Maternal Condition but Not Corticosterone Is Linked to Offspring Sex Ratio in a Passerine Bird

There is evidence of offspring sex ratio adjustment in a range of species, but the potential mechanisms remain largely unknown. Elevated maternal corticosterone (CORT) is associated with factors that can favour brood sex ratio adjustment, such as reduced maternal condition, food availability and partner attractiveness. Therefore, the steroid hormone has been suggested to play a key role in sex ratio manipulation. However, despite correlative and causal evidence CORT is linked to sex ratio manipulation in some avian species, the timing of adjustment varies between studies. Consequently, whether CORT is consistently involved in sex-ratio adjustment, and how the hormone acts as a mechanism for this adjustment remains unclear. Here we measured maternal baseline CORT and body condition in free-living blue tits (Cyanistes caeruleus) over three years and related these factors to brood sex ratio and nestling quality. In addition, a non-invasive technique was employed to experimentally elevate maternal CORT during egg laying, and its effects upon sex ratio and nestling quality were measured. We found that maternal CORT was not correlated with brood sex ratio, but mothers with elevated CORT fledged lighter offspring. Also, experimental elevation of maternal CORT did not influence brood sex ratio or nestling quality. In one year, mothers in superior body condition produced male biased broods, and maternal condition was positively correlated with both nestling mass and growth rate in all years. Unlike previous studies maternal condition was not correlated with maternal CORT. This study provides evidence that maternal condition is linked to brood sex ratio manipulation in blue tits. However, maternal baseline CORT may not be the mechanistic link between the maternal condition and sex ratio adjustment. Overall, this study serves to highlight the complexity of sex ratio adjustment in birds and the difficulties associated with identifying sex biasing mechanisms.     

The behavioral context of common dolphin (Delphinus sp.) vocalizations

Correlations between surface behavior and concurrent underwater vocalizations were modeled for common dolphins (Delphinus spp.) in the Southern California Bight (SCB) over multiple field seasons. Clicks, pulsed calls, and whistles were examined, with a total of 50 call features identified. Call features were used to classify behavior using random forest decision trees, with rates of correct classification reaching 80.6% for fast travel, 84.6% for moderate travel, 59.8% for slow travel, and 58% for foraging behavior. Common dolphins spent most of their time traveling. The highest number of clicks, pulsed calls, and complex whistles were produced during fast travel. In contrast, during foraging there were few pulsed calls and whistles produced, and the whistles were simple with narrow bandwidths and few harmonics. Behavior and vocalization patterns suggest nocturnal foraging in offshore waters as the primary feeding strategy. Group size and spacing were strongly correlated with behavior and rates of calling, with higher call rates in dispersed traveling groups and lower call rates in loosely aggregated foraging groups. These results demonstrate that surface behavior can be classified using vocalization data, which builds the framework for behavioral studies of common dolphins using passive acoustic monitoring techniques.     

Human endonuclease III acts preferentially on DNA damage opposite guanine residues in DNA

The human endonuclease III homologue (hNTH1) removes premutagenic cytosine damage from DNA. This includes 5-hydroxycytosine, which has increased potential for pairing with adenine, resulting in C --> T transition mutations. Here we report that hNTH1 acts on both 5-hydroxycytosine and abasic sites preferentially when these are situated opposite guanines in DNA. Discrimination against other opposite bases is strongly dependent on the presence of magnesium. To further elucidate this effect, we have introduced mutations in the helix-hairpin-helix domain of hNTH1 (K212S, P211R, +G212, and DeltaP211), and measured the kinetics of 5-hydroxycytosine removal of the mutants relative to wild type. The K212S and DeltaP211 (truncated hairpin) mutant proteins were both inactive, whereas the extended hairpin in the +G212 mutant diminished recognition and binding to 5-hydroxycytosine-containing DNA. The P211R mutant resembled native hNTH1, except for decreased specificity of binding. Despite the altered kinetic parameters, the active mutants retained the ability to discriminate against the pairing base, indicating that enzyme interactions with the opposite strand relies on other domains than the active site helix-hairpin-helix motif.     

Chaperonin 60: a paradoxical,evolutionarily conserved protein family with multiple moonlighting functions

Chaperonin 60 is the prototypic molecular chaperone, an essential protein in eukaryotes and prokaryotes, whose sequence conservation provides an excellent basis for phylogenetic analysis. Escherichia coli chaperonin 60 (GroEL), the prototype of this family of proteins, has an established oligomeric‐structure‐based folding mechanism and a defined population of folding partners. However, there is a growing number of examples of chaperonin 60 proteins whose crystal structures and oligomeric composition are at variance with GroEL, suggesting that additional complexities in the protein‐folding function of this protein should be expected. In addition, many organisms have multiple chaperonin 60 proteins, some of which have lost their protein‐folding ability. It is emerging that this highly conserved protein has evolved a bewildering variety of additional biological functions – known as moonlighting functions – both within the cell and in the extracellular milieu. Indeed, in some organisms, it is these moonlighting functions that have been left after the loss of the protein‐folding activity. This highlights the major paradox in the biology of chaperonin 60. This article reviews the relationship between the folding and non‐folding (moonlighting) activities of the chaperonin 60 family and discusses current knowledge on their molecular evolution focusing on protein domains involved in the non‐folding chaperonin functions in an attempt to understand the emerging biology of this evolutionarily ancient protein family.     

Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals

The US National Cancer Institute has recently sponsored the formation of a Cohort Consortium (http://2002.cancer.gov/scpgenes.htm) to facilitate the pooling of data on very large numbers of people, concerning the effects of genes and environment on cancer incidence. One likely goal of these efforts will be generate a large population-based case-control series for which a number of candidate genes will be investigated using SNP haplotype as well as genotype analysis. The goal of this paper is to outline the issues involved in choosing a method of estimating haplotype-specific risk estimates for such data that is technically appropriate and yet attractive to epidemiologists who are already comfortable with odds ratios and logistic regression. Our interest is to develop and evaluate extensions of methods, based on haplotype imputation, that have been recently described (Schaid et al., Am J Hum Genet, 2002, and Zaykin et al., Hum Hered, 2002) as providing score tests of the null hypothesis of no effect of SNP haplotypes upon risk, which may be used for more complex tasks, such as providing confidence intervals, and tests of equivalence of haplotype-specific risks in two or more separate populations. In order to do so we (1) develop a cohort approach towards odds ratio analysis by expanding the E-M algorithm to provide maximum likelihood estimates of haplotype-specific odds ratios as well as genotype frequencies; (2) show how to correct the cohort approach, to give essentially unbiased estimates for population-based or nested case-control studies by incorporating the probability of selection as a case or control into the likelihood, based on a simplified model of case and control selection, and (3) finally, in an example data set (CYP17 and breast cancer, from the Multiethnic Cohort Study) we compare likelihood-based confidence interval estimates from the two methods with each other, and with the use of the single-imputation approach of Zaykin et al. applied under both null and alternative hypotheses. We conclude that so long as haplotypes are well predicted by SNP genotypes (we use the Rh2 criteria of Stram et al. [1]) the differences between the three methods are very small and in particular that the single imputation method may be expected to work extremely well.     

Compartmentation of intracellular nucleotides in mammalian cells

The important role of nucleotides in cellular metabolism requires that serious consideration be given to the question of the homogeneity or inhomogeneity of nucleotide pools in cells. The purpose of this review is to summarize the existing evidence for compartmentation of nucleotide pools, discuss the limitations of this evidence, and to discuss the implications of compartmentation for the interpretation of nucleotide concentration measurements. Evidence for nucleotide compartmentation comes from the following types of evidence: compartmentation of RNA precursors; compartmentation of deoxynucleoside triphosphates; mitochondrial compartmentation; the existence of tightly bound nucleotides; pools derived from alternative synthetic routes; compartmentation in cyclic nucleotide metabolism; channeling in the synthesis of pyrimidine nucleotides; and others. The types of evidence adduced for compartmentation will be considered critically and in detail, and alternative explanations considered, as well. Implications of the data and hypotheses on nucleotide compartmentation for the interpretation of nucleotide pool measurements in various types of experiments will be discussed.     

Reproductive biology of the milk shark Rhizoprionodon acutus and the bigeye houndshark Iago omanensis in the coastal waters of Oman

Female Rhizoprionodon acutus were found to mature between 62 and 74 cm total length ( L _T) whereas males matured between 63 and 71 cm L _T. The L _T at 50% maturity was 64·3 cm for females and 64·7 cm for males. Litter size varied from one to six embryos, and was positively correlated with maternal L _T. Female embryos outnumbered males by a ratio of 2·3:1. The size at birth was c . 37 cm L _T. Full‐term embryos and post‐partum females were observed during all seasons although their occurrence was highest in spring. Spermatozoa were rarely recorded in the oviducal gland, indicating that this species does not store sperm. It was not possible to generate maturity curves for Iago omanensis but it was evident that females matured by the time they reached 35 cm and males were mature by 31 cm L _T. This species displayed a clearly defined reproductive cycle with parturition occurring primarily in spring, after a gestation period of c . 1 year. Maximal embryo size was 19 cm L _T while maximal litter size was 24 embryos. The oviducal gland appeared to act as a seminal receptacle and it appeared that females may utilize these stores by not mating every year.     

Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging

The arsenal of engineered variants of the GFP [green FP (fluorescent protein)] from Aequorea jellyfish provides researchers with a powerful set of tools for use in biochemical and cell biology research. The recent discovery of diverse FPs in Anthozoa coral species has provided protein engineers with an abundance of alternative progenitor FPs from which improved variants that complement or supersede existing Aequorea GFP variants could be derived. Here, we report the engineering of the first monomeric version of the tetrameric CFP (cyan FP) cFP484 from Clavularia coral. Starting from a designed synthetic gene library with mammalian codon preferences, we identified dimeric cFP484 variants with fluorescent brightness significantly greater than the wild-type protein. Following incorporation of dimer-breaking mutations and extensive directed evolution with selection for blue-shifted emission, high fluorescent brightness and photostability, we arrived at an optimized variant that we have named mTFP1 [monomeric TFP1 (teal FP 1)]. The new mTFP1 is one of the brightest and most photostable FPs reported to date. In addition, the fluorescence is insensitive to physiologically relevant pH changes and the fluorescence lifetime decay is best fitted as a single exponential. The 1.19 A crystal structure (1 A=0.1 nm) of mTFP1 confirms the monomeric structure and reveals an unusually distorted chromophore conformation. As we experimentally demonstrate, the high quantum yield of mTFP1 (0.85) makes it particularly suitable as a replacement for ECFP (enhanced CFP) or Cerulean as a FRET (fluorescence resonance energy transfer) donor to either a yellow or orange FP acceptor.     

Sources,fates, and impacts of nitrogen inputs to terrestrial ecosystems: review and synthesis

The relative importance of nitrogen inputs from atmospheric deposition and biological fixation is reviewed in a number of diverse, non-agricultural terrestrial ecosystems. Bulk precipitation inputs of N (l–l2 kg N ha^–1 yr^–1) are the same order of magnitude as, or frequently larger than, the usual range of inputs from nonsymbiotic fixation (< 1=" –=" 5=" kg=" n=">^–1 yr^–1), especially in areas influenced by industrial activity. Bulk precipitation measurements may underestimate total atmospheric deposition by 30–40% because they generally do not include all forms of wet and dry deposition. Symbiotic fixation generally ranges from 10–160 kg N ha^–1 yr^–1) in ecosystems where N-fixing species are present during early successional stages, and may exceed the range under unusual conditions.Rates of both symbiotic and nonsymbiotic fixation appear to be greater during early successional stages of forest development, where they have major impacts on nitrogen dynamics and ecosystem productivity. Fates and impacts of these nitrogen inputs are important considerations that are inadequately understood. These input processes are highly variable in space and time, and few sites have adequate comparative information on both nitrogen deposition and fixation.