Spring migration patterns of red knots in the Southeast United States disentangled using automated telemetry.

Red Knots use the Southeast United States as a stopover during north and southbound migration and during the winter. We examined northbound red knot migration routes and timing using an automated telemetry network. Our primary goal was to evaluate the relative use of an Atlantic migratory route through Delaware Bay versus an inland route through the Great Lakes en route to Arctic breeding grounds and to identify areas of apparent stopovers. Secondarily, we explored the association of red knot routes and ground speeds with prevailing atmospheric conditions. Most Red Knots migrating north from the Southeast United States skipped or likely skipped Delaware Bay (73%) while 27% of the knots stopped in Delaware Bay for at least 1 day. A few knots used an Atlantic Coast strategy that did not include Delaware Bay, relying instead on the areas around Chesapeake Bay or New York Bay for stopovers. Nearly 80% of migratory trajectories were associated with tailwinds at departure. Most knots tracked in our study traveled north through the eastern Great Lake Basin, without stopping, thus making the Southeast United States the last terminal stopover for some knots before reaching boreal or Arctic stopover sites.

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria.

Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.

Time resolved detection of the S(1D) product of the UV induced dissociation of CS2.

The products formed following the photodissociation of UV (200 nm) excited CS2 are monitored in a time resolved photoelectron spectroscopy experiment using femtosecond XUV (21.5 eV) photons. By spectrally resolving the electrons, we identify separate photoelectron bands related to the CS2 + hν → S(1D) + CS and CS2 + hν → S(3P) + CS dissociation channels, which show different appearance and rise times. The measurements show that there is no delay in the appearance of the S(1D) product contrary to the results of Horio et al. [J. Chem. Phys. 147, 013932 (2017)]. Analysis of the photoelectron yield associated with the atomic products allows us to obtain a S(3P)/S(1D) branching ratio and the rate constants associated with dissociation and intersystem crossing rather than the effective lifetime observed through the measurement of excited state populations alone.

Protamine loops DNA in multiple steps.

Protamine proteins dramatically condense DNA in sperm to almost crystalline packing levels. Here, we measure the first step in the in vitro pathway, the folding of DNA into a single loop. Current models for DNA loop formation are one-step, all-or-nothing models with a looped state and an unlooped state. However, when we use a Tethered Particle Motion (TPM) assay to measure the dynamic, real-time looping of DNA by protamine, we observe the presence of multiple folded states that are long-lived (∼100 s) and reversible. In addition, we measure folding on DNA molecules that are too short to form loops. This suggests that protamine is using a multi-step process to loop the DNA rather than a one-step process. To visualize the DNA structures, we used an Atomic Force Microscopy (AFM) assay. We see that some folded DNA molecules are loops with a ∼10-nm radius and some of the folded molecules are partial loops-c-shapes or s-shapes-that have a radius of curvature of ∼10 nm. Further analysis of these structures suggest that protamine is bending the DNA to achieve this curvature rather than increasing the flexibility of the DNA. We therefore conclude that protamine loops DNA in multiple steps, bending it into a loop.

Femtosecond Soft-X-ray Absorption Spectroscopy of Liquids with a Water-Window High-Harmonic Source.

Femtosecond X-ray absorption spectroscopy (XAS) is a powerful method to investigate the dynamical behavior of a system after photoabsorption in real time. So far, the application of this technique has remained limited to large-scale facilities, such as femtosliced synchrotrons and free-electron lasers (FEL). In this work, we demonstrate femtosecond time-resolved soft-X-ray absorption spectroscopy of liquid samples by combining a sub-micrometer-thin flat liquid jet with a high-harmonic tabletop source covering the entire water-window range (284-538 eV). Our work represents the first extension of tabletop XAS to the oxygen edge of a chemical sample in the liquid phase. In the time domain, our measurements resolve the gradual appearance of absorption features below the carbon K-edge of ethanol and methanol during strong-field ionization and trace the valence-shell ionization dynamics of the liquid alcohols with a temporal resolution of ∼30 fs. This technique opens unique opportunities to study molecular dynamics of chemical systems in the liquid phase with elemental, orbital, and site sensitivity.

Single cell fluorescence imaging of glycan uptake by intestinal bacteria.

Microbes in the intestines of mammals degrade dietary glycans for energy and growth. The pathways required for polysaccharide utilization are functionally diverse; moreover, they are unequally dispersed between bacterial genomes. Hence, assigning metabolic phenotypes to genotypes remains a challenge in microbiome research. Here we demonstrate that glycan uptake in gut bacteria can be visualized with fluorescent glycan conjugates (FGCs) using epifluorescence microscopy. Yeast α-mannan and rhamnogalacturonan-II, two structurally distinct glycans from the cell walls of yeast and plants, respectively, were fluorescently labeled and fed to Bacteroides thetaiotaomicron VPI-5482. Wild-type cells rapidly consumed the FGCs and became fluorescent; whereas, strains that had deleted pathways for glycan degradation and transport were non-fluorescent. Uptake of FGCs, therefore, is direct evidence of genetic function and provides a direct method to assess specific glycan metabolism in intestinal bacteria at the single cell level.

Mapping the Complete Reaction Path of a Complex Photochemical Reaction.

We probe the dynamics of dissociating CS_{2} molecules across the entire reaction pathway upon excitation. Photoelectron spectroscopy measurements using laboratory-generated femtosecond extreme ultraviolet pulses monitor the competing dissociation, internal conversion, and intersystem crossing dynamics. Dissociation occurs either in the initially excited singlet manifold or, via intersystem crossing, in the triplet manifold. Both product channels are monitored and show that, despite being more rapid, the singlet dissociation is the minor product and that triplet state products dominate the final yield. We explain this by a consideration of accurate potential energy curves for both the singlet and triplet states. We propose that rapid internal conversion stabilizes the singlet population dynamically, allowing for singlet-triplet relaxation via intersystem crossing and the efficient formation of spin-forbidden dissociation products on longer timescales. The study demonstrates the importance of measuring the full reaction pathway for defining accurate reaction mechanisms.

The ADAMTS5 Metzincin Regulates Zebrafish Somite Differentiation.

The ADAMTS5 metzincin, a secreted zinc-dependent metalloproteinase, modulates the extracellular matrix (ECM) during limb morphogenesis and other developmental processes. Here, the role of ADAMTS5 was investigated by knockdown of zebrafish adamts5 during embryogenesis. This revealed impaired Sonic Hedgehog (Shh) signaling during somite patterning and early myogenesis. Notably, synergistic regulation of myod expression by ADAMTS5 and Shh during somite differentiation was observed. These roles were not dependent upon the catalytic activity of ADAMTS5. These data identify a non-enzymatic function for ADAMTS5 in regulating an important cell signaling pathway that impacts on muscle development, with implications for musculoskeletal diseases in which ADAMTS5 and Shh have been associated.

Resonant multiphoton ionisation probe of the photodissociation dynamics of ammonia.

The dissociation dynamics of the Ã-state of ammonia have been studied using a resonant multiphoton ionisation probe in a photoelectron spectroscopy experiment. The use of a resonant intermediate in the multiphoton ionisation process changes the ionisation propensity, allowing access to different ion states when compared with equivalent single photon ionisation experiments. Ionisation through the E' 1A1' Rydberg intermediate means we maintain overlap with the ion state for an extended period, allowing us to monitor the excited state population for several hundred femtoseconds. The vibrational states in the photoelectron spectrum show two distinct timescales, 200 fs and 320 fs, that we assign to the non-adiabatic and adiabatic dissociation processes respectively. The different timescales derive from differences in the wavepacket trajectories for the two dissociation pathways that resonantly excite different vibrational states in the intermediate Rydberg state. The timescales are similar to those obtained from time resolved ion kinetic energy release measurements, suggesting we can measure the different trajectories taken out to the region of conical intersection.

Two seconds is all it takes: European starlings (Sturnus vulgaris) increase levels of circulating glucocorticoids after witnessing a brief raptor attack.

Researchers typically study "acute" activation of the hypothalamic-pituitary-adrenal (HPA) axis by measuring levels of circulating glucocorticoids in animals that have been exposed to a predator or a cue from a predator (e.g., odor), or have experienced a standardized capture-and-restraint protocol, all of which are many minutes in duration. However, exposure to predators in the "wild", either as the subject of an attack or as a witness to an attack, is generally much shorter as most depredation attempts upon free-living animals last <5s. Yet, whether a stimulus lasting only seconds can activate the HPA axis is unknown. To determine if a stimulus of a few seconds triggers a glucocorticoid response, we measured levels of corticosterone (CORT; the primary avian glucocorticoid) in wild-caught European starlings (Sturnus vulgaris) after they witnessed a brief (<2-8s) raptor attack upon a conspecific, a human "attack" (i.e., a researcher handling a conspecific), and an undisturbed control. Witnesses of a raptor attack responded with CORT levels comparable to that induced by a standardized capture-and-restraint protocol. Glucocorticoid levels of individuals following the control treatment were similar to baseline levels, and those that witnessed a human "attack" had intermediate levels. Our results demonstrate that witnessing a predator attack of very brief duration triggers a profound adrenocortical stress response. Given the considerable evidence of a role for glucocorticoids in learning and memory, such a response may affect how individuals learn to recognize and appropriately react to predators.

Two nights of sleep deprivation with or without energy restriction does not impair the thermal response to cold.

PURPOSE: In persons completing exhaustive daily exercise, sleep and energy restriction have been highlighted as risk factors for hypothermia in cold environments. The present study therefore sought to determine the effect of sleep deprivation (SDEP), with and without energy restriction, on the thermal response to cold. METHODS: In a random order, ten recreationally active men (mean ± SD: age 25 ± 6 years, body fat 17 ± 5 %) completed three 53 h trials: a control (CON: 436 min/night sleep), SDEP (0 min sleep), and sleep deprivation and energy restriction (SDEP + ER: 0 min sleep and 10% daily energy requirements). Exhaustive exercise was completed after 5 and 29 h. After 53 h participants completed a semi-nude seated cold air test (CAT, 0 °C), for 4 h or until rectal core temperature (T re) reached 36 °C. RESULTS: Two nights of sleep and energy restriction did not impair the thermal response to cold (T re, CON 36.15 ± 0.20 °C, SDEP 36.30 ± 0.15 °C, SDEP + ER 36.25 ± 0.20 °C, P = 0.25). Rewarming was also similar as indicated by 1 h post-CAT T re (P = 0.78). In contrast, perceived thermal discomfort during the initial hour of the CAT tended to be greater after SDEP and SDEP + ER (P ≤ 0.1). CONCLUSION: Sleep and energy restriction, at least as evaluated within this experiment, should be considered minimal risk factors for hypothermia. The greater perception of cold discomfort at the same body temperature suggests that sleep and energy restriction may actually reduce cold injury risk, as people are likely to engage earlier in normal behavioral cold adaptation.

The evolutionary conservation of the A Disintegrin-like and Metalloproteinase domain with Thrombospondin-1 motif metzincins across vertebrate species and their expression in teleost zebrafish.

BACKGROUND: The A Disintegrin-like and Metalloproteinase domain with Thrombospondin-1 motifs (ADAMTS) enzymes comprise 19 mammalian zinc-dependent metalloproteinases (metzincins) with homologues in a wide range of invertebrates. ADAMTS enzymes have a broad range of functions in development and diseases due to their extracellular matrix remodelling activity. Here, we report a detailed characterisation of their evolutionary conservation across vertebrates. RESULTS: Using bioinformatics complemented with de novo sequencing, gene sequences for ADAMTS enzymes were obtained from a variety of organisms. Detailed evolutionary analyses revealed a high level of conservation across vertebrates with evidence of ADAMTS gene expansion during two rounds of whole genome duplication (WGD) in vertebrates, while tandem duplication events and gene loss were also apparent. However, the additional round of teleost-specific WGD did not have a significant effect on ADAMTS gene family members suggesting their conserved roles have remained constant in teleost fish. Quantitative reverse-transcriptase polymerase chain reaction analysis revealed dynamic expression of adamts genes throughout zebrafish embryonic development reflecting the key conserved roles they play in vertebrate embryogenesis. Notably, several adamts mRNAs were maternally expressed with a dramatic increase in mRNA levels coinciding with zygotic expression and organogenesis. Broad adamts mRNA expression was also demonstrated in several adult organs indicating potential roles in adult homeostasis. CONCLUSIONS: Our data highlight the evolution of the ADAMTS gene family through duplication processes across metazoans supplemented by a burst of amplification through vertebrate WGD events. It also strongly posits the zebrafish as a potential model species to further elucidate the function of ADAMTS enzymes during vertebrate development.

Using nocturnal flight calls to assess the fall migration of warblers and sparrows along a coastal ecological barrier.

Atmospheric conditions fundamentally influence the timing, intensity, energetics, and geography of avian migration. While radar is typically used to infer the influence of weather on the magnitude and spatiotemporal patterns of nocturnal bird migration, monitoring the flight calls produced by many bird species during nocturnal migration represents an alternative methodology and provides information regarding the species composition of nocturnal migration. We used nocturnal flight call (NFC) recordings of at least 22 migratory songbirds (14 warbler and 8 sparrow species) during fall migration from eight sites along the mainland and island coasts of Rhode Island to evaluate five hypotheses regarding NFC detections. Patterns of warbler and sparrow NFC detections largely supported our expectations in that (1) NFC detections associated positively and strongly with wind conditions that influence the intensity of coastal bird migration and negatively with regional precipitation; (2) NFCs increased during conditions with reduced visibility (e.g., high cloud cover); (3) NFCs decreased with higher wind speeds, presumably due mostly to increased ambient noise; and (4) coastal mainland sites recorded five to nine times more NFCs, on average, than coastal nearshore or offshore island sites. However, we found little evidence that (5) nightly or intra-night patterns of NFCs reflected the well-documented latitudinal patterns of migrant abundance on an offshore island. Despite some potential complications in inferring migration intensity and species composition from NFC data, the acoustic monitoring of NFCs provides a viable and complementary methodology for exploring the spatiotemporal patterns of songbird migration as well as evaluating the atmospheric conditions that shape these patterns.

Fruit removal rate depends on neighborhood fruit density, frugivore abundance, and spatial context.

Fleshy-fruited plants depend fundamentally on interactions with frugivores for effective seed dispersal. Recent models of frugivory within spatially explicit networks make two general predictions regarding these interactions: rate of fruit removal increases (i.e., is facilitated) as densities of conspecific neighborhood fruits increase, and fruit removal rate varies positively with frugivore abundance. We conducted a field experiment that constitutes the first empirical and simultaneous test of these two primary predictions. We manipulated neighborhood abundances of arrowwood (Viburnum recognitum and Viburnum dentatum) fruits in southern New England's maritime shrub community and monitored removal rates by autumn-migrating birds. Focal arrowwood plants in neighborhoods with high conspecific fruit density sustained moderately decreased fruit removal rates (i.e., competition) relative to those in low-density neighborhoods, a result that agrees with most field research to date but contrasts with theoretical expectation. We suggest the spatial contexts that favor competition (i.e., high-abundance neighborhoods and highly aggregated landscapes) are considerably more common than the relatively uniform, low-aggregation fruiting landscapes that promote facilitation. Patterns of arrowwood removal by avian frugivores generally varied positively with, and apparently in response to, seasonal changes in migratory frugivore abundance. However, we suggest that dense stands of arrowwood concentrated frugivore activity at the neighborhood scale, thus counteracting geographic patterns of frugivore abundance. Our results underscore the importance of considering spatial context (e.g., fruit distribution and aggregation, frugivory hubs) in plant-avian frugivore interactions.

Biosynthesis and expression of a disintegrin-like and metalloproteinase domain with thrombospondin-1 repeats-15: a novel versican-cleaving proteoglycanase.

The proteoglycanase clade of the ADAMTS superfamily shows preferred proteolytic activity toward the hyalectan/lectican proteoglycans as follows: aggrecan, brevican, neurocan, and versican. ADAMTS15, a member of this clade, was recently identified as a putative tumor suppressor gene in colorectal and breast cancer. However, its biosynthesis, substrate specificity, and tissue expression are poorly described. Therefore, we undertook a detailed study of this proteinase and its expression. We report propeptide processing of the ADAMTS15 zymogen by furin activity, identifying RAKR(212)↓ as a major furin cleavage site within the prodomain. ADAMTS15 was localized on the cell surface, activated extracellularly, and required propeptide processing before cleaving V1 versican at position (441)E↓A(442). In the mouse embryo, Adamts15 was expressed in the developing heart at E10.5 and E11.5 days post-coitum and in the musculoskeletal system from E13.5 to E15.5 days post-coitum, where it was co-localized with hyaluronan. Adamts15 was also highly expressed in several structures within the adult mouse colon. Our findings show overlapping sites of Adamts15 expression with other members of ADAMTS proteoglycanases during embryonic development, suggesting possible cooperative roles during embryogenesis, consistent with other ADAMTS proteoglycanase combinatorial knock-out mouse models. Collectively, these data suggest a role for ADAMTS15 in a wide range of biological processes that are potentially mediated through the processing of versican.

High altitude impairs in vivo immunity in humans.

The aim was to assess the effect of high altitude on the development of new immune memory (induction) using a contact sensitization model of in vivo immunity. We hypothesized that high-altitude exposure would impair induction of the in vivo immune response to a novel antigen, diphenylcyclopropenone (DPCP). DPCP was applied (sensitization) to the lower back of 27 rested controls at sea level and to ten rested mountaineers 28 hours after passive ascent to 3777 m. After sensitization, mountaineers avoided strenuous exercise for a further 24 hours, after which they completed alpine activities for 11-18 days. Exactly 4 weeks after sensitization, the strength of immune memory induction was quantified in rested mountaineers and controls at sea level, by measuring the response to a low, dose-series DPCP challenge, read at 48 hours as skin measures of edema (skinfold thickness) and redness (erythema). Compared with control responses, skinfold thickness and erythema were reduced in the mountaineers (skinfold thickness,-52%, p=0.01, d=0.86; erythema, -36%, p=0.02, d=0.77). These changes in skinfold thickness and erythema were related to arterial oxygen saturation (r=0.7, p=0.04), but not cortisol (r<0.1, p>0.79), at sensitization. In conclusion, this is the first study to show, using a contact sensitization model of in vivo immunity, that high altitude exposure impairs the development of new immunity in humans.

Three nights of sleep deprivation does not alter thermal strain during exercise in the heat.

PURPOSE: Individuals exposed to total sleep deprivation may experience an increased risk of impaired thermoregulation and physiological strain during prolonged physical activity in the heat. However, little is known of the impact of more relevant partial sleep deprivation (PSD). This randomized counterbalanced study investigated the effect of PSD on thermal strain during an exercise-heat stress. METHODS: Ten healthy individuals performed two stress tests (45 min running, 70 % [Formula: see text] 33 °C, 40 % RH). Each trial followed three nights of controlled sleep: normal [479 (SD 2) min sleep night(-1); Norm] and PSD [116 (SD 4) min sleep night(-1)]. Energy balance and hydration state were controlled throughout the trials. Rectal temperatures (T re), mean skin temperature ([Formula: see text]), heart rate (HR), RPE, and thermal sensations (TS) were measured at regular intervals during each heat stress trial. RESULTS: There was a significant main effect of time (P < 0.05) for all of these variables. However, no differences (P > 0.05) were observed between PSD and Norm, respectively, for T re [39.0 (0.5) vs. 39.1 (0.5) °C], [Formula: see text], [36.1 (0.6) vs. 36.0 (0.7) °C] and HR [181 (13) vs. 182 (13) beats min(-1))] at the end of exercise-heat stress. There were no differences (P > 0.05) in [Formula: see text], PSI, RPE, TS and whole-body sweat rate between PSD versus Norm. CONCLUSION: Since greater physiological strain during exercise-heat stress did not follow three nights of PSD, it appears that sleep loss may have minimal impact upon thermal strain during exercise in the heat, at least as evaluated within this experiment.

Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases.

Protein-tyrosine phosphatase-like inositol polyphosphatases are microbial enzymes that catalyze the stepwise removal of one or more phosphates from highly phosphorylated myo-inositols via a relatively ordered pathway. To understand the substrate specificity and kinetic mechanism of these enzymes we have determined high resolution, single crystal, x-ray crystallographic structures of inactive Selenomonas ruminantium PhyA in complex with myo-inositol hexa- and pentakisphosphate. These structures provide the first glimpse of a myo-inositol polyphosphatase-ligand complex consistent with its known specificity and reveal novel features of the kinetic mechanism. To complement the structural studies, fluorescent binding assays have been developed and demonstrate that the K(d) for this enzyme is several orders of magnitude lower than the K(m). Together with rapid kinetics data, these results suggest that the protein tyrosine phosphatase-like inositol polyphosphatases have a two-step, substrate-binding mechanism that facilitates catalysis.

Exercise-induced stress inhibits both the induction and elicitation phases of in vivo T-cell-mediated immune responses in humans.

Little is known about the influence of exercise on induction and elicitation phases of in vivo immunity in humans. We used experimental contact-hypersensitivity, a clinically relevant in vivo measure of T cell-mediated immunity, to investigate the effects of exercise on induction and elicitation phases of immune responses to a novel antigen. The effects of 2 h-moderate-intensity-exercise upon the induction (Study One) and elicitation of in vivo immune memory (Study Two) to diphenylcyclopropenone (DPCP) were examined. Study One: matched, healthy males were randomly-assigned to exercise (N=16) or control (N=16) and received a primary DPCP exposure (sensitization), 20 min after either 2 h running at 60% V O(2peak) (EX) or 2 h seated rest (CON). Four weeks later, participants received a low, dose-series DPCP challenge (elicitation) on their upper inner arm, which was read at 24 and 48 h as clinical score, oedema (skinfold thickness) and redness (erythema). Study Two: pilot; 13 healthy males were sensitized to DPCP. Elicitation challenges were repeated every 4 weeks until responses reached a reproducible plateau. Then, N=9 from the pilot study completed both EX and CON trials in a randomized order. Elicitation challenges were applied and evaluated as in Study One. Results demonstrate that exercise-induced stress significantly impairs both the induction (oedema -53% at 48 h; P<0.001) and elicitation (oedema -19% at 48 h; P<0.05) phases of the in vivo T-cell-mediated immune response. These findings demonstrate that prolonged moderate-intensity exercise impairs the induction and elicitation phases of in vivo T-cell-mediated immunity. Moreover, the induction component of new immune responses appears more sensitive to systemic-stress-induced modulation than the elicitation component.