Systems-biology dissection of eukaryotic cell growth

A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth

Reproductive success through high pollinator visitation rates despite self incompatibility in an endangered wallflower

PREMISE OF THE STUDY: Self incompatibility (SI) in rare plants presents a unique challenge—SI protects plants from inbreeding depression, but requires a sufficient number of mates and xenogamous pollination. Does SI persist in an endangered polyploid? Is pollinator visitation sufficient to ensure reproductive success? Is there evidence of inbreeding/outbreeding depression? We characterized the mating system, primary pollinators, pollen limitation, and inbreeding/outbreeding depression in Erysimum teretifolium to guide conservation efforts. METHODS: We compared seed production following self pollination and within- and between-population crosses. Pollen tubes were visualized after self pollinations and between-population pollinations. Pollen limitation was tested in the field. Pollinator observations were quantified using digital video. Inbreeding/outbreeding depression was assessed in progeny from self and outcross pollinations at early and later developmental stages. KEY RESULTS: Self-pollination reduced seed set by 6.5× and quadrupled reproductive failure compared with outcross pollination. Pollen tubes of some self pollinations were arrested at the stigmatic surface. Seed-set data indicated strong SI, and fruit-set data suggested partial SI. Pollinator diversity and visitation rates were high, and there was no evidence of pollen limitation. Inbreeding depression (δ) was weak for early developmental stages and strong for later developmental stages, with no evidence of outbreeding depression. CONCLUSIONS: The rare hexaploid E. teretifolium is largely self incompatible and suffers from late-acting inbreeding depression. Reproductive success in natural populations was accomplished through high pollinator visitation rates consistent with a lack of pollen limitation. Future reproductive health for this species will require large population sizes with sufficient mates and a robust pollinator community

Auditory reafferences: The influence of real-time feedback on movement control

© 2015 Kennel, Streese, Pizzera, Justen, Hohmann and Raab. Auditory reafferences are real-time auditory products created by a person's own movements. Whereas the interdependency of action and perception is generally well studied, the auditory feedback channel and the influence of perceptual processes during movement execution remain largely unconsidered. We argue that movements have a rhythmic character that is closely connected to sound, making it possible to manipulate auditory reafferences online to understand their role in motor control. We examined if step sounds, occurring as a by-product of running, have an influence on the performance of a complex movement task. Twenty participants completed a hurdling task in three auditory feedback conditions: a control condition with normal auditory feedback, a white noise condition in which sound was masked, and a delayed auditory feedback condition. Overall time and kinematic data were collected. Results show that delayed auditory feedback led to a significantly slower overall time and changed kinematic parameters. Our findings complement previous investigations in a natural movement situation with non-artificial auditory cues. Our results support the existing theoretical understanding of action-perception coupling and hold potential for applied work, where naturally occurring movement sounds can be implemented in the motor learning processes

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects

BACKGROUND: A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a molecular clock approach, in which DNA or amino acid substitution rates are calibrated with fossils or geological/climatic events, can provide indirect estimates of clade ages and diversification rates. The utility of this approach depends on the rate constancy of molecular evolution at a genetic locus across time and across lineages. Although the nuclear ribosomal internal transcribed spacer region (nrITS) is increasingly being used to infer clade ages in plants, little is known about the sources or magnitude of variation in its substitution rate. Here, we systematically review the literature to assess substitution rate variation in nrITS among angiosperms, and we evaluate possible correlates of the variation. RESULTS: We summarize 28 independently calibrated nrITS substitution rates ranging from 0.38 × 10(-9 )to 8.34 × 10(-9 )substitutions/site/yr. We find that herbaceous lineages have substitution rates almost twice as high as woody plants, on average. We do not find any among-lineage phylogenetic constraint to the rates, or any effect of the type of calibration used. Within life history categories, both the magnitude of the rates and the variance among rates tend to decrease with calibration age. CONCLUSION: Angiosperm nrITS substitution rates vary by approximately an order of magnitude, and some of this variation can be attributed to life history categories. We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results. We also suggest that for lineages with independent calibrations, much of the variation in nrITS substitution rates may come from uncertainty in calibration date estimates, highlighting the importance of accurate and/or multiple calibration dates

Terahertz hot electron bolometer waveguide mixers for GREAT

Supplementing the publications based on the first-light observations with the German Receiver for Astronomy at Terahertz frequencies (GREAT) on SOFIA, we present background information on the underlying heterodyne detector technology. We describe the superconducting hot electron bolometer (HEB) detectors that are used as frequency mixers in the L1 (1400 GHz), L2 (1900 GHz), and M (2500 GHz) channels of GREAT. Measured performance of the detectors is presented and background information on their operation in GREAT is given. Our mixer units are waveguide-based and couple to free-space radiation via a feedhorn antenna. The HEB mixers are designed, fabricated, characterized, and flight-qualified in-house. We are able to use the full intermediate frequency bandwidth of the mixers using silicon-germanium multi-octave cryogenic low-noise amplifiers with very low input return loss. Superconducting HEB mixers have proven to be practical and sensitive detectors for high-resolution THz frequency spectroscopy on SOFIA. We show that our niobium-titanium-nitride (NbTiN) material HEBs on silicon nitride (SiN) membrane substrates have an intermediate frequency (IF) noise roll-off frequency above 2.8 GHz, which does not limit the current receiver IF bandwidth. Our mixer technology development efforts culminate in the first successful operation of a waveguide-based HEB mixer at 2.5 THz and deployment for radioastronomy. A significant contribution to the success of GREAT is made by technological development, thorough characterization and performance optimization of the mixer and its IF interface for receiver operation on SOFIA. In particular, the development of an optimized mixer IF interface contributes to the low passband ripple and excellent stability, which GREAT demonstrated during its initial successful astronomical observation runs.Comment: Accepted for publication in A&A (SOFIA/GREAT special issue

Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests

Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions

Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort.

BACKGROUND: Better understanding of drug resistance patterns in HIV-infected children on antiretroviral therapy (ART) is required to inform public health policies in high prevalence settings. The aim of this study was to characterise the acquired drug resistance in HIV-infected children failing first-line ART in a decentralised rural HIV programme. METHODS: Plasma samples were collected from 101 paediatric patients (≤15 yrs of age) identified as failing ART. RNA was extracted from the plasma, reverse transcribed and a 1.3 kb region of the pol gene was amplified and sequenced using Sanger sequencing protocols. Sequences were edited in Geneious and drug resistance mutations were identified using the RegaDB and the Stanford resistance algorithms. The prevalence and frequency of mutations were analysed together with selected clinical and demographic data in STATA v11. RESULTS: A total of 101 children were enrolled and 89 (88%) were successfully genotyped; 73 on a non-nucleoside reverse-transcriptase inhibitor (NNRTI)-based regimen and 16 on a protease inhibitor (PI)-based regimen at the time of genotyping. The majority of patients on an NNRTI regimen (80%) had both nucleoside reverse-transcriptase inhibitor (NRTI) and NNRTI resistance mutations. M184V and K103N were the most common mutations amongst children on NNRTI-based and M184V among children on PI-based regimens. 30.1% had one or more thymidine analogue mutation (TAM) and 6% had ≥3 TAMs. Only one child on a PI-based regimen harboured a major PI resistance mutation. CONCLUSIONS: Whilst the patterns of resistance were largely predictable, the few complex resistance patterns seen with NNRTI-based regimens and the absence of major PI mutations in children failing PI-based regimens suggest the need for wider access to genotypic resistance testing in this setting

Population-specific association of Clock gene polymorphism with annual cycle timing in stonechats

Timing is essential for survival and reproduction of organisms across the tree of life. The core circadian clock gene Clk has been implicated in annual timing and shows highly conserved sequence homology across vertebrates except for one variable region of poly Glutamine repeats. Clk genotype varies in some species with latitude, seasonal timing and migration. However, findings are inconsistent, difficult to disentangle from environmental responses, and biased towards high latitudes. Here we combine field data with a common-garden set up to study associations of Clk with latitude, migration and annual-cycle timing within the stonechat species complex with trans-equatorial distribution range. Including 950 individuals from nine populations with diverse migratory strategies. Gene diversity was lowest in resident African and Canary Island populations and increased with latitude, independently of migration distance. Repeat length and annual-cycle timing was linked in a population-specific way. Specifically, equatorial African stonechats showed delayed timing with longer repeat length for all annual-cycle stages. Our data suggest that at low latitudes with constant photoperiod, Clk genotype might orchestrate a range of consistent, individual chronotypes. In contrast, the influence of Clk on annual-cycle timing at higher latitudes might be mediated by its interactions with genes involved in (circadian) photoperiodic pathways

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes