Morphometry of sculpins ( Cottus ) in the Clearwater drainage, Idaho

The morphometry of four Idaho species of Cottidae were compared. Pectoral ray counts allowed separation of Cottus beldingi and C. confusus from C. bairdi and C. rhotheus but not from each other. Preopercular armature also allowed identification of the same two groups of two species. Palatine tooth development generally allowed separation of each species as did body prickle development. Body ratios involving caudal peduncle depth allowed separation of C. rhotheus and C. bairdi. Development of lateral lines allowed differentiation of C. rhotheus from the other three species. A key was developed based on the combination of characters studied.     

Sexual imprinting of a Barn Owl ( Tyto alba ) on humans

The sexual imprinting of a Barn Owl ( Tyto alba ) on humans is reported.     

A germline variant in the TP53 polyadenylation signal confers cancer susceptibility

To identify new risk variants for cutaneous basal cell carcinoma, we performed a genome-wide association study of 16 million SNPs identified through whole-genome sequencing of 457 Icelanders. We imputed genotypes for 41,675 Illumina SNP chip-typed Icelanders and their relatives. In the discovery phase, the strongest signal came from rs78378222[C] (odds ratio (OR) = 2.36, P = 5.2 × 10(-17)), which has a frequency of 0.0192 in the Icelandic population. We then confirmed this association in non-Icelandic samples (OR = 1.75, P = 0.0060; overall OR = 2.16, P = 2.2 × 10(-20)). rs78378222 is in the 3' untranslated region of TP53 and changes the AATAAA polyadenylation signal to AATACA, resulting in impaired 3'-end processing of TP53 mRNA. Investigation of other tumor types identified associations of this SNP with prostate cancer (OR = 1.44, P = 2.4 × 10(-6)), glioma (OR = 2.35, P = 1.0 × 10(-5)) and colorectal adenoma (OR = 1.39, P = 1.6 × 10(-4)). However, we observed no effect for breast cancer, a common Li-Fraumeni syndrome tumor (OR = 1.06, P = 0.57, 95% confidence interval 0.88-1.27).     

Sequence variant on 8q24 confers susceptibility to urinary bladder cancer

We conducted a genome-wide SNP association study on 1,803 urinary bladder cancer (UBC) cases and 34,336 controls from Iceland and The Netherlands and follow up studies in seven additional case-control groups (2,165 cases and 3,800 controls). The strongest association was observed with allele T of rs9642880 on chromosome 8q24, 30 kb upstream of MYC (allele-specific odds ratio (OR) = 1.22; P = 9.34 x 10(-12)). Approximately 20% of individuals of European ancestry are homozygous for rs9642880[T], and their estimated risk of developing UBC is 1.49 times that of noncarriers. No association was observed between UBC and the four 8q24 variants previously associated with prostate, colorectal and breast cancers, nor did rs9642880 associate with any of these three cancers. A weaker signal, but nonetheless of genome-wide significance, was captured by rs710521[A] located near TP63 on chromosome 3q28 (allele-specific OR = 1.19; P = 1. 15 x 10(-7)).     

ASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinoma

Fair color increases risk of cutaneous melanoma (CM) and basal cell carcinoma (BCC). Recent genome-wide association studies have identified variants affecting hair, eye and skin pigmentation in Europeans. Here, we assess the effect of these variants on risk of CM and BCC in European populations comprising 2,121 individuals with CM, 2,163 individuals with BCC and over 40,000 controls. A haplotype near ASIP, known to affect a similar spectrum of pigmentation traits as MC1R variants, conferred significant risk of CM (odds ratio (OR) = 1.45, P = 1.2 x 10(-9)) and BCC (OR = 1.33, P = 1.2 x 10(-6)). The variant in TYR encoding the R402Q amino acid substitution, previously shown to affect eye color and tanning response, conferred risk of CM (OR = 1.21, P = 2.8 x 10(-7)) and BCC (OR = 1.14, P = 6.1 x 10(-4)). An eye color variant in TYRP1 was associated with risk of CM (OR = 1.15, P = 4.6 x 10(-4)). The association of all three variants is robust with respect to adjustment for the effect of pigmentation.     

Lagomorphs and the dispersal of seeds into communities dominated by exotic annual weeds

Large areas of western rangeland are presently dominated by alien annual weeds such as Bromus tectorum (cheatgrass). These communities resist succession to perennial communities primarily because the annuals are competitively superior to establishing perennial seedlings and they promote fires that favor weeds over perennials. Succession may be further slowed, however, by low rates of seed dispersal into annual grasslands. We investigated the role of lagomorphs ( Sylvilagus nuttalli , Nuttall's cottontail; S. audubonii , desert cottontail; and Lepus californicus , black-tailed jackrabbit) in seed dispersal across an ecotone: 50 m into woodland, border, and 20 m, 50 m, and 100 m into grassland. We searched pellets for juniper seeds visually and for any other species through germination from crushed pellets after cold, moist stratification. Pellets were not even distributed across transects, but there was no trend with respect to position of transect. Juniperus osteosperma (Utah juniper) was the most abundant seed. Both the number of juniper seeds and the proportion of pellets with juniper seeds decreased steadily from a high in woodland to absence at 100 m into grassland. Only 2 dicot seedlings emerged from pellets, 1 Salsola pestifer and 1 unknown that died prior to identification. Consequently, there was little seed movement into grassland; 72% of all seeds were collected from either woodland or border transects. Lagomorphs apparently do not effectively replenish the native perennial seed pool of cheatgrass-dominated disturbances at Dugway.     

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.     

Muted climate variations in continental Siberia during the mid-Pleistocene epoch

The large difference in carbon and oxygen isotope data from the marine record between marine oxygen isotope stage 12 (MIS 12) and MIS 11, spanning the interval between about 480 and 380 kyr ago, has been interpreted as a transition between an extremely cold glacial period and an unusually warm interglacial period, with consequences for global ice volume, sea level and the global carbon cycle. The extent of the change is intriguing, because orbital forcing is predicted to have been relatively weak at that time. Here we analyse a continuous sediment record from Lake Baikal, Siberia, which reveals a virtually continuous interglacial diatom assemblage, a stable littoral benthic diatom assemblage and lithogenic sediments with 'interglacial' characteristics for the period from MIS 15a to MIS 11 (from about 580 to 380 kyr ago). From these data, we infer significantly weaker climate contrasts between MIS 12 and 11 than during more recent glacial-interglacial transitions in the late Pleistocene epoch (about 130 to 10 kyr ago). For the period from MIS 15a to MIS 11, we also infer an apparent lack of extensive mountain glaciation.     

Physiology: Dynamic instabilities in the inflating lung

In lung diseases such as asthma, expiratory flow becomes limited, airways can collapse and the vital exchange of gases is compromised. Here we model the inflation of collapsed regions of the lung during inspiration in terms of avalanches propagating through a bifurcating network of airways, and find that the accompanying cascade of dynamic pressure instabilities -- avalanche 'shocks' -- manifests as negative elastic resistance of the lung. Our analysis of this apparent thermodynamic paradox provides a better understanding of aeration in the deep regions of the lung, which may find application in medical conditions in which gas exchange is impaired.     

Metal-insulator transition in chains with correlated disorder

According to Bloch's theorem, electronic wavefunctions in perfectly ordered crystals are extended, which implies that the probability of finding an electron is the same over the entire crystal. Such extended states can lead to metallic behaviour. But when disorder is introduced in the crystal, electron states can become localized, and the system can undergo a metal-insulator transition (also known as an Anderson transition). Here we theoretically investigate the effect on the physical properties of the electron wavefunctions of introducing long-range correlations in the disorder in one-dimensional binary solids, and find a correlation-induced metal-insulator transition. We perform numerical simulations using a one-dimensional tight-binding model, and find a threshold value for the exponent characterizing the long-range correlations of the system. Above this threshold, and in the thermodynamic limit, the system behaves as a conductor within a broad energy band; below threshold, the system behaves as an insulator. We discuss the possible relevance of this result for electronic transport in DNA, which displays long-range correlations and has recently been reported to be a one-dimensional disordered conductor.