Effects of nitrogen supply on the anatomy and chemical composition of leaves of four grass species belonging to the genus Poa, as determined by image-processing analysis and pyrolysis–mass spectrometry

Previous experiments have shown that the anatomy and chemical composition of leaves of inherently fast- and slow-growing grass species, grown at non-limiting nitrogen supply, differ systematically. The present experiment was carried out to investigate whether these differences persist when the plants are grown at an intermediate or a very low nitrogen supply. To this end, the inherently fast-growing Poa annua L. and Poa trivialis L., and the inherently slow-growing Poa compressa L. and Poa pratensis (L.) Schreb. were grown hydroponically at three levels of nitrate supply: at optimum (RGR_max) and at relative addition rates of 100 and 50 mmol N (mol N)^?1 d^?1 (RAR₁₀₀ and RAR₅₀), respectively. As expected, at the lowest N supply, the potentially fast-growing species grew at the same rate as the inherently slow-growing ones. Similarly, the differences in leaf area ratio (LAR, leaf area:total dry mass), specific leaf area (SLA, leaf arear:leaf dry mass) and leaf mass ratio (LMR, leaf dry mass:total dry mass) disappeared. Under optimal conditions, the fast-growing species differed from the slow-growing ones in that they had a higher N concentration. There were no significant differences in C concentration. With decreasing N supply, the total N concentration decreased and the differences between the species disappeared. The total C concentration increased for the fast-growing species and decreased for the slow-growing ones, i.e. the small, but insignificant, difference in C concentration between the species at RGR_max increased with decreasing N supply. The chemical composition of the leaves at low N supply, analysed in more detail by pyrolysis–mass spectrometry, showed an increase in the relative amounts of guaiacyl lignin, cellulose and hemicellulose, whereas those of syringyl lignin and protein decreased. The anatomy and morphology of the leaves of the four grass species differing in RGR_max were analysed by image-processing analysis. The proportion of the total volume occupied by mesophyll plus intercellular spaces and epidermis did not correlate with the amount of leaf mass per unit leaf area (specific leaf mass, SLM) at different N supply. The higher SLM at low N supply was caused partly by a high proportion of non-veinal sclerenchymatic cells per cross-section and partly by the smaller volume of epidermal cells. We conclude that the decrease in relative growth rate (and increase in SLM) at decreasing N supply is partly due to chemical and anatomical changes. The differences between the fast- and slow-growing grass species at an optimum nutrient supply diminished when plants were growing at a limiting nitrogen supply.     

Whole-plant ABA flux and the regulation of water loss in Cedrella odorata

Three-month-old Cedrella odorata seedlings were exposed to a soil-drying treatment. During this period, xylem sap was periodically collected from the plant by applying pneumatic pressure to the roots. This also allowed whole-plant water status to be measured by recording the balancing pressure applied. The concentration of ABA in xylem sap (C) was related to the whole-plant transpiration rate (V) which was measured with a sap flow gauge. The analysis of these paired measurements centred on how the reciprocal of C (R) varied with respect to V. This revealed that (1) the observed increases in C could not be explained by the reductions in V alone, (2) initially, decreases in V were associated with proportional increases in the whole-plant ABA flux (M), and (3) this relationship broke down at low values of V since zero flow was associated with a finite value for C estimated to be 41 pmol ABA mmol^?1 H₂O. A simple static model is developed from the observations that is able to explain the data well, and the results are discussed in terms of the effects of ABA on stomatal conductance (g_sw).     

Mean growth rate when rare is not a reliable metric for persistence of species

The coexistence of many species within ecological communities poses a long‐standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, , is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on and show that it fails to capture the effect of temporal random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in , since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as increases.     

The Rate of Cu,Zn Superoxide Dismutase Evolution

The rate of amino acid replacement in Cu, Zn SOD greatly departs from the expectations of the molecular clock. We examine 27 Cu, Zn SOD sequences available and conclude that: (I) the SOD enzymes from different mammal families differ from each other by roughly the same number of replacements, which is consistent with a simultaneous mammalian radiation; (2) over the most recent 60 million years (MY) the rate of SOD evolution is fairly high (15aa/100aa/100MYR) and may be considered constant; (3) the rate of accumulation of amino acid replacements since the divergence of fungi. plants and animals to the present is inconstant along different branches of the evolutionary tree; moreover it steadily decreases with time, to the same extent in all lineages; (4) some comparisons exhibit divergences that are in any case greater than expected from a Poisson process on the assumption of a molecular clock; (5) plant chloroplast enzymes display fewer differences from each other than cytoplasmic ones; (6) bacteriocuprein (from Photobacterium leiognathi), fluke and human extracellular SOD are all three extremely remotely related to one another and to the SOD of other eukaryotes.

The process of consistent decline of the rate of evolution of Cu. Zn SOD can be described by a number of mathematical functions. We explore simple models that assume constant rates and might be applicable to other proteins or genes that apparently evolve at disparate rates.     

Synchronization of the Circadian Activity Rhythm in Hamsters Following Intermittent Schedule Shifts

The time course of resynchronization of the circadian activity rhythm of hamsters was observed following a 10-hr advance or delay in the light-dark cycle (LD 12:12). Twenty-six shift patterns of the lighting schedule were studied; they consisted of continuous (daily), three-step, two-step and one-step shifting. So long as the daily shift of the lighting schedule was 1 hr or less, the locomotor rhythm followed the continuous shift perfectly. As the amount of daily shift increased, the time course of activity onset deviated more from the time of lights off; the tendency was more marked in advancing than in delaying shifts. Responses of the activity rhythm to stepwise shifting were essentially the same as those to a continuous shift. They were, however, characterized by larger individual variations, and it took additional days before entrainment was achieved. By fitting the time course of entrainment to an exponential model with a constant term, estimates of time constant and shift error were derived. The time constant became shorter with increasing amounts of daily shifts up to 2 hr per day, increasing the number of shift steps, and/or reducing the amount of the initial shift of the seies. The shift error estimated was 0.51 ± 0.12 hr, indicating precise resynchronization. Accordingly, a quicker resynchronization may be expected when a multiple step shift with a moderate initial shift are employed. In the case of a 10-hr shift, for example, a shift of 3 hr followed by another 7 hr may be recommended.     

Continued use of soft‐metal bands on gulls in North America reduces the value of recovery data

Use of soft‐metal (aluminum alloy) bands on gulls (Laridae) is known to result in high rates of band loss and, as a result, hard‐metal (monel, incoloy, or stainless steel) bands are superior for most studies. However, the U.S. Bird Banding Laboratory (BBL) and the Canadian Wildlife Service Bird Banding Office continue to issue soft bands for use on gulls, and the BBL does not make specific recommendations about use of hard bands so many banders continue to use soft bands. For wholly marine species of gulls banded in North America since 1996, ～20% have been banded with soft bands; the proportion of soft bands used on partially freshwater gulls was ～70% up to 2009, but has since fallen to 40%. Using hierarchical Bayesian models in program MARK, we analyzed recovery data for three gull species and found that estimates of annual survival rates derived from soft bands (0.68–0.81) were lower than those derived from hard bands (0.85–0.96). Comparison of survival rates of Herring Gulls (Larus argentatus) in the Great Lakes basin and on the Atlantic coast provided no evidence that soft bands last longer in freshwater than saltwater. Band loss compromises many types of studies, including those assessing the possible effects of climate change. We recommend that use of soft bands on gulls be discontinued, and that banders be required to use hard bands on these species in the future. The same consideration applies to other long‐lived species, including some waterfowl and all albatrosses, pelicans, cormorants, shearwaters, petrels, terns, shorebirds, and alcids. Use of hard bands should be based on expectations about a species’ longevity and evidence of band wear, rather than on whether or not it occurs in saltwater.     

Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer’s Disease Brain

Molecular changes in the brain of individuals afflicted with Alzheimer's disease (AD) are an intense area of study. Little is known about the role of protein abundance and posttranslational modifications in AD progression and treatment, in particular large-scale intact N-linked glycoproteomics analysis. To elucidate the N-glycoproteome landscape, we developed an approach based on multi-lectin affinity enrichment, hydrophilic interaction chromatography, and LC-MS–based glycoproteomics. We analyzed brain tissue from 10 persons with no cognitive impairment or AD, 10 with asymptomatic AD, and 10 with symptomatic AD, detecting over 300 glycoproteins and 1900 glycoforms across the samples. The majority of glycoproteins have N-glycans that are high-mannosidic or complex chains that are fucosylated and bisected. The Man5 N-glycan was found to occur most frequently at >20% of the total glycoforms. Unlike the glycoproteomes of other tissues, sialylation is a minor feature of the brain N-glycoproteome, occurring at <9% among the glycoforms. We observed AD-associated differences in the number of antennae, frequency of fucosylation, bisection, and other monosaccharides at individual glycosylation sites among samples from our three groups. Further analysis revealed glycosylation differences in subcellular compartments across disease stage, including glycoproteins in the lysosome frequently modified with paucimannosidic glycans. These results illustrate the N-glycoproteomics landscape across the spectrum of AD clinical and pathologic severity and will facilitate a deeper understanding of progression and treatment development.     

Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases

Muscle-specific receptor tyrosine kinase (MuSK) agonist antibodies were developed 2 decades ago to explore the benefits of receptor activation at the neuromuscular junction. Unlike agrin, the endogenous agonist of MuSK, agonist antibodies function independently of its coreceptor low-density lipoprotein receptor–related protein 4 to delay the onset of muscle denervation in mouse models of ALS. Here, we performed dose–response and time-course experiments on myotubes to systematically compare site-specific phosphorylation downstream of each agonist. Remarkably, both agonists elicited similar intracellular responses at known and newly identified MuSK signaling components. Among these was inducible tyrosine phosphorylation of multiple Rab GTPases that was blocked by MuSK inhibition. Importantly, mutation of this site in Rab10 disrupts association with its effector proteins, molecule interacting with CasL 1/3. Together, these data provide in-depth characterization of MuSK signaling, describe two novel MuSK inhibitors, and expose phosphorylation of Rab GTPases downstream of receptor tyrosine kinase activation in myotubes.     

MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics

Identifying protein–protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an “abortive” biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity-dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist. Here we modified the structure of BioID2, derived from Aquifex aeolicus BirA, to create a smaller, highly active, biotin ligase that we named MicroID2. Truncation of the C terrminus of BioID2 and addition of mutations to alleviate blockage of biotin/ATP binding at the active site of BioID2 resulted in a smaller and highly active construct with lower background labeling. Several additional point mutations improved the function of our modified MicroID2 construct compared with BioID2 and other biotin ligases, including TurboID and miniTurbo. MicroID2 is the smallest biotin ligase reported so far (180 amino acids [AAs] for MicroID2 versus 257 AAs for miniTurbo and 338 AAs for TurboID), yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurbo. MicroID2 also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we in addition developed a MicroID2 mutant, termed lbMicroID2 (low background MicroID2), that has lower labeling efficiency but significantly reduced biotin scavenging compared with BioID2. Finally, we demonstrate utility of MicroID2 in mass spectrometry experiments by localizing MicroID2 constructs to subcellular organelles and measuring proximal interactions.