Cas9 knockout of RP genes did not affect cell viability. Matched RP ribosome profiling and mRNA data in humans and rodents stratified by tissue and development stage and were strongly correlated, showing that RP translation rates were proportional to mRNA levels. In a small dataset of human adult and fetal tissues, RP protein levels showed development stage and tissue specific heterogeneity of RP levels. Our results suggest that heterogeneous RP levels play a significant functional role in cellular physiology, in both normal and disease states.

A reference map of the human binary protein interactome.

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships1,2. Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome3, transcriptome4 and proteome5 data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.

Precision medicine - networks to the rescue.

Genetic variants are often not predictive of the phenotypic outcome. Individuals carrying the same pathogenic variant, associated with Mendelian or complex disease, can manifest to different extents, from severe-to-mild to no disease. Improving the accuracy of predicted clinical manifestations of genetic variants has emerged as one of the biggest challenges in precision medicine, which can only be addressed by understanding the mechanisms underlying genotype-phenotype relationships. Efforts to understand the molecular basis of these relationships have identified complex systems of interacting biomolecules that underlie cellular function. Here, we review recent advances in how modeling cellular systems as networks of interacting proteins has fueled identification of disease-associated processes, delineation of underlying molecular mechanisms, and prediction of the pathogenicity of variants. This review is intended to be inspiring for clinicians, geneticists, and network biologists alike who aim to jointly advance our understanding of human disease and accelerate progress toward precision medicine.

Broadband transparent optical phase change materials for high-performance nonvolatile photonics.

Optical phase change materials (O-PCMs), a unique group of materials featuring exceptional optical property contrast upon a solid-state phase transition, have found widespread adoption in photonic applications such as switches, routers and reconfigurable meta-optics. Current O-PCMs, such as Ge-Sb-Te (GST), exhibit large contrast of both refractive index (Δn) and optical loss (Δk), simultaneously. The coupling of both optical properties fundamentally limits the performance of many applications. Here we introduce a new class of O-PCMs based on Ge-Sb-Se-Te (GSST) which breaks this traditional coupling. The optimized alloy, Ge2Sb2Se4Te1, combines broadband transparency (1-18.5 µm), large optical contrast (Δn = 2.0), and significantly improved glass forming ability, enabling an entirely new range of infrared and thermal photonic devices. We further demonstrate nonvolatile integrated optical switches with record low loss and large contrast ratio and an electrically-addressed spatial light modulator pixel, thereby validating its promise as a material for scalable nonvolatile photonics.

Long-lived monolithic micro-optics for multispectral GRIN applications.

The potential for realizing robust, monolithic, near-surface refractive micro-optic elements with long-lived stability is demonstrated in visible and infrared transmitting glasses capable of use in dual band applications. Employing an enhanced understanding of glass chemistry and geometric control of mobile ion migration made possible with electrode patterning, flat, permanent, thermally-poled micro-optic structures have been produced and characterized. Sub-surface (t~5-10 µm) compositional and structural modification during the poling process results in formation of spatially-varying refractive index profiles, exhibiting induced Δn changes up to 5 × 10-2 which remain stable for >15 months. The universality of this approach applied to monolithic vis-near infrared [NIR] oxide and NIR-midwave infrared [MIR] chalcogenide glass materials is demonstrated for the first time. Element size, shape and gradient profile variation possible through pattern design and fabrication is shown to enable a variety of design options not possible using other GRIN process methodologies.

Gene-gene and gene-environment interactions in complex traits in yeast.

One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context-dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene-gene interactions (GGI) and gene-environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype-phenotype map.

Monolithically integrated stretchable photonics.

Mechanically stretchable photonics provides a new geometric degree of freedom for photonic system design and foresees applications ranging from artificial skins to soft wearable electronics. Here we describe the design and experimental realization of the first single-mode stretchable photonic devices. These devices, made of chalcogenide glass and epoxy polymer materials, are monolithically integrated on elastomer substrates. To impart mechanical stretching capability to devices built using these intrinsically brittle materials, our design strategy involves local substrate stiffening to minimize shape deformation of critical photonic components, and interconnecting optical waveguides assuming a meandering Euler spiral geometry to mitigate radiative optical loss. Devices fabricated following such design can sustain 41% nominal tensile strain and 3000 stretching cycles without measurable degradation in optical performance. In addition, we present a rigorous analytical model to quantitatively predict stress-optical coupling behavior in waveguide devices of arbitrary geometry without using a single fitting parameter.

Metabolic shift in sugars and amino acids regulates sprouting in Saffron corm.

Saffron is one of the most expensive spices of the world. Since this spice is triploid and meiosis is unusual, it cannot reproduce sexually like other plants; rather, it is propagated vegetatively via an underground corm, which can withstand a long dry dormant period before sprouting. Thus, corms are indispensable to saffron propagation. To identify and analyse signature metabolites associated with the 'dormancy-sprouting' process, non-targeted GC-MS was performed at different stages of corm development. Comparative metabolite profiling reflected dissimilar profiles among the stages as portrayed by differential cluster patterns of metabolites in the PCA and PLS-DA analysis. Correlation analysis revealed the interdependencies of individual metabolites and metabolic pathway. At the onset of stage 2, characterized by the initiation and differentiation of leaf primordia, a shift from dormancy to active metabolism occurred as derived from the increased abundance of sugars and other metabolites involved in the tricarboxylic acid cycle, glycolytic, amino acid and fatty acid pathways. These changes contribute to sprouting and vegetative growth of the corm. The present study provides new insights into saffron corm composition and metabolite changes associated with various stages of corm development and may pave the way for achieving agronomical improvements in this economically important spice.

The Modular Adaptive Ribosome.

The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.

Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth.

The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it's evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with the environment specific regulators is not well understood. Saccharomyces cerevisiae is highly sensitive to the environment, which acts as not just external stimulus but also as signalling cue for this unicellular, sessile organism. We used a previously published dataset of a biparental yeast population grown in 34 diverse environments and mapped genetic loci regulating variation in phenotypic plasticity, plasticity QTL, and compared them with environment-specific QTL. Plasticity QTL is one whose one allele exhibits high plasticity whereas the other shows a relatively canalised behaviour. We mapped phenotypic plasticity using two parameters-environmental variance, an environmental order-independent parameter and reaction norm (slope), an environmental order-dependent parameter. Our results show a partial overlap between pleiotropic QTL and plasticity QTL such that while some plasticity QTL are also pleiotropic, others have a significant effect on phenotypic plasticity without being significant in any environment independently. Furthermore, while some plasticity QTL are revealed only in specific environmental orders, we identify large effect plasticity QTL, which are order-independent such that whatever the order of the environments, one allele is always plastic and the other is canalised. Finally, we show that the environments can be divided into two categories based on the phenotypic diversity of the population within them and the two categories have differential regulators of phenotypic plasticity. Our results highlight the importance of identifying genetic regulators of phenotypic plasticity to comprehensively understand the genotype-phenotype map.

Differential Regulation of Cryptic Genetic Variation Shapes the Genetic Interactome Underlying Complex Traits.

Cryptic genetic variation (CGV) refers to genetic variants whose effects are buffered in most conditions but manifest phenotypically upon specific genetic and environmental perturbations. Despite having a central role in adaptation, contribution of CGV to regulation of quantitative traits is unclear. Instead, a relatively simplistic architecture of additive genetic loci is known to regulate phenotypic variation in most traits. In this paper, we investigate the regulation of CGV and its implication on the genetic architecture of quantitative traits at a genome-wide level. We use a previously published dataset of biparental recombinant population of Saccharomyces cerevisiae phenotyped in 34 diverse environments to perform single locus, two-locus, and covariance mapping. We identify loci that have independent additive effects as well as those which regulate the phenotypic manifestation of other genetic variants (variance QTL). We find that whereas additive genetic variance is predominant, a higher order genetic interaction network regulates variation in certain environments. Despite containing pleiotropic loci, with effects across environments, these genetic networks are highly environment specific. CGV is buffered under most allelic combinations of these networks and perturbed only in rare combinations resulting in high phenotypic variance. The presence of such environment specific genetic networks is the underlying cause of abundant gene­environment interactions. We demonstrate that overlaying identified molecular networks on such genetic networks can identify potential candidate genes and underlying mechanisms regulating phenotypic variation. Such an integrated approach applied to human disease datasets has the potential to improve the ability to predict disease predisposition and identify specific therapeutic targets.

Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation.

Antagonistic pleiotropy (AP), the ability of a gene to show opposing effects in different phenotypes, has been identified in various life history traits and complex disorders, indicating its fundamental role in balancing fitness over the course of evolution. It is intuitive that natural selection might maintain AP to allow organisms phenotypic flexibility in different environments. However, despite several attempts, little evidence exists for its role in adaptation. We performed a meta-analysis in yeast to identify the genetic basis of AP in bi-parental segregants, natural isolates, and a laboratory strain genome-wide deletion collection, by comparing growth in favorable and stress conditions. We found that whereas AP was abundant in the synthetic populations, it was absent in the natural isolates. This finding indicated resolution of trade-offs, i.e., mitigation of trade-offs over evolutionary history, probably through accumulation of compensatory mutations. In the deletion collection, organizational genes showed AP, suggesting ancient resolutions of trade-offs in the basic cellular pathways. We find abundant AP in the segregants, greater than estimated in the deletion collection or observed in previous studies, with IRA2, a negative regulator of the Ras/PKA signaling pathway, showing trade-offs across diverse environments. Additionally, IRA2 and several other Ras/PKA pathway genes showed balancing selection in isolates of S. cerevisiae and S. paradoxus, indicating that multiple alleles maintain AP in this pathway in natural populations. We propose that during AP resolution, retaining the ability to vary signaling pathways such as Ras/PKA, may provide organisms with phenotypic flexibility. However, with increasing organismal complexity AP resolution may become difficult. A partial resolution of AP could manifest as complex human diseases, and the inability to resolve AP may play a role in speciation. Our findings suggest that testing a universal phenomenon like AP across multiple experimental systems may elucidate mechanisms underlying its regulation and evolution.

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

For a unicellular, nonmotile organism like Saccharomyces cerevisiae, carbon sources act as nutrients and as signaling molecules; consequently, these sources affect various fitness parameters, including growth. It is therefore advantageous for yeast strains to adapt their growth to carbon source variation. The ability of a given genotype to manifest different phenotypes in varying environments is known as phenotypic plasticity. To identify quantitative trait loci (QTL) that drive plasticity in growth, two growth parameters (growth rate and biomass) were measured for a set of meiotic recombinants of two genetically divergent yeast strains grown in different carbon sources. To identify QTL contributing to plasticity across pairs of environments, gene-environment interaction mapping was performed, which identified several QTL that have a differential effect across environments, some of which act antagonistically across pairs of environments. Multi-QTL analysis identified loci interacting with previously known growth affecting QTL as well as novel two-QTL interactions that affect growth. A QTL that had no significant independent effect was found to alter growth rate and biomass for several carbon sources through two-QTL interactions. Our study demonstrates that environment-specific epistatic interactions contribute to the growth plasticity in yeast. We propose that a targeted scan for epistatic interactions, such as the one described here, can help unravel mechanisms regulating phenotypic plasticity.