Stomatal conductance, not biochemistry, drives low temperature acclimation of photosynthesis in Populus balsamifera, regardless of nitrogen availability

Low-temperature thermal acclimation may require adjustments to N and water use to sustain photosynthesis because of slow enzyme functioning and high water viscosity. However, understanding of photosynthetic acclimation to temperatures below 11 °C is limited. We acclimated Populus balsamifera to 6 °C and 10 °C (6A and 10A, respectively) and provided the trees with either high or low N fertilizer. We measured net CO₂ assimilation (A_net ), stomatal conductance (g_s ), maximum rates of Rubisco carboxylation (V_cmax ), electron transport (J_max ) and dark respiration (R_d ) at leaf temperatures of 2, 6, 10, 14 and 18 °C, along with leaf N concentrations. The 10A trees had higher A_net than the 6A trees at warmer leaf temperatures, which was correlated with higher g_s in the 10A trees. The instantaneous temperature responses of V_cmax , J_max and R_d were similar for trees from both acclimation temperatures. While soil N availability increased leaf N concentrations, this had no effect on acclimation of photosynthesis or respiration. Our results indicate that acclimation below 11 °C occurred primarily through changes in stomatal conductance, not photosynthetic biochemistry, and was unaffected by short-term N supply. Thermal acclimation of stomatal conductance should therefore be a priority for future carbon cycle model development.

A constraint on historic growth in global photosynthesis due to increasing CO2

The global terrestrial carbon sink is increasing^1-3, offsetting roughly a third of anthropogenic CO₂ released into the atmosphere each decade¹, and thus serving to slow⁴ the growth of atmospheric CO₂. It has been suggested that a CO₂-induced long-term increase in global photosynthesis, a process known as CO₂ fertilization, is responsible for a large proportion of the current terrestrial carbon sink^4-7. The estimated magnitude of the historic increase in photosynthesis as result of increasing atmospheric CO₂ concentrations, however, differs by an order of magnitude between long-term proxies and terrestrial biosphere models^7-13. Here we quantify the historic effect of CO₂ on global photosynthesis by identifying an emergent constraint^14-16 that combines terrestrial biosphere models with global carbon budget estimates. Our analysis suggests that CO₂ fertilization increased global annual photosynthesis by 11.85 ± 1.4%, or 13.98 ± 1.63 petagrams carbon (mean ± 95% confidence interval) between 1981 and 2020. Our results help resolve conflicting estimates of the historic sensitivity of global photosynthesis to CO₂, and highlight the large impact anthropogenic emissions have had on ecosystems worldwide.

"Spshing noise": biological significance of its attraction and nonattraction by birds

Many New World passerine birds, especially migrants which join mixed flocks of local species in the Neotropics, are attracted to a noise termed "spshing" used by humans to attract birds into view. The noise is effective because it mimics the vocalizations of certain bird species which play a central bonding role in mixed species flocks. Migrants join these flocks to gain local expertise about food sources and/or potential enemies in unfamiliar environments. Old World passerine migrants do not react to "spshing." In Africa, they do not join mixed flocks of local species because of more favorable environmental conditions negating the need to do so. In tropical Asia, many migrants join mixed flocks but the local bonding species give vocalizations unlike those of their counterparts in the Neotropics, and thus not like "spshing."

Evaluation of novel injectable hydrogels for nucleus pulposus replacement

Branched copolymers composed of poly(N-isopropylacrylamide) (PNIPAAm) and poly(ethylene glycol) (PEG) are being investigated as an in situ forming replacement for the nucleus pulposus of the intervertebral disc. A family of copolymers was synthesized by varying the molecular weight of the PEG blocks and molar ratio of NIPAAm monomer units to PEG branches. Gel swelling, dissolution, and compressive mechanical properties were characterized over 90 days and stress relaxation behavior over 30 days immersion in vitro. It was found that the NIPAAm to PEG molar ratio did not affect the equilibrium swelling and compressive mechanical properties. However, gel elasticity exhibited a dependency on both the PEG block molecular weight and content. The equilibrium gel water content increased and compressive modulus decreased with increasing PEG block size. While all of the branched copolymers showed significant increases in stress relaxation time constant compared to the homopolymer (p < 0.05), the high PEG content PNIPAAm-PEG (4600 and 8000 g/mol) exhibited the maximum elasticity. Because of its high water content, requisite stiffness and high elastic response, PNIPAAm-PEG (4600 g/mol) will be further evaluated as a candidate material for nucleus pulposus replacement.

Capillary-loaded particle fluid dynamics: effect on estimation of sperm concentration

Capillary loaded chambers are frequently used for semen analysis. Poiseuille flow of specimen into these chambers causes migration of suspended particles or cells in a direction transverse to the flow, which results in their preferential accumulation in the Segre-Silberberg (SS) planes. This SS effect depends on the transverse velocity gradient in the laminar flow. For semen analysis in thin capillary-loaded slides, the SS effect can lead to erroneous estimation of sample sperm-cell concentration. To better understand chamber flow dynamics and SS effect significance, we assessed flow uniformity, inflow cell velocity, and results of concentration measurements under different flow conditions for latex bead and porcine and human sperm suspensions. Overall, a concentration peak was present at the meniscus, which continued through chamber loading. High-velocity SS preferred planes, which channeled particles toward the meniscus, were located at the fractional positions of beta = .27 and beta = .73, where beta is the distance from wall to plane normalized to the chamber depth. In computer-automated semen analysis, a standard 20-microm x 18-mm x 6-mm chamber is commonly used, and these studies supported our previously published fluid-flow theory for this type of chamber. Conversely, the SS effect does not appear to have time to develop in the 100-microm-depth hemacytometer, which is deeper than the standard slide, has lower transverse velocity gradient, and consequently does not exhibit concentration variation due to the SS effect. These findings provide further support that hemacytometry, when performed properly, remains the gold standard. Applicability of our findings to routine semen analyses was then tested in 2 studies performed with independent boar studs. These studies compared diluted boar semen concentrations estimated by standard hemacytometry and in capillary-loaded 20-microm slides, using a computer-automated semen-analysis system designed to compensate for the SS effect. Good numerical agreement for sperm concentration with a high degree of correlation (r(2) = .936) was found between the 2 techniques. These findings reaffirm the need to critically assess new technologies for accuracy, repeatability, and precision.

Particle distribution in low-volume capillary-loaded chambers

Accurate determination of sperm concentration in fluid suspension is a critical component in a semen analysis. Inaccurate estimations can lead to misinterpretation of the spermiogram and, in the case of livestock production, can lead to faulty insemination doses, which can adversely affect stud power, fertility, fecundity, and cost effectiveness of breeding programs. Capillary-loaded slides, like the hemacytometer, have been the standard for calibration of other concentration estimation modalities such as photometry, Coulter counter, flow cytometry, and computer-automated semen analysis (CASA). Single-use capillary-loaded slides, much smaller than the hemacytometer, are frequently used by many of the current CASA systems. As the use of CASA increases, more field reports are suggesting differences between CASA results and hemacytometry. In this article, we establish that these differences are, in large part, due to the Segre-Silberberg effect, which occurs during Poiseuille flow in high-gradient fluid flow in thin capillary-loaded slides. We develop the theory of this phenomenon and derive the scaling and significance of the effect. Finally, we graphically provide a means for predicting the necessary compensation factor when using capillary-loaded slides to determine sperm concentration.

Why are translationally sub-optimal synonymous codons used in Escherichia coli?

Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force, so there is a balance between mutation, selection, and drift; (2) at some sites there is no selection on codon usage, so some synonymous sites are unaffected by translational selection; and (3) translationally sub-optimal codons are favored by alternative selection pressures at certain synonymous sites. We find that when all the data is considered, model 1 is supported and both models 2 and 3 are rejected as sole explanations for the existence of translationally sub-optimal codons. However, we find evidence in favor of both models 2 and 3 when the data is partitioned between groups of amino acids and between regions of the genes. Thus, all three mechanisms appear to contribute to the existence of translationally sub-optimal codons in E. coli.

Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans

It is has been suggested that synonymous codon bias is a consequence of mutation bias in mammals. We tested this hypothesis in humans using single-nucleotide polymorphism data. We found a pattern of polymorphism which was inconsistent with the mutation bias hypothesis in G+C-rich genes. However, the data were consistent with the action of natural selection or biased gene conversion. Similar patterns of polymorphism were also observed in noncoding DNA, suggesting that natural selection or biased gene conversion may affect large tracts of the human genome.

A test of amino acid reversibility

In studies of molecular evolution, the assumption that protein evolution is reversible has often been made, but rarely tested. Here we use a large set of orthologous murid protein coding sequences to perform a simple test of reversibility, and find no evidence to reject the assumption of reversibility in protein evolution.

In-depth morphological changes and embrittlement near the wear surface of UHMWPE inserts from uncemented hip systems

Polyethylene hip cups were examined with optical and electron microscopy after permanganic etching, a technique that allows in-depth examination from the articulating surface downward. In addition to wear features present on the surface, novel defects were revealed in implants after retrieval from the body but not in as-manufactured controls. They were incipient cracks that indicated the existence of an embrittled layer extending 10 microm or more into the implant from the wear surface after exposure to the body environment. The lengths of the cracks, which were perpendicular to the tensile stresses responsible for their formation, were mostly more or less parallel to the wear surface. The embrittlement and cracking revealed are probably major contributors to the wear of polyethylene implants in the body. Poor particle consolidation may be a contributory factor, but it was not observed to be the primary cause of implant wear within the body.

The evolution of haplodiploidy under inbreeding

Although haplodiploid organisms tend to be inbred, previous models of the evolution of haplodiploidy have assumed outbred populations. Here a model for the evolution of haplodiploidy is developed which incorporates sib mating, deleterious mutations generated by mutation, and fitness differences between haploids and diploids. Simulations of the model allow an assessment of the effect of inbreeding on the deleterious mutation and maternal transmission theories for the evolution of haplodiploidy. As expected from intuitive arguments, inbreeding favours haplodiploidy under the deleterious mutation hypothesis but disfavours haplodiploidy under the maternal transmission hypothesis. It appears that the effect of inbreeding is greater on the maternal transmission theory, and thus inbreeding may restrict the evolution of haplodiploidy.

The evolutionary dynamics of male-killers and their hosts

Male-killing bacteria are cytoplasmic sex-ratio distorters that are transmitted vertically through females of their insect hosts. The killing of male hosts by their bacteria is thought to be an adaptive bacterial trait because it augments the fitness of female hosts carrying clonal relatives of those bacteria. Here we attempt to explain observations of multiple male-killers in natural host populations. First we show that such male-killer polymorphism cannot be explained by a classical model of male-killing. We then show that more complicated models incorporating the evolution of resistance in hosts can explain male-killer polymorphism. However, this is only likely if resistance genes are very costly. We also consider the long-term evolutionary dynamics of male-killers, and show that evolution towards progressively more 'efficient' male-killers can be thwarted by the appearance of host resistance. The presence of a resistance gene can allow a less efficient male-killer to outcompete its rival and hence reverse the trend towards more efficient transmission and reduced metabolic load on the host.

On morphology of consolidated UHMWPE resin in hip cups

The microstructure of replacement hip cups made from ultra-high molecular weight polyethylene (UHMWPE) has been revealed by permanganic etching to bring out the fine details. Specimens are examined by optical microscopy according to the Nomarski technique, and by scanning and transmission electron microscopy. In all cups the original reactor particles are visible. Optical microscopy is most productive in revealing variations not only in the texture of different individual particles, but also in the degree of consolidation of a particle with its neighbours. Both these factors differ according to the material and process. Electron microscopy reveals the existence of pockets of lower molecular weight material which has been expelled from the particles by the original sintering process.

The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents

Nonsynonymous substitutions in DNA cause amino acid substitutions while synonymous substitutions in DNA leave amino acids unchanged. The cause of the correlation between the substitution rates at nonsynonymous (K(A)) and synonymous (K(S)) sites in mammals is a contentious issue, and one that impacts on many aspects of molecular evolution. Here we use a large set of orthologous mammalian genes to investigate the causes of the K(A)-K(S) correlation in rodents. The strength of the K(A)-K(S) correlation exceeds the neutral theory expectation when substitution rates are estimated using algorithmic methods, but not when substitution rates are estimated by maximum likelihood. Irrespective of this methodological uncertainty the strength of the K(A)-K(S) correlation appears mostly due to tandem substitutions, an excess of which is generated by substitutional nonindependence. Doublet mutations cannot explain the excess of tandem synonymous-nonsynonymous substitutions, and substitution patterns indicate that selection on silent sites is the likely cause. We find no evidence for selection on codon usage. The nature of the relationship between synonymous divergence and base composition is unclear because we find a significant correlation if we use maximum-likelihood methods but not if we use algorithmic methods. Finally, we find that K(S) is reduced at the start of genes, which suggests that selection for RNA structure may affect silent sites in mammalian protein-coding genes.

Vertebrate genome evolution: a slow shuffle or a big bang?

In vertebrates it is often found that if one considers a group of genes clustered on a certain chromosome, then the homologues of those genes often form another cluster on a different chromosome. There are four explanations, not necessarily mutually exclusive, to explain how such homologous clusters appeared. Homologous clusters are expected at a low probability even if genes are distributed at random. The duplication of a subset of the genome might create homologous clusters, as would a duplication of the entire genome. Alternatively, it may be adaptive for certain combinations of genes to cluster, although clearly the genes must have duplicated prior to rearrangement into clusters. Molecular phylogenetics provides a means to examine the origins of homologous clusters, although it is difficult to discriminate between the different explanations using current data. However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters.

Do essential genes evolve slowly?

Approximately two thirds of all knockouts of individual mouse genes give rise to viable fertile mice. These genes have thus been termed 'non-essential' in contrast to 'essential' genes, the knockouts of which result in death or infertility. Although non-essential genes are likely to be under selection that favours sequence conservation [1], it is predicted that they are less subject to such stabilising selection than essential genes, and hence evolve faster [2]. We have addressed this issue by analysing the molecular evolution of 108 non-essential and 67 essential genes that have been sequenced in both mouse and rat. On preliminary analysis, the non-essential genes appeared to be faster evolving than the essential ones. We found, however, that the non-essential class contains a disproportionate number of immune-system genes that may be under directional selection (that is, selection favouring change) because of host-parasite coevolution. After correction for this bias, we found that the rate at which genes evolve does not correlate with the severity of the knockout phenotype. This was corroborated by the finding that, whereas neuron-specific genes have significantly lower rates of change than other genes, essential and non-essential neuronal genes have comparable rates of evolution. Our findings most probably reflect strong selection acting against even very subtle deleterious phenotypes, and indicate that the putative involvement of directional selection in host-parasite coevolution and gene expression within the nervous system explains much more of the variance in rates of gene evolution than does the knockout phenotype.

The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?

Miyata et al. have suggested that the male-to-female mutation rate ratio (alpha) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of alpha. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of alpha are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution.

Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager

Employing a set of 43 othologous mouse and rat genes, Hughes and Yeager (J. Mol. Evol. 45:125-130, 1997) reported (1) no correlation between synonymous and nonsynonymous rates of nucleotide substitution, (2) a positive correlation between intronic GC contents (GCi) and intronic substitution rates (Ki), (3) that the average Ki value was very similar to the average Ks value, and (4) that the compositional correlation between the rat and the mouse genes is stronger at the third codon position (GC3) than at the first and second codon positions (GC12). We have examined the robustness of these results to alterations in substitution rate estimation protocol, alignment protocol, and statistical procedure. We find that a significant correlation between Ka and Ks is observed either if a rank correlation statistic is used instead of regression analysis, if one outlier is excluded from the analysis, or if a regression weighted by gene size is employed. The correlation between Ki and GCi we find to be sensitive to changes in alignment protocol and disappears on the use of weighted means. The finding that Ks and Ki are approximately the same is dependent on the method for estimating Ks values. Finally, the variance around the regression line of rat GC3 versus mouse GC3 we find to be significantly higher than that in GC12. The source of the discrepancy between this and Hughes and Yeager's result is unclear. The variance around the line for GC4 is higher still, as might be expected. Using a methodology that may be considered preferable to that of Hughes and Yeager, we find that all four of their results are contradicted. More importantly this analysis reinforces the need for caution in assembling and analyzing data sets, as the degree of sensitivity to what many might consider minor methodological alterations is unexpected.

Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor

The repeatability of patterns of variation in Ka/Ks and Ks is expected if such patterns are the result of deterministic forces. We have contrasted the molecular evolution of the mammalian insulin-like growth factor type II receptor (Igf2r) in the mouse-rat comparison with that in the human-cow comparison. In so doing, we investigate explanations for both the evolution of genomic imprinting and for Ks variation (and hence putatively for mutation rate evolution). Previous analysis of Igf2r, in the mouse-rat comparison, found Ka/Ks patterns that were suggested to be contrary to those expected under the conflict theory of imprinting. We find that Ka/Ks variation is repeatable and hence confirm these patterns. However, we also find that the molecular evolution of Igf2r signal sequences suggests that positive selection, and hence conflict, may be affecting this region. The variation in Ks across Igf2r is also repeatable. To the best of our knowledge this is the first demonstration of such repeatability. We consider three explanations for the variation in Ks across the gene: (1) that it is the result of mutational biases, (2) that it is the result of selection on the mutation rate, and (3) that it is the product of selection on codon usage. Explanations 2 and 3 predict a Ka-Ks correlation, which is not found. Explanation 3 also predicts a negative correlation between codon bias and Ks, which is also not found. However, in support of explanation 1 we do find that in rodents the rate of silent C --> T mutations at CpG sites does covary with Ks, suggesting that methylation-induced mutational patterns can explain some of the variation in Ks. We find evidence to suggest that this CpG effect is due to both variation in CpG density, and to variation in the frequency with which CpGs mutate. Interestingly, however, a GC4 analysis shows no covariance with Ks, suggesting that to eliminate methyl-associated effects CpG rates themselves must be analyzed. These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations.

The dynamics of maternal-effect selfish genetic elements

Maternal-effect selfish genes such as Medea or Scat act to kill progeny that do not bear a copy of the selfish gene present in the mother. Previous models of this system allowed for two types of allele, the selfish (killer) type and the sensitive (susceptible) wild-type. These models predict that the invasion conditions of the selfish allele are quite broad and that if invasion is possible a high frequency equilibrium is to be expected. The selfish element is therefore predicted to persist. Here a hypothetical third allele that neither kills nor is killed (i.e. insensitive) is considered. Such an allele could enter a population by recombination, mutation or migration. The incorporation of this third allele profoundly affects the dynamics of the system and, under some parameter values, it is possible for the spread of the insensitive allele to lead, eventually, to the fixation of the wild-type allele (reversible evolution). This is most likely if the death of progeny provides no direct benefit to the surviving sibs (i.e. in the absence of fitness compensation), as in insects without gregarious broods. Under these circumstances the selfish element cannot spread when infinitely rare, only after having risen to some finite frequency. A fitness cost to bearing the killer allele then causes its loss. However, if fitness compensation is found (e.g. in placental mammals) the invasion of the selfish element from an infinitely low level is possible for a wide range of costs and both stable coexistences of all three alleles and limit cycles of all three are then found. It is therefore to be expected that in mammals selfish maternal-effect genes are more likely both to spread and to persist than in insects, due to their different levels of fitness compensation.

Alcohol and drug abuse treatment of homeless persons: results from the NIAAA Community Demonstration Program

In a national evaluation, we assessed the implementation and outcomes of a multisite demonstration program for homeless persons with alcohol and other drug problems. We developed comprehensive case studies from data on client characteristics, utilization of services, implementation of interventions, and community systems of care at nine project sites. Client-level outcome data were analyzed to estimate the effectiveness of the interventions in a subset of projects with experimental or quasi-experimental evaluation designs. After controlling for baseline predictors, treatment clients in the majority of sites were significantly more likely than comparison clients to report improvement on one or more outcome dimensions. On alcohol use, for example, under conservative assumptions the average treatment client was drinking less at follow-up than were 57 percent of comparison clients. Analyses of predictor-by-treatment interactions suggested that clients with fewer problems benefited most from the interventions. The implementation analysis yielded a number of lessons for policymakers and program planners.

A systemwide quality assurance/risk management program

Physician involvement throughout this systemwide quality assurance and risk management program is a key element in the program's success. Physicians report through their own medical staff organization to a centralized quality assurance committee that interfaces between the board of directors and the medical staff of each hospital. The program is bolstered by complete support from the board and administration.

The photosynthetic capacity of stubble leaves and their contribution to growth of the lucerne plant after low level cutting

The net carbon dioxide exchange rate (NCE) of lucerne (Medicago sativa cv. Hunter River) stubble leaves was found to be low (c. 55 ng CO2 cm-2 sec-1) immediately after removing shoots 15 cm above the stem base. However, within several days the NCE rose to a maximum of 130 ng CO2 cm-2 sec-1 on day 8. This peak rate was similar to that of recently expanded new leaves and held for about 3 days before declining. Leaves of similar age and position on uncut plants showed a steady decline in NCE. Leaf resistance, r'l, was low (c. 0.8 sec cm-1) and did not change as the NCE increased during the first 8 days. Mesophyll resistance, r'm, to carbon dioxide diffusion was initially high and declined from c. 9 to 2 sec cm-1 during this period. Comparison of dry weight changes of plant parts after stubble leaves were either retained or removed suggested that the tap-root benefited most by stubble leaf retention. The contribution to new shoots from stubble leaves appeared to be slight. However, when stubble leaves were exposed to 14CO2 on day 11, photosynthate was mainly exported into the shoot arising from the axil of the exposed leaf. This suggests that stubble leaves substitute, in part or completely, for the supply of carbohydrate to stubble shoots normally derived from reserves mobilized in the tap-root. The likely causes of rejuvenation in NCE of stubble leaves after partial shoot removal are discussed along with the significance of this photosynthetic contribution to regrowth of the lucerne plant.