Two distinct conformational states define the interaction of human RAD51‐ATP with single‐stranded DNA

An essential mechanism for repairing DNA double‐strand breaks is homologous recombination (HR). One of its core catalysts is human RAD51 (hRAD51), which assembles as a helical nucleoprotein filament on single‐stranded DNA, promoting DNA‐strand exchange. Here, we study the interaction of hRAD51 with single‐stranded DNA using a single‐molecule approach. We show that ATP‐bound hRAD51 filaments can exist in two different states with different contour lengths and with a free‐energy difference of ~4 k_BT per hRAD51 monomer. Upon ATP hydrolysis, the filaments convert into a disassembly‐competent ADP‐bound configuration. In agreement with the single‐molecule analysis, we demonstrate the presence of two distinct protomer interfaces in the crystal structure of a hRAD51‐ATP filament, providing a structural basis for the two conformational states of the filament. Together, our findings provide evidence that hRAD51‐ATP filaments can exist in two interconvertible conformational states, which might be functionally relevant for DNA homology recognition and strand exchange.     

Neuroethology of Melibe leonina Swimming Behavior

The nudibranch Melibe leonina swims by rhythmically flexingits body from side to side at a frequency of 1 cycle every 2–5sec. Melibe swim spontaneously, when they are dislodged fromthe substrate, or when they come in contact with predatory seastars,such as Pycnopodia helianthoides. Intracellular recordings obtainedfrom semi-intact swimming Melibe reveal a population of 15 swimmotoneurons (SMNs) in each pedal ganglion. In general, SMNsin one pedal ganglion fire out-of-phase with SMNs in the oppositepedal ganglion, resulting in rhythmic side-to-side bending movements.In isolated brains, recordings from SMNs yield similar results,indicating the existence of a swim central pattern generator(CPG). There is no evidence for synaptic interactions betweenSMNs and either inhibiting or exciting SMNs has no impact onthe swim pattern. The SMNs are driven by a CPG consisting of4 interneurons; 2 in the cerebropleural ganglia and 1 in eachpedal ganglion. Appropriate bursting activity in the swim interneuronsis necessary for swimming to occur. Either hyperpolarizationor depolarization of any of the 4 CPG interneurons disruptsthe normal swim pattern. Swimming behavior, and the fictiveswim motor program expressed by the isolated brain, are inhibitedby light and nitric oxide donors. NADPH-diaphorase stainingand nitric oxide synthase (NOS) immunocytochemistry of Melibebrains suggests the source of nitric oxide might be a pair ofbilaterally symmetrical cells located in the cerebropleuralganglia.     

Temperature can interact with landscape factors to affect songbird productivity

Increased temperatures and more extreme weather patterns associated with global climate change can interact with other factors that regulate animal populations, but many climate change studies do not incorporate other threats to wildlife in their analyses. We used 20 years of nest‐monitoring data from study sites across a gradient of habitat fragmentation in Missouri, USA, to investigate the relative influence of weather variables (temperature and precipitation) and landscape factors (forest cover and edge density) on the number of young produced per nest attempt (i.e., productivity) for three species of songbirds. We detected a strong forest cover × temperature interaction for the Acadian Flycatcher (Empidonax virescens) on productivity. Greater forest cover resulted in greater productivity because of reduced brood parasitism and increased nest survival, whereas greater temperatures reduced productivity in highly forested landscapes because of increased nest predation but had no effect in less forested landscapes. The Indigo Bunting (Passerina cyanea) exhibited a similar pattern, albeit with a marginal forest cover × temperature interaction. By contrast, productivity of the Northern Cardinal (Cardinalis cardinalis) was not influenced by landscape effects or temperature. Our results highlight a potential difficulty of managing wildlife in response to global change such as habitat fragmentation and climate warming, as the habitat associated with the greatest productivity for flycatchers was also that most negatively influenced by high temperatures. The influence of high temperatures on nest predation (and therefore, nest predators) underscores the need to acknowledge the potential complexity of species' responses to climate change by incorporating a more thorough consideration of community ecology in the development of models of climate impacts on wildlife.     

Nonnative plant invasion increases urban vegetation structure and influences arthropod communities

Aim

Ecological theory and empirical evidence indicate that greater structural complexity and diversity in plant communities increases arthropod abundance and diversity. Nonnative plants are typically associated with low arthropod abundance and diversity due to lack of evolutionary history. However, nonnative plants increase the structural complexity of forests, as is common in urban forests. Therefore, urban forests are ideal ecosystems to determine whether structural complexity associated with nonnative plants will increase abundance and diversity of arthropods, as predicted by complexity literature, or whether structural complexity associated with nonnative plants will be depauperate of arthropods, as predicted by nonnative plant literature.

Location

We sampled 24 urban temperate deciduous and mixed forests in two cites, Raleigh, North Carolina and Newark, Delaware, in the eastern United States.

Methods

We quantified ground cover vegetation and shrub layer vegetation in each forest and created structural complexity metrics to represent total, nonnative and native understory vegetation structural complexity. We vacuum sampled arthropods from vegetation and quantified the abundance, biomass, richness and diversity of spiders and non-spider arthropods.

Results

Nonnative plants increase understory vegetation complexity in urban forests. In Raleigh and Newark, we found support for the hypotheses that dense vegetation will increase arthropod abundance and biomass, and against the hypothesis that nonnative vegetation will decrease arthropods. Urban forest arthropod abundance and biomass, but not diversity, increased with greater nonnative and native structural complexity.

Main Conclusions

Invaded urban forests may provide adequate food in the form of arthropod biomass to transfer energy to the next trophic level, but likely fail to provide ecological services and functions offered by diverse species, like forest specialists. Urban land managers should survey urban forests for nonnative and native plant communities and prioritize replacing dense nonnative plants with native species when allocating vegetation maintenance resources.     

Mandarin Speech Perception in Combined Electric and Acoustic Stimulation

For deaf individuals with residual low-frequency acoustic hearing, combined use of a cochlear implant (CI) and hearing aid (HA) typically provides better speech understanding than with either device alone. Because of coarse spectral resolution, CIs do not provide fundamental frequency (F0) information that contributes to understanding of tonal languages such as Mandarin Chinese. The HA can provide good representation of F0 and, depending on the range of aided acoustic hearing, first and second formant (F1 and F2) information. In this study, Mandarin tone, vowel, and consonant recognition in quiet and noise was measured in 12 adult Mandarin-speaking bimodal listeners with the CI-only and with the CI+HA. Tone recognition was significantly better with the CI+HA in noise, but not in quiet. Vowel recognition was significantly better with the CI+HA in quiet, but not in noise. There was no significant difference in consonant recognition between the CI-only and the CI+HA in quiet or in noise. There was a wide range in bimodal benefit, with improvements often greater than 20 percentage points in some tests and conditions. The bimodal benefit was compared to CI subjects’ HA-aided pure-tone average (PTA) thresholds between 250 and 2000 Hz; subjects were divided into two groups: “better” PTA (<50 dB HL) or “poorer” PTA (>50 dB HL). The bimodal benefit differed significantly between groups only for consonant recognition. The bimodal benefit for tone recognition in quiet was significantly correlated with CI experience, suggesting that bimodal CI users learn to better combine low-frequency spectro-temporal information from acoustic hearing with temporal envelope information from electric hearing. Given the small number of subjects in this study (n = 12), further research with Chinese bimodal listeners may provide more information regarding the contribution of acoustic and electric hearing to tonal language perception.     

The production of lipids alternately labelled with carbon-13

Chlorella cells were shown to have similar fatty acid profiles when grown photoautotrophically or if grown photoheterotrophically with ethanoate (acetate) as carbon source. When supplied with ethanoate labelled with carbon-13 in the methyl group, the alga incorporated it into fatty acids with retention of the sequence of labelling on alternate carbon atoms, thus providing a convenient method for synthesising lipids in a form useful for nuclear magnetic resonance (NMR) studies of lipids in situ in membranes. Marine algae used in fish farming may have higher levels of very highly unsaturated fatty acids; proposals for producing these compounds labelled with carbon-13 are, therefore, presented, based on using centrally labelled glycerol. The scope for producing other substances labelled in a form suitable for NMR studies, such as carotenoids, is discussed.     

Discovery of synthesis and secretion of polyol esters of fatty acids by four basidiomycetous yeast species in the order Sporidiobolales

Polyol esters of fatty acids (PEFA) are amphiphilic glycolipids produced by yeast that could play a role as natural, environmentally friendly biosurfactants. We recently reported discovery of a new PEFA-secreting yeast species, Rhodotorula babjevae, a basidiomycetous yeast to display this behavior, in addition to a few other Rhodotorula yeasts reported on the 1960s. Additional yeast species within the taxonomic order Sporidiobolales were screened for secreted glycolipid production. PEFA production equal or above 1 g L^?1 were detected in 19 out of 65 strains of yeast screened, belonging to 6 out of 30 yeast species tested. Four of these species were not previously known to secrete glycolipids. These results significantly increase the number of yeast species known to secrete PEFA, holding promise for expanding knowledge of PEFA synthesis and secretion mechanisms, as well as setting the groundwork towards commercialization.     

HIV-1 Subtype C-Infected Individuals Maintaining High Viral Load as Potential Targets for the “Test-and-Treat” Approach to Reduce HIV Transmission

The first aim of the study is to assess the distribution of HIV-1 RNA levels in subtype C infection. Among 4,348 drug-naïve HIV-positive individuals participating in clinical studies in Botswana, the median baseline plasma HIV-1 RNA levels differed between the general population cohorts (4.1–4.2 log₁₀) and cART-initiating cohorts (5.1–5.3 log₁₀) by about one log₁₀. The proportion of individuals with high (≥50,000 (4.7 log₁₀) copies/ml) HIV-1 RNA levels ranged from 24%–28% in the general HIV-positive population cohorts to 65%–83% in cART-initiating cohorts. The second aim is to estimate the proportion of individuals who maintain high HIV-1 RNA levels for an extended time and the duration of this period. For this analysis, we estimate the proportion of individuals who could be identified by repeated 6- vs. 12-month-interval HIV testing, as well as the potential reduction of HIV transmission time that can be achieved by testing and ARV treating. Longitudinal analysis of 42 seroconverters revealed that 33% (95% CI: 20%–50%) of individuals maintain high HIV-1 RNA levels for at least 180 days post seroconversion (p/s) and the median duration of high viral load period was 350 (269; 428) days p/s. We found that it would be possible to identify all HIV-infected individuals with viral load ≥50,000 (4.7 log₁₀) copies/ml using repeated six-month-interval HIV testing. Assuming individuals with high viral load initiate cART after being identified, the period of high transmissibility due to high viral load can potentially be reduced by 77% (95% CI: 71%–82%). Therefore, if HIV-infected individuals maintaining high levels of plasma HIV-1 RNA for extended period of time contribute disproportionally to HIV transmission, a modified “test-and-treat” strategy targeting such individuals by repeated HIV testing (followed by initiation of cART) might be a useful public health strategy for mitigating the HIV epidemic in some communities.     

Effects of transketolase cofactors on its conformation and stability

In studying transketolase (TK) from Saccharomyces cerevisiae, the majority of researchers use as cofactors Mg(2+) and thiamine diphosphate (ThDP) (by analogy with other ThDP-dependent enzymes), whereas the active site of native holoTK is known to contain only Ca(2+). Experiments in which Mg(2+) was substituted for Ca(2+) demonstrated that the kinetic properties of TK varied with the bivalent cation cofactor. This led to the assumption that TK species obtained by reconstitution from apoTK and ThDP in the presence of Ca(2+) or Mg(2+), respectively, adopt different conformations. Kinetic study of the H103A mutant yeast transketolase. FEBS Letters 567, 270-274]. Analysis of far-UV circular dichroism (CD) spectra and of data, obtained using methods of thermal denaturing, differential scanning calorimetry (DSC) and tryptophan fluorescence spectroscopy, corroborated this assumption. Indeed, the ratios of secondary structure elements in the molecule of apoTK, recorded in the presence of Ca(2+) or Mg(2+), respectively, turned out to be different. The two forms of the holoenzyme, obtained by reconstitution from apoTK and ThDP in the presence of Ca(2+) or Mg(2+), respectively, also differed in stability: the holoenzyme was more stable in the presence of Ca(2+) than Mg(2+).