Delayed herbivory by migratory geese increases summer‐long CO2 uptake in coastal western Alaska

The advancement of spring and the differential ability of organisms to respond to changes in plant phenology may lead to “phenological mismatches” as a result of climate change. One potential for considerable mismatch is between migratory birds and food availability in northern breeding ranges, and these mismatches may have consequences for ecosystem function. We conducted a three‐year experiment to examine the consequences for CO₂ exchange of advanced spring green‐up and altered timing of grazing by migratory Pacific black brant in a coastal wetland in western Alaska. Experimental treatments represent the variation in green‐up and timing of peak grazing intensity that currently exists in the system. Delayed grazing resulted in greater net ecosystem exchange (NEE) and gross primary productivity (GPP), while early grazing reduced CO₂ uptake with the potential of causing net ecosystem carbon (C) loss in late spring and early summer. Conversely, advancing the growing season only influenced ecosystem respiration (ER), resulting in a small increase in ER with no concomitant impact on GPP or NEE. The experimental treatment that represents the most likely future, with green‐up advancing more rapidly than arrival of migratory geese, results in NEE changing by 1.2 µmol m^?2 s^?1 toward a greater CO₂ sink in spring and summer. Increased sink strength, however, may be mitigated by early arrival of migratory geese, which would reduce CO₂ uptake. Importantly, while the direct effect of climate warming on phenology of green‐up has a minimal influence on NEE, the indirect effect of climate warming manifest through changes in the timing of peak grazing can have a significant impact on C balance in northern coastal wetlands. Furthermore, processes influencing the timing of goose migration in the winter range can significantly influence ecosystem function in summer habitats.     

Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta

To elucidate how human DNA polymerase β (pol β) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol β. Analyses reveal that the thumb closing of pol β before chemistry is hampered when the incorrect nucleotide dATP is bound opposite 8-oxoG; the unfavorable interaction between active-site residue Tyr²⁷¹ and dATP that causes an anti to syn change in the 8-oxoG (syn):dATP complex explains this slow motion, in contrast to the 8-oxoG (anti):dCTP system. Such differences in conformational pathways before chemistry for mismatched versus matched complexes help explain the preference for correct insertion across 8-oxoG by pol β. Together with reference studies with a nonlesioned G template, we propose that 8-oxoG leads to lower efficiency in pol β's incorporation of dCTP compared with G by affecting the requisite active-site geometry for the chemical reaction before chemistry. Furthermore, because the active site is far from ready for the chemical reaction after partial closing or even full thumb closing, we suggest that pol β is tightly controlled not only by the chemical step but also by a closely related requirement for subtle active-site rearrangements after thumb movement but before chemistry.     

Relationship between thermodynamic driving force and one-way fluxes in reversible processes

Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and reverse fluxes and free energy for any chemical process operating in a steady state. This relationship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state in dilute solution, provides a novel equivalent definition for chemical reaction free energy. In addition, it is shown that previously unrelated theories introduced by Ussing and Hodgkin and Huxley for transport of ions across membranes, Hill for catalytic cycle fluxes, and Crooks for entropy production in microscopically reversible systems, are united in a common framework based on this relationship.     

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels.     

Middle Eocene primate tarsals from China: implications for haplorhine evolution

We describe tarsal remains of primates recovered from the Middle Eocene (approximately 45 mya) Shanghuang fissures in southern Jiangsu Province, China. These tarsals document the existence of four higher-level taxa of haplorhine primates and at least two adapid species. The meager and poorly preserved adapid material exhibits some similarities to European adapines like Adapis. The haplorhine primates are divided into two major groups: a "prosimian group" consisting of Tarsiidae and an unnamed group that is anatomically similar to Omomyidae; and an "anthropoid group" consisting of Eosimiidae and an unnamed group of protoanthropoids. The anthropoid tarsals are morphologically transitional between omomyids (or primitive haplorhines) and extant telanthropoids, providing the first postcranial evidence for primates which bridge the prosimian-anthropoid gap. All of the haplorhines are extremely small (most are between 50-100 g), and the deposits contain the smallest euprimates ever documented. The uniqueness of this fauna is further highlighted by the fact that no modern primate community contains as many tiny primates as does the fauna from Shanghuang.     

The unique N-terminal domain of the cAMP phosphodiesterase PDE4D4 allows for interaction with specific SH3 domains

Of the five PDE4D isoenzymes, only the PDE4D4 cAMP specific phosphodiesterase was able to bind to SH3 domains. Only PDE4D4 and PDE4A5, but not any other PDE4A, B, C and D isoforms expressed in rat brain, bound to src, lyn and fyn kinase SH3 domains. Purified PDE4D4 could bind to purified lyn SH3. PDE4D4 and PDE4A5 both exhibited selectivity for binding the SH3 domains of certain proteins. PDE4D4 did not bind to WW domains. We suggest that an important function of the unique N-terminal region of PDE4D4 may be to allow for association with certain SH3 domain-containing proteins.     

Effects of season of birth on the prepubertal pattern of gonadotropin secretion and age at puberty in beef heifers

There is an early transient rise in gonadotropin secretion in spring-born prepubertal heifers and there is an indication that this pattern is different in autumn-born heifers. The effect of season of birth on age and weight at puberty is equivocal. This study was designed to compare the temporal patterns of LH and FSH secretion between spring- and autumn-born heifers and to determine the effects of season of birth on age and weight at puberty. Blood samples from 2 groups of heifer calves born in spring (last week of March, n = 5) or autumn (last week of October, n = 5) were collected every other week from birth to puberty and every 15 min for 10 h at 6, 12, 18, 24 and 32 wk of age. Timing of puberty was determined by measuring progesterone in plasma samples collected every 2 to 3 d starting at 42 wk of age. Age and weight at onset of puberty did not differ between the 2 groups of heifers (P > 0.05); however, the autumn-born heifers tended to mature in a wider range of ages and weights. Based on the 10-h sampling periods, mean serum concentrations of LH and LH pulse frequency and amplitude were higher in spring-born heifers at 18 wk of age than in autumn-born heifers (P < 0.05). In spring-born heifers, LH pulse frequency increased over time to 32 wk of age, and LH pulse amplitude was higher at 12 and 18 wk than at 32 wk of age (P < 0.05). Autumn-born heifers had higher LH pulse frequency at 6 wk and showed a decrease in mean concentrations of LH at 12 and 18 wk of age (P < 0.05). The FSH pulse frequency of spring-born heifers was higher at 12 wk of age than in autumn-born heifers (P < 0.05), FSH pulse amplitude in autumn-born heifers decreased from 6 to 32 wk of age. It was concluded that although the mean age and weight at puberty did not differ between spring- and autumn-born heifers, the range in age and weight at puberty was wider in the autumn-born heifers. The patterns of LH secretion differed between spring- and autumn-born prepubertal heifers, with spring-born calves exhibiting an early rise in LH secretion, while mean serum concentrations of LH decreased during this period in autumn-born heifers.     

The evolution of endothermy and its diversity in mammals and birds

Many elements of mammalian and avian thermoregulatory mechanisms are present in reptiles, and the changes involved in the transition to endothermy are more quantitative than qualitative. Drawing on our experience with reptiles and echidnas, we comment on that transition and on current theories about how it occurred. The theories divide into two categories, depending on whether selection pressures operated directly or indirectly on mechanisms producing heat. Both categories of theories focus on explaining the evolution of homeothermic endothermy but ignore heterothermy. However, noting that hibernation and torpor are almost certainly plesiomorphic (=ancestral, primitive), and that heterothermy is very common among endotherms, we propose that homeothermic endothermy evolved via heterothermy, with the earliest protoendotherms being facultatively endothermic and retaining their ectothermic capacity for "constitutional eurythermy." Thus, unlike current models for the evolution of endothermy that assume that hibernation and torpor are specialisations arising from homeothermic ancestry, and therefore irrelevant, we consider that they are central. We note the sophistication of thermoregulatory behavior and control in reptiles, including precise control over conductance, and argue that brooding endothermy seen in some otherwise ectothermic Boidae suggests an incipient capacity for facultative endothermy in reptiles. We suggest that the earliest insulation in protoendotherms may have been internal, arising from redistribution of the fat bodies that are typical of reptiles. We note that short-beaked echidnas provide a useful living model of what an (advanced) protoendotherm may have been like. Echidnas have the advantages of endothermy, including the capacity for homeothermic endothermy during incubation, but are very relaxed in their thermoregulatory precision and minimise energetic costs by using ectothermy facultatively when entering short- or long-term torpor. They also have a substantial layer of internal dorsal insulation. We favor theories about the evolution of endothermy that invoke direct selection for the benefits conferred by warmth, such as expanding daily activity into the night, higher capacities for sustained activity, higher digestion rates, climatic range expansion, and, not unrelated, control over incubation temperature and the benefits for parental care. We present an indicative, stepwise schema in which observed patterns of body temperature are a consequence of selection pressures, the underlying mechanisms, and energy optimization, and in which homeothermy results when it is energetically desirable rather than as the logical endpoint.     

Zygospores of selected Trichomycetes in larval Diptera of the families Chironomidae and Simuliidae

The midgut-inhabiting fungi (Harpellaceae) Harpella melusinae and Stachylina pedifer were induced to form zygospores, using an application of a pH 10 potassium hydroxide solution with culture media. The previously unknown zygospores of S. pedifer are borne perpendicular to the zygosporophore, as in Harpella melusinae. The zygospores of the hindgut-inhabiting species Smittium coloradense, borne obliquely to the zygosporophore (in vivo), are described for the first time.