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At least 163 records · Page 9Linked to original sources

bioRxiv2017

To Beard, Or Not To Beard: Linking Sexual Selection On Masculinity, Embryonic Neural Crest Cells, And Human Self-Domestication

ObjectivesPre-historic decline in human craniofacial masculinity has been proposed as evidence of selection for elevated sociability and a process of human self-domestication thought to have promoted complex capacities including language, culture, and cumulative technological development. This follows experimental observation of similar changes in non-human animals under selection for reduced aggression. Two distinct domestication hypotheses posit developmental explanations, involving hypoplasia of embryonic neural crest cells (NCCs), and declining androgen influence, respectively. Here, I assess the operation and potential interactions between these two mechanisms and consider their role in enhanced human adaptation to a cooperative sociocultural niche. MethodsI provide a review and synthesis of related literature with a focus on physiological mechanisms effecting domesticated reductions in masculinity and sexual dimorphism. Further, I examine pre-historic modes of socio-sexual selection likely to drive human self-domestication via reduced aggression and masculinity. ResultsI find pluripotent NCCs provide progenitors for a wide range of vertebrate masculine features, acting as regular targets for sexually driven evolutionary change; suggesting domesticated hypoplasia of NCC-derived tissues would be sufficient to explain declines in masculine traits and features. However, lineage specific androgen receptor variability likely moderates these NCC-based effects. ConclusionsThese findings extend theorised mechanisms driving noted physiological, morphological, and behavioural changes thought to indicate enhanced sociability and human and self-domestication. Multiple current explanations for human sociability are consistent with physiological domestication under socio-sexual selection favouring dampened masculine physiology and behaviour as adaptations to an enhanced sociocultural niche. The analysis highlights multiple avenues for further investigation.

evolutionary biology↗

bioRxiv2017

Bundle sheath extensions in tomato affect leaf phenotypic plasticity in response to irradiance

Coordination between structural and physiological traits is key to plants responses to environmental fluctuations. In heterobaric leaves, bundle sheath extensions (BSEs) increase photosynthetic performance (light-saturated rates of photosynthesis, Amax) and water transport capacity (leaf hydraulic conductance, Kleaf). However, it is not clear how BSEs affect these and other leaf developmental and physiological parameters in response to environmental conditions. The obscuravenosa (obv) mutation, found in many commercial tomato varieties, leads to absence of BSEs. We examined structural and physiological traits of tomato heterobaric and homobaric (obv) near-isogenic lines (NILs) grown at two different irradiance levels. Kleaf, minor vein density and stomatal pore area index decreased with shading in heterobaric but not in homobaric leaves, which show similarly lower values in both conditions. Homobaric plants, on the other hand, showed increased Amax, leaf intercellular air spaces and mesophyll surface area exposed to intercellular airspace (Smes) in comparison with heterobaric plants when both were grown in the shade. BSEs further affected carbon isotope discrimination, a proxy for long-term water-use efficiency. BSEs confer plasticity in traits related to leaf structure and function in response to irradiance levels and might act as a hub integrating leaf structure, photosynthetic function and water supply and demand.\n\nSummary statementThe presence of bundle sheath extension (BSEs) defines leaves as heterobaric, as opposed to homobaric leaves that lack them. Multiple functions have been proposed for BSEs, but their impact on different environmental conditions is still unclear. Here, we compared a tomato (Solanum lycopersicum) homobaric mutant lacking BSEs with its corresponding heterobaric wild-type, grown under two irradiance conditions. We show that the presence of BSEs differentially alters various physiological and anatomical parameters in response to growth irradiance. We propose that BSEs could act as hubs coordinating leaf plasticity in response to environmental factors.\n\nArticle typeResearch article

plant biology↗

bioRxiv2017

High-dimensional microbiome interactions shape host fitness

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host in turn shapes the gut microbiome. Microbiomes co-evolve with their hosts and have been implicated in host speciation. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. We find that the same microbial interactions that shape host fitness also shape microbiome abundances, suggesting a potential evolutionary mechanism by which microbiome communities (rather than just individual species) may be intertwined in co-selection with their hosts. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which in turn accelerated development, reproduction, and aging: flies that reproduced more died sooner. From these measurements we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Host physiology phenotypes were highly dependent on interactions between bacterial species. Higher-order interactions (involving 3, 4, and 5 species) were widely prevalent and impacted both host physiology and the maintenance of gut diversity. The parallel impacts of bacterial interactions on the microbiome and on host fitness suggest that microbiome interactions may be key drivers of evolution.\n\nSignificanceAll animals have associated microbial communities called microbiomes that can influence the physiology and fitness of their host. It is unclear to what extent individual microbial species versus ecology of the microbiome influences fitness of the host. Here we mapped all the possible interactions between individual species of bacteria with each other and with the hosts physiology. Our approach revealed that the same bacterial interactions that shape microbiome abundances also shape host fitness traits. This relationship provides a feedback that may favor the emergence of co-evolving microbiome-host units.

microbiology↗

bioRxiv2018

Locomotor response to acute stressors requires hypothalamic-pituitary-interrenal axis activation and glucocorticoid receptors in zebrafish

When vertebrates face acute stressors, their bodies rapidly undergo a repertoire of physiological and behavioral adaptations, which is termed the stress response (SR). Rapid physiological changes in heart rate and blood sugar levels occur via the interaction of glucocorticoids and their cognate receptors following hypothalamic-pituitary-adrenal (HPA) axis activation. These physiological changes are observed within minutes of encountering a stressor and the rapid time domain rules out genomic responses that require gene expression changes. Although behavioral changes corresponding to physiological changes are commonly observed, it is not clearly understood to what extent HPA axis activation dictates adaptive behavior. We hypothesized that rapid locomotor response to acute stressors in zebrafish requires HPI axis activation. In teleost fish, interrenal cells (I) are functionally homologous to the adrenal gland cortical layer. We derived 8 frameshift mutants in genes involved in HPI axis function: two mutants in exon 2 of mc2r (adrenocorticotropic hormone receptor), two in each of exon 2 and exon 5 of nr3c1 (glucocorticoid receptor), and two in exon 2 of nr3c2 (mineralocorticoid receptor). Exposing larval zebrafish to mild environmental stressors, acute changes in salinity or light illumination, results in a rapid locomotor response. We show here that this locomotor response requires a functioning HPI axis via the action of mc2r (adrenocorticotropic hormone receptor) and the canonical glucocorticoid receptor encoded by nr3c1 gene, but not mineralocorticoid receptor (nr3c2). Our rapid behavioral assay paradigm based on HPI axis biology may prove useful to screen for genetic, pharmacological, or environmental modifiers of the HPA axis.\n\nSignificanceAltered HPA axis activity is acknowledged as a causative and critical prognostic factor in many psychiatric disorders including depression. Nonetheless, genome wide association studies (GWAS) on depression have revealed conflicting findings about susceptibility loci, while identifying several genetic loci that warrant further investigations in the process. Such findings indicate that psychiatric disorders with complex genetic foundations require functional studies as well as genetic analyses. We developed a sensitive behavioral assay paradigm that leverages the genetic amenability and rapid development of zebrafish and demonstrated that our assay system reliably detects changes in HPA axis responsiveness. Our functional genetics and behavioral assay approach provides a useful platform to discover novel genetic, pharmacological, or environmental modifiers of the HPA axis.

neuroscience↗

bioRxiv2018

Quantification of Enterohemorrhagic Escherichia coli O157:H7 proteome using TMT-Based Analysis

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a human pathogen responsible for diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS). EHEC infection is distributed worldwide and numerous outbreaks of diseases caused by enterohemorrhagic have been reported. To promote a comprehensive insight into the molecular basis of EHEC O157:H7 physiology and pathogenesis, the combined proteome of EHEC O157:H7 strains, Clade 8 and Clade 6 isolated from cattle in Argentina, and the standard EDL933 (clade 3) strain has been analyzed. TMT (Tandem Mass Tags)-based quantitative proteomic and emPAI analyses were performed to estimate the protein abundance in EHEC proteome. 2,234 non-redundant proteins of EHEC O157:H7 were identified. A comparison of this result with in silico data of EHEC O157:H7 genome showed that approximately 40% of the predicted proteome of this pathogen were covered. According to the emPAI analysis, 85 proteins were among the most abundant (e.g. GAPDH, FliC H-antigen, Enolase, and GroEL). Tellurite resistance proteins were also highly abundant. COG analysis showed that although most of the identified proteins are related to cellular metabolism, the majority of the most abundant proteins are associated with translation processes. A KEGG enrichment analysis revealed that Glycolysis / Gluconeogenesis was the most significant pathway. On the other hand, the less abundant detected proteins are those related to DNA processes, cell respiration and prophage. Among the proteins that composed the Type III Secretion System, the most abundant protein was EspA. Altogether, the results show a subset of important proteins that contribute to physiology and pathogenicity of EHEC O157:H7.\n\nIMPORTANCEThe study of the abundance of proteins present within a complex mixture of proteins in a cell, under different conditions, can provide important information about the activities of individual protein components and protein networks that are cornerstones for the comprehension of physiological adaptations in response to biological demands promoted by environmental changes. We generated a comprehensive and accurate quantitative list of EHEC O157:H7 proteome, which provides a description of the most abundant proteins produced by this pathogen that were related to physiology and pathogenesis of EHEC. This study provides information and extends the understanding on functional genomics and the biology of this pathogen.

microbiology↗

bioRxiv2018

Entrainment of circadian rhythms depends on firing rates and neuropeptide release of VIP SCN neurons

The mammalian suprachiasmatic nucleus (SCN) functions as a master circadian pacemaker, integrating environmental input to align physiological and behavioral rhythms to local time cues. Approximately 10% of SCN neurons express vasoactive intestinal polypeptide (VIP); however, it is unknown how firing activity of VIP neurons releases VIP to entrain circadian rhythms. To identify physiologically relevant firing patterns, we optically tagged VIP neurons and characterized spontaneous firing over three days. VIP neurons had circadian rhythms in firing rate and exhibited two classes of instantaneous firing activity. We next tested whether physiologically relevant firing affected circadian rhythms through VIP release. We found that VIP neuron stimulation with high, but not low, frequencies shifted gene expression rhythms in vitro through VIP signaling. In vivo, high frequency VIP neuron activation rapidly entrained circadian locomotor rhythms. Thus, increases in VIP neuronal firing frequency release VIP and entrain molecular and behavioral circadian rhythms.\n\nHighlightsO_LIMazuski et al. identified three classes of circadian SCN neurons based on their distinct firing patterns consistent over multiple days\nC_LIO_LIThere are two distinct classes (tonic and irregular firing) of VIP SCN neurons.\nC_LIO_LIStimulation of VIP SCN neurons at physiologically relevant frequencies phase shifts whole-SCN circadian rhythms in gene expression through VIP release. These effects are blocked with VIP antagonists.\nC_LIO_LIFiring of VIP SCN neurons entrains circadian rhythms in locomotor behavior in a frequency and time-of-day dependent manner.\nC_LI

neuroscience↗

bioRxiv2018

Life history trade-offs in ectotherms impart a pseudo-hormetic response, not hormesis.

All organisms are faced with survival and fitness challenges. However, differences in how ectotherms and endotherms deal with these challenges causes confusion when theoretical explanations are proposed. Herein, an immunochallenged, immature ectothermic vertebrate increased growth in the face of immunochallenge, reminiscent of up-regulated physiological efficiency termed hormesis. The immunochallenged subjects increased food intake relative to control animals, a largely ignored possibility in previous studies. This likely led to an energy surplus that fueled additional growth. Although there was increased resource demand from the immune response that exceeded internal stores, the acceptably sized food items contained more resources than immunologically-driven demand required. We theorize that because ectotherms lack significant internally-stored resources compared to endotherms, they must feed to fuel increased physiological demand. This can lead to excess resource intake because the minimum acceptably sized prey contains more available resources than upregulation required. This creates a pseudo-hormetic hormetic response, fueled by excess food intake rather than significant improved physiological efficiency. Further, we speculate that lifespan and/or maturity may interact with resource management ectotherms, though our data are inconclusive on this matter. Ultimately, our data suggest additional growth when ectotherms face stressors is a pseudo-hormetic response stemming from increased food intake instead of upregulated physiological efficiency.

evolutionary biology↗

bioRxiv2018

Specialized mechanoreceptor systems in rodent glabrous skin

Rodents use their forepaws to actively interact with their tactile environment. Studies on the physiology and anatomy of glabrous skin that makes up the majority of the forepaw are almost non-existent in the mouse. Here we developed a preparation to record from single sensory fibers of the forepaw and compared anatomical and physiological receptor properties to those of the hind paw glabrous and hairy skin. We found that the mouse forepaw skin is equipped with a very high density of mechanoreceptors; >3 fold more than hind paw glabrous skin. In addition, rapidly adapting mechanoreceptors that innervate Meissners corpuscles of the forepaw were several-fold more sensitive to slowly moving mechanical stimuli compared to their counterparts in the hind paw glabrous skin. All other mechanoreceptors types as well as myelinated nociceptors had physiological properties that were invariant regardless of which skin area they occupied. We discovered a novel D-hair receptor innervating a small group of hairs in the middle of the hind paw glabrous skin in mice. Glabrous D-hair receptors were direction sensitive albeit with an orientation sensitivity opposite to that described for hairy skin D-hair receptors. Glabrous D-hair receptors do not occur in all rodents, but are present in North American and African rodent species that diverged more than 65 million years ago. The function of these specialized hairs is unknown, but they are nevertheless evolutionarily very ancient. Our study reveals novel physiological specializations of mechanoreceptors in the glabrous skin that likely evolved to facilitate tactile exploration.

neuroscience↗

bioRxiv2018

Systems genetic discovery of host-microbiome interactions reveals mechanisms of microbial involvement in disease

The role of the microbiome in health and disease involves complex networks of host genetics, genomics, microbes and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in the laboratory mouse enables data-driven discovery of network components and mechanisms of host-microbial interactions underlying multiple disease phenotypes. To examine the interplay among the whole host genome, transcriptome and microbiome, we mapped quantitative trait loci and correlated the abundance of cecal mRNA, luminal microflora, physiology and behavior in incipient strains of the highly diverse Collaborative Cross mouse population. The relationships that are extracted can be tested experimentally to ascribe causality among host and microbe in behavior and physiology, providing insight into disease. Application of this strategy in the Collaborative Cross population revealed experimentally validated mechanisms of microbial involvement in models of autism, inflammatory bowel disease and sleep disorder.\n\neTOC BlurbHost genetic diversity provides a variable selection environment and physiological context for microbiota and their interaction with host physiology. Using a highly diverse mouse population Bubier et al. identified a variety of host, microbe and potentially disease interactions.\n\nHighlights* 18 significant species-specific QTL regulating microbial abundance were identified\n* Cis and trans eQTL for 1,600 cecal transcripts were mapped in the Collaborative Cross\n* Sleep phenotypes were highly correlated with the abundance of B.P. Odoribacter\n* Elimination of sleep-associated microbes restored normal sleep patterns in mice.

genetics↗

bioRxiv2018

Population dynamics and transcriptomic responses of Pseudomonas aeruginosa in a complex laboratory microbial community

Pseudomonas aeruginosa is one of the dominant species when it co-exists with many other bacterial species in diverse environments. To understand its physiology and interactions with co-existing bacterial species in different conditions, we established physiologically reproducible eighteen-species communities, and found that P. aeruginosa became the dominant species in mixed-species biofilm community but not in the planktonic community. P. aeruginosa H1 type VI secretion system was highly induced in the mixed-species biofilm community compare to its mono-species biofilm, which was further demonstrated to play a key role for P. aeruginosa to gain fitness over other bacterial species. In addition, the type IV pili and Psl exopolysaccharide were shown to be required for P. aeruginosa to compete with other bacterial species in the biofilm community. Our study showed that the physiology of P. aeruginosa is strongly affected by interspecies interactions, and both biofilm determinants and H1 type VI secretion system contribute to P. aeruginosa fitness over other species in complex biofilm communities.\n\nImportancePseudomonas aeruginosa usually coexists with different bacterial species in natural environment. However, systematic comparative characterization of P. aeruginosa in complex microbial communities with its mono-species communities is lacking. We constructed mixed-species planktonic and biofilm communities consisting P. aeruginosa and seventeen other bacterial species to study the physiology and interaction of P. aeruginosa in complex multiple-species community. A single molecule detection platform, NanoString nCounter(R) 16S rRNA array, was used to shown that P. aeruginosa can become the dominant species in the biofilm communities while not in the planktonic communities. Comparative transcriptomic analysis and fluorescence-based quantification further revealed that P. aeruginosa H1 type VI secretion system and biofilm determinants are both required for its fitness in mixed-species biofilm communities.

microbiology↗

bioRxiv2018

Quantitative variations of ADF/cofilin’s multiple actions on actin filaments with pH

Actin Depolymerizing Factor (ADF)/cofilin is the main protein family promoting the disassembly of actin filaments, which is essential for numerous cellular functions. ADF/cofilin proteins disassemble actin filaments through different reactions, as they bind to their sides, sever them, and promote the depolymerization of the resulting ADF/cofilin-saturated filaments. Moreover, the efficiency of ADF/cofilin is known to be very sensitive to pH. ADF/cofilin thus illustrates two challenges in actin biochemistry: separating the different regulatory actions of a single protein, and characterizing them as a function of specific biochemical conditions. Here, we investigate the different reactions of ADF/cofilin on actin filaments, over four different values of pH ranging from pH 6.6 to pH 7.8, using single filament microfluidics techniques. We show that lowering pH reduces the effective filament severing rate by increasing the rate at which filaments become saturated by ADF/cofilin, thereby reducing the number of ADF/cofilin domain boundaries, where severing can occur. The severing rate per domain boundary, however, remains unchanged at different pH values. The ADF/cofilin-decorated filaments (refered to as \"cofilactin\" filaments) depolymerize from both ends. We show here that, at physiological pH (pH 7.0 to 7.4), the pointed end depolymerization of cofilactin filaments is barely faster than that of bare filaments. In contrast, cofilactin barbed ends undergo an \"unstoppable\" depolymerization (depolymerizing for minutes despite the presence of free actin monomers and capping protein in solution), throughout our range of pH. We thus show that, at physiological pH, the main contribution of ADF/cofilin to filament depolymerization is at the barbed end.\n\nA number of key cellular processes rely on the proper assembly and disassembly of actin filament networks 1. The central regulator of actin disassembly is the ADF/cofilin protein family 2, 3, which comprises three isoforms in mammals: cofilin-1 (cof1, found in nearly all cell types), cofilin-2 (cof2, found primarily in muscles) and Actin Depolymerization Factor (ADF, found mostly in neurons and epithelial cells). We refer to them collectively as \"ADF/cofilin\".\n\nOver the years, the combined efforts of several labs have led to the following understanding of actin filament disassembly by ADF/cofilin. Molecules of ADF/cofilin bind stoechiometrically 4, 5 to the sides of actin filaments, with a strong preference for ADP-actin subunits 6-10. Though ADF/cofilin molecules do not contact each other 11, they bind in a cooperative manner, leading to the formation of ADF/cofilin domains on the filaments 5, 7, 9, 12, 13. Compared to bare F-actin, the filament portions decorated by ADF/cofilin (refered to as \"cofilactin\") are more flexible 14, 15 and exhibit a shorter right-handed helical pitch, with a different subunit conformation 11, 16-19. Thermal fluctuations are then enough to sever actin filaments at (or near) domain boundaries8, 9, 13, 20, 21. Cofilactin filaments do not sever, but depolymerize from both ends 13 thereby renewing the actin monomer pool.\n\nADF/cofilin thus disassembles actin filaments through the combination of different actions. As such, it vividly illustrates a current challenge in actin biochemistry: identifying and quantifying the multiple reactions involving a single protein. This is a very difficult task for bulk solution assays, where a large number of reactions take place simultaneously, and single-filament techniques have played a key role in deciphering ADF/cofilins actions 9, 13, 20, 22-24. In particular, the microfluidics-based method that we have developed over the past years, is a powerful tool for such investigations 25. It has recently allowed us to quantify the kinetics of the aforementioned reactions, and to discover that ADF/cofilin-saturated filament (cofilactin) barbed ends can hardly stop depolymerizing, even when ATP-G-actin and capping protein are present in solution 13.\n\nIn addition, ADF/cofilin is very sensitive to pH 4, 5, 26-29. In cells, pH can be a key regulatory factor 30. It can vary between compartments, between cell types, and be specifically modulated. We can consider that a typical cytoplasmic pH would be comprised between 7.0 and 7.4. Recently, we have quantified the different reactions involving ADF/cofilin at pH 7.8 13, leaving open the question of how these reaction rates are indivdually affected by pH variations. For instance, it has been reported that ADF/cofilin is a more potent filament disassembler at higher pH values 4, 5, 26-29 but the actual impact of pH on the rate constants of individual reactions has yet to be characterized. Moreover, whether the unstoppable barbed end depolymerization that we have recently discovered for ADF/cofilin-saturated filaments at pH 7.8 13 remains significant at lower, more physiological pH values is an open question.\n\nHere, we investigate how the different contributions of ADF/cofilin (using unlabeled ADF, unlabeled cof1 and eGFP-cof1) to actin filament disassembly depend on pH, which we varied from 6.6 to 7.8. We first present the methods which we have used to do so, based on the observation of individual filaments, using microfluidics (Fig. 1). We measured cofilins abitility to decorate actin filament by binding to its sides (Fig. 2), and the rate at which individual cofilin domains severed actin filaments (Fig. 3). We next quantified the kinetic parameters of filament ends, for bare and ADF/cofilin-saturated (cofilactin) filaments (Fig. 4), and we specifically quantified the extent to which the barbed ends of cofilactin filaments are in a state which can hardly stop depolymerizing (Fig. 5). We finally summarize our results (Fig. 6).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC=\"FIGDIR/small/422824_fig1.gif\" ALT=\"Figure 1\">\nView larger version (38K):\norg.highwire.dtl.DTLVardef@5a6fdorg.highwire.dtl.DTLVardef@1165d4borg.highwire.dtl.DTLVardef@146f0b7org.highwire.dtl.DTLVardef@658f72_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Using microfluidics to monitor individual actin filaments and the binding of cofilin. (A) Experiments are performed in microfluidic chambers, sketched from above. The main channel is connected through three inlets to different protein solutions. Controlling the pressure in each inlet allows one to rapidly change the solution in the field of view.\n\n(B) Sketch of a typical experiment (side view). Filaments are elongated from coverslip-anchored spectrin-actin seeds, by flowing in with ATP-G-actin. Filaments are then aged by flowing in a solution of ATP-G-actin at the critical concentration, for at least 15 min. This results in >99% of the monomers in the ADP-state. Finally, filaments are exposed to ADF/cofilin.\n\n(C) Example of a field of view, imaged with TIRFm. ADP-F-actin labelled with Alexa-488 is exposed to mCherry-cofilin-1, which forms observable domains on the filaments.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC=\"FIGDIR/small/422824_fig2.gif\" ALT=\"Figure 2\">\nView larger version (47K):\norg.highwire.dtl.DTLVardef@1aca24borg.highwire.dtl.DTLVardef@d2f404org.highwire.dtl.DTLVardef@1924892org.highwire.dtl.DTLVardef@daaaac_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Cofilin binds more slowly to filaments at higher pH values. (A). Experimental configuration. Actin filaments are grown from spectrin-actin seeds with a long middle segment of unlabelled ADP-actin.\n\n(B). Time-lapse showing an unlabeled ADP-actin filament become saturated by eGFP-cof1 over time.\n\n(C-D). Mean normalized eGFP-cofilin-1 fluorescence signal, binding onto unlabelled ADP-F-actin. 150 nM (C) and 400 nM (D) eGFP-cofilin-1 was injected in the chamber from time t=0 onwards. The fluorescence signal was averaged along 20 to 35 pixels (3.5 to 6 {micro}m) for each filment. Number of filaments (C) N = 10, 10, 18, 20, for pH 6.6 Hepes, 7.0 Hepes, 7.0 Tris and 7.4 Tris, respectively, and\n\n(D) N = 10 in all conditions.\n\n(E). Number of cofilin subunits in individual domains, increasing over time. For clarity, the time origin has been shifted for each curve. Lines: linear fit. Condition: 400 nM eGFP-cofilin-1, pH 7.0 Hepes.\n\n(F). Growth rate of individual cofilin domains at different eGFP-cofilin-1 concentrations and pH. Value: median, error bars: interquartile range. N = 10 domains, except N = 9 for pH 6.6 Hepes 150 nM cof1, and for pH 7.8 Tris 400 nM cof1.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=41 SRC=\"FIGDIR/small/422824_fig3.gif\" ALT=\"Figure 3\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@1fb31d4org.highwire.dtl.DTLVardef@846198org.highwire.dtl.DTLVardef@12379d0org.highwire.dtl.DTLVardef@127b96_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO The severing rate per cofilin domain is unaffected by pH. (A). Experimental setup. Alexa-568-labelled actin filaments are polymerized from actin-spectrin seeds, and aged before being exposed to eGFP-cof1.\n\n(B). Typical kymograph. 200 nM eGFP-cof1 (green) is constantly injected, binds F-actin (red) and induces severing (lightning symbols).\n\n(C). Fraction of cofilin domains with no severing event detected near their edges, over time. Time t=0 is defined for each domain as the last frame before they become visible. The survival fraction curves are calculated using the Kaplan-Meier method over 22 to 43 filaments, 78 to 90 cofilin domains and 30 to 33 severing events, for each data set.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC=\"FIGDIR/small/422824_fig4.gif\" ALT=\"Figure 4\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@16fdad8org.highwire.dtl.DTLVardef@889caborg.highwire.dtl.DTLVardef@e5b14aorg.highwire.dtl.DTLVardef@1da73c9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Higher pH slows down polymerization and depolymerization of bare F-actin but accelerates depolymerization of ADF/cofilin-saturated filaments at both ends. (A-C) Polymerization from the barbed-end.\n\n(A) Sketch of the experimental configuration, where filaments were grown from actin-spectrin seeds with G-ATP-actin and profilin.\n\n(B) Kymograph of a typical elongating filament.\n\n(C) Polymerization rate at different pH. N = 20 filaments for each condition.\n\n(D-E) Depolymerization from the barbed-end.\n\n(D) Sketch of the experimental configuration. ADP-F-actin is exposed either to buffer only, or to 1-2{micro}M unlabelled ADF or cofilin-1 in order to fully saturate the filament in less than a minute.\n\n(E) Depolymerization rate for different pH values. Right: zoom into the 0-5 sub/s range. From left to right, N = 20, 32, 22, 32, 31 (buffer only); N=9, 14, 23, 33, 34 (ADF-saturated); N=17, 18, 16 (cofilin-1-saturated).\n\n(F-H) Depolymerization from the pointed-end.\n\n(F) Sketch of the experimental configuration. ADP-F-actin was bound to the surface by gelsolin. Filaments were exposed to buffer only (supplemented with 0.4 mM CaCl2 to ensure gelsolin-actin tight binding), containing 1 to 2 {micro}M unlabelled ADF or cofilin-1 to rapidly saturate filaments.\n\n(G) Typical kymograph of a depolymerizing filament saturated with ADF.\n\n(H) Pointed-end depolymerization rate at different pH. N = 14, 20, 15, 20, 20 (buffer); N=20, 20, 16, 20, 20 (ADF-saturated); N= 20, 20, 20 (cofilin-1-saturated).\n\n(C, E, H) Symbol: median, error bars: interquartile range.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC=\"FIGDIR/small/422824_fig5.gif\" ALT=\"Figure 5\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@e79318org.highwire.dtl.DTLVardef@16a4bb1org.highwire.dtl.DTLVardef@18f8fbdorg.highwire.dtl.DTLVardef@25dab6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 5.C_FLOATNO The \"unstoppable\" depolymerization of cofilactin barbed ends is observed throughout our pH range. (A-C) Synergy of CP and ADF/cofilin to saturate filaments and initiate barbed end depolymerization.\n\n(A) Sketch of experimental configuration and events. Filaments grow until they are capped with CP. ADF/cofilin can then saturate the filaments, up to their BE which thus uncaps and depolymerizes.\n\n(B) Kymograph of a filament continuously exposed to the same solution containing 0.8 {micro}M G-ATP-actin, 1 {micro}M ADF and 2 nM CP. The filament polymerizes, pauses as it is capped by CP, and eventually depolymerizes.\n\n(C) Fraction of barbed ends that transitioned from a pause to depolymerization. Time t = 0 corresponds to the beginning of the pause (as shown on B). N = 24, 32, 32 filaments for pH 7.0 Hepes, pH 7.0 Tris, pH 7.4 Tris, respectively.\n\n(D-F) Cofilactin barbed ends sustain depolymerization in the presence of ATP-G-actin.\n\n(D) Sketch of the experimental configuration and events. Filaments are polymerized from spectrin-actin seeds and saturated with ADF. Depolymerizing cofilactin filaments are then constantly exposed to a solution of ATP-G-actin.\n\n(E) Fraction of barbed ends that transitioned from depolymerization to polymerization over time, when exposed to 1 {micro}M ATP-G-actin and 0.5 {micro}M ADF (to keep filaments saturated). N = 25, 16, 25, 24, 31 for pH 6.6 Hepes, 7.0 Hepes, 7.0 Tris, 7.4 Tris, 7.8 Tris, respectively.\n\n(F) Same as (E), with 1 {micro}M profilin added to the solution. N= 21, 27, 30 for pH 6.6 Hepes, 7.4 Tris, 7.8 Tris, respectively.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC=\"FIGDIR/small/422824_fig6.gif\" ALT=\"Figure 6\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@13a07bborg.highwire.dtl.DTLVardef@d19d2forg.highwire.dtl.DTLVardef@1a697daorg.highwire.dtl.DTLVardef@3b9d59_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO Summary of results: barbed end depolymerization is an important contribution of cofilin disassembly at physiological pH. Within the range of pH that we have explored (pH 6.6 to 7.8) we have made the following observations (from top to bottom, on this sketch). A lower pH favors the rapid decoration of filaments by ADF/cofilin, but the severing rate per cofilin domain does not vary with pH. As a consequence, at a higher pH, domain boundaries persist longer (before domains merge) and severing is more efficient. The acceleration of pointed end depolymerization for cofilactin filaments is mostly observed at high pH. The \"unstoppable\" depolymerization of cofilactin barbed ends is observed at all pH, and is more pronounced at lower pH values.\n\nC_FIG

biochemistry↗

bioRxiv2026

Predictability failure in glucose-insulin system for ICU patients

Modern medicine implicitly assumes that physiological responses to intervention are predictably determined by administered treatments. However, physiological systems containing intrinsic delays between the detection of a stimulus and the biological response may violate this assumption. We investigate the human glucose-insulin system as described by the Ultradian model and mathematically demonstrate that clinically relevant forcing protocols-such as pulsatile insulin delivery and step-wise glucose infusion, both commonly used in intensive care units (ICUs)-can induce sustained temporal chaos that may hamper accurate prediction of the physiological response. If not accounted for, these chaotic dynamics could create difficulties in achieving optimal dosing and timing when administering glucose and insulin in clinical or home care settings. This phenomenon, termed delay-induced uncertainty (DIU), arises from the interaction between physiological delay, intrinsic shear near a limit cycle, and external forcing. Using the Ultradian glucose-insulin model, we compute top Lyapunov exponents to quantify predictability. Across a range of pulsatile and step-wise forcing regimes, including stochastic amplitudes drawn from Markov processes, we observe positive Lyapunov exponents, indicating sustained chaos. Our results suggest that delayed endocrine regulation may fundamentally limit the predictive value of the models used to develop glycemic management strategies, with implications for clinical protocols in the ICU.

systems biology↗

bioRxiv2015

Two phases of aging separated by the Smurf transition as a public path to death

Agings most obvious characteristic is the time dependent increase of an individuals probability to die. This lifelong process is accompanied by a large number of molecular and physiological changes. Although numerous genes involved in aging have been identified in the past decades its leading factors have yet to be determined. To identify the very processes driving aging we have developed in the past years an assay to identify physiologically old individuals in a synchronized population of Drosophila melanogaster. Those individuals show an age-dependent increase of intestinal permeability followed by a high risk of death. Here we show that this physiological marker of aging is conserved in 3 invertebrate species Drosophila mojavensis, Drosophila virilis, Caenorhabditis elegans and 1 vertebrate specie Danio rerio. Our findings suggest that intestinal barrier dysfunction may be an important event in the aging process conserved across a broad range of species, thus raising the possibility that it may also be the case in Homo sapiens.

Physiology↗

bioRxiv2017

Transcriptomes of major renal collecting-duct cell types in mouse identified by single-cell RNA-Seq

Prior RNA sequencing (RNA-Seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical physiological roles in the regulation of blood pressure, extracellular fluid volume and extracellular fluid composition. To enrich these cell types, we used fluorescence-activated cell sorting (FACS) that employed well established lectin cell surface markers for PCs and type B ICs, as well as a newly identified cell surface marker for type A ICs, viz. c-Kit. Single-cell RNA-Seq using the 1C- and PC-enriched populations as input enabled identification of complete transcriptomes of A-ICs, B-ICs and PCs. The data were used to create a freely-accessible online gene-expression database for collecting duct cells. This database allowed identification of genes that are selectively expressed in each cell type including cell-surface receptors, transcription factors, transporters and secreted proteins. The analysis also identified a small fraction of hybrid cells expressing both aquapor{inverted exclamation}n-2 and either anion exchanger 1 or pendrin transcripts. In many cases, mRNAs for receptors and their ligands were identified in different cells (e.g. Notch2 chiefly in PCs vs Jag1 chiefly in ICs) suggesting signaling crosstalk among the three cell types. The identified patterns of gene expression among the three types of collecting duct cells provide a foundation for understanding physiological regulation and pathophysiology in the renal collecting duct.\n\nSIGNIFICANCE STATEMENTA long-term goal in mammalian biology is to identify the genes expressed in every cell type of the body. In kidney, the expressed genes (\"transcriptome\") of all epithelial cell types have already been identified with the exception of the cells that make up the renal collecting duct, responsible for regulation of blood pressure and body fluid composition. Here, a technique called \"single-cell RNA-Seq\" was used in mouse to identify transcriptomes for the major collecting-duct cell types: type A intercalated cells, type B intercalated cells and principal cells. The information was used to create a publicly-accessible online resource. The data allowed identification of genes that are selectively expressed in each cell type, informative for cell-level understanding of physiology and pathophysiology.

physiology↗

bioRxiv2014

Spatial variation in water loss predicts terrestrial salamander distribution and population dynamics

Many patterns observed in ecology, such as species richness, life history variation, habitat use, and distribution have physiological underpinnings. For many ectothermic organisms temperature relations shape these patterns, but for terrestrial amphibians, water balance may supersede temperature as the most critical physiologically-limiting factor. Many amphibian species have little resistance to water loss, which restricts them to moist microhabitats and may significantly affect foraging, dispersal, and courtship. Using plaster models as surrogates for terrestrial plethodontid salamanders, we measured water loss under ecologically-relevant field conditions to estimate the duration of surface activity time across the landscape. Surface activity time was significantly affected by topography, solar exposure, canopy cover, maximum air temperature, and time since rain. Spatially, surface activity times were highest in ravine habitats and lowest on ridges. Surface activity time was a significant predictor of salamander abundance, as well as a predictor of successful recruitment; the probability of a juvenile salamander occupying an area with high surface activity time was two times greater than an area with limited predicted surface activity. Our results suggest that survival, recruitment, or both are demographic processes that are affected by water loss and the ability of salamanders to be surface active. Results from our study extend our understanding of plethodontid salamander ecology, emphasize the limitations imposed by their unique physiology, and highlight the importance of water loss to spatial population dynamics. These findings are timely to understanding the effects that fluctuating temperature and moisture conditions predicted for future climates will have on plethodontid salamanders.

Ecology↗

bioRxiv2014

Collecting reward to defend homeostasis: A homeostatic reinforcement learning theory

Efficient regulation of internal homeostasis and defending it against perturbations requires complex behavioral strategies. However, the computational principles mediating brains homeostatic regulation of reward and associative learning remain undefined. Here we use a definition of primary rewards, as outcomes fulfilling physiological needs, to build a normative theory showing how learning motivated behavior is modulated by the internal state of the animal. The theory proves that seeking rewards is equivalent to the fundamental objective of physiological stability, defining the notion of physiological rationality of behavior. We further give a formal basis for temporal discounting of reward. It also explains how animals learn to act predictively to preclude prospective homeostatic challenges, and attributes a normative computational role to the modulation of midbrain dopaminergic activity by hypothalamic signals.

Neuroscience↗

bioRxiv2016

Construction and Experimental Validation of a Petri net Model of Wnt/β-catenin Signaling

The Wnt/{beta}-catenin signaling pathway is important for multiple developmental processes and tissue maintenance in adults. Consequently, deregulated signaling is involved in a range of human diseases including cancer and developmental defects. A better understanding of the intricate regulatory mechanism and effect of physiological (active) and pathophysiological (hyperactive) WNT signaling is important for predicting treatment response and developing novel therapies. The constitutively expressed CTNNB1 (commonly and hereafter referred to as {beta}-catenin) is degraded by a destruction complex, composed of amongst other AXIN1 and GSK3. The destruction complex is inhibited during active signaling leading to {beta}-catenin stabilization and induction of {beta}-catenin/TCF target genes. In this study we investigated the mechanism and effect of {beta}-catenin stabilization during active and hyperactive WNT signaling in a combined in silico and in vitro approach. We constructed a Petri net model of Wnt/{beta}-catenin signaling including main players from the plasma membrane (WNT ligands and receptors), cytoplasmic effectors and the downstream negative feedback target gene AXIN2. We simulated the model with active (i.e. WNT stimulation) and hyperactive (i.e. GSK3 inhibition) signaling, which led to the following observations: 1) A dose- and time-dependent response was observed for both WNT stimulation and GSK3 inhibition. 2) The Wnt-pathway activity was 2-fold higher for GSK3 inhibition compared to WNT stimulation. Both of these observations were corroborated by TCF/LEF luciferase reporter assays. Using this experimentally validated model we simulated the effect of the negative feedback regulator AXIN2 upon WNT stimulation and observed an attenuated {beta}-catenin stabilization. We furthermore simulated the effect of APC inactivating mutations, yielding a stabilization of {beta}-catenin levels comparable to the Wnt-pathway activities observed in colorectal and breast cancer. Our model can be used for further investigation and viable predictions of the role of Wnt/{beta}-catenin signaling in oncogenesis and development.\n\nAuthor SummaryDeregulated Wnt/{beta}-catenin signaling is implicated in cancer and developmental defects. In this study we combined in silico and in vitro efforts to investigate the behavior of physiological and pathophysiological WNT signaling. We created a model of Wnt/{beta}-catenin signaling that describes the core interactions: receptor activation, inhibition of downstream effectors and an important negative feedback mechanism. Simulations with the model demonstrated the expected dose- and time-dependent response for both conditions, and the Wnt-pathway activity was significantly higher for pathophysiological compared to physiological signaling. These observations were experimentally validated, which allowed us to investigate and predict the effect of the negative feedback and an inactivating cancer mutation on the Wnt-pathway activity. Our model provides mechanistic insight on the different conditions and can easily be extended and used to answer other questions on Wnt/{beta}-catenin signaling in the area of cancer research and regenerative medicine.

Bioinformatics↗

bioRxiv2016

Characterization of a Male Reproductive Transcriptome for Peromyscus eremicus (Cactus mouse)

AbstractRodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology and behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. However, well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. This study characterizes a reproductive transcriptome of male Peromyscus eremicus (Cactus mouse), a desert specialist with extreme physiological adaptations to water limitation. We describe a reproductive transcriptome comprising three tissues in order to expand upon existing research in this species and to facilitate further studies elucidating the genetic basis of potential desert adaptations in male reproductive physiology.

Genomics↗