The Valley-of-Death: Reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment

The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However, empirical data as to the topography of fitness landscapes are limited, owing to difficulties in measuring fitness for large numbers of genotypes under any condition. We previously reported a case of reciprocal sign epistasis (RSE), where two mutations individually increased yeast fitness in a glucose-limited environment, but reduced fitness when combined, suggesting the existence of two peaks on the fitness landscape. We sought to determine whether a ridge connected these peaks so that populations founded by one mutant could reach the peak created by the other, avoiding the low-fitness Valley-of-Death between them. Sequencing clones after 250 generations of further evolution provided no evidence for such a ridge, but did reveal many presumptive beneficial mutations, adding to a growing body of evidence that clonal interference pervades evolving microbial populations

Evaluation of the vector competence of a native UK mosquito Ochlerotatus detritus (Aedes detritus) for dengue, chikungunya and West Nile viruses

BACKGROUND: To date there has been no evidence of mosquito-borne virus transmission of public health concern in the UK, despite the occurrence of more than 30 species of mosquito, including putative vectors of arboviruses. The saltmarsh mosquito Ochlerotatus detritus [syn. Aedes (Ochlerotatus) detritus] is locally common in parts of the UK where it can be a voracious feeder on people. METHODS: Here, we assess the competence of O. detritus for three major arboviruses: dengue virus (DENV), chikungunya virus (CHIKV) and West Nile virus (WNV) using adult mosquitoes reared from wild, field-obtained immatures. RESULTS: We demonstrate laboratory competence for WNV at 21 °C, with viral RNA detected in the mosquito’s saliva 17 days after oral inoculation. By contrast, there was no evidence of laboratory competence of O. detritus for either DENV or CHIKV. CONCLUSIONS: To our knowledge, this is the first study to demonstrate competence of a UK mosquito for WNV and confirms that O. detritus may present a potential risk for arbovirus transmission in the UK and that further investigation of its vector role in the wild is required

Data Gathering in UWA Sensor Networks : Practical Considerations and Lessons from Sea Trials

Underwater acoustic (UWA) network protocol design is a challenging task due to several factors, such as slow propagation of acoustic waves, low frequency bandwidth and high bit error and frame error rates often encountered in real UWA environments. In this paper, we consider the design of a robust and scalable data gathering protocol for UWA sensor networks (UASNs), focusing on practical considerations and lessons learnt from multiple lake and sea trials. A cross-layer protocol is presented that integrates a network discovery process, intelligent routing, scheduling via Transmit Delay Allocation MAC (TDA-MAC) and multi-node Automatic Repeat Request (ARQ), to facilitate reliable data gathering in practical UASN deployments. Furthermore, this paper presents the details of a novel experimental testbed and underwater sensor node prototype that were used for the trials reported in this study. Based on the results of the trials, important conclusions are drawn on the protocol features required to achieve reliable networked communication in realistic UWA environments. The insights gained from the trials are valuable both for further development of the proposed data gathering protocol, and for the wider UWA networking research community concerned with developing practical solutions for real-world UASN deployments

IL-23 past, present, and future: a roadmap to advancing IL-23 science and therapy

Interleukin (IL)-23, an IL-12 cytokine family member, is a hierarchically dominant regulatory cytokine in a cluster of immune-mediated inflammatory diseases (IMIDs), including psoriasis, psoriatic arthritis, and inflammatory bowel disease. We review IL-23 biology, IL-23 signaling in IMIDs, and the effect of IL-23 inhibition in treating these diseases. We propose studies to advance IL-23 biology and unravel differences in response to anti–IL-23 therapy. Experimental evidence generated from these investigations could establish a novel molecular ontology centered around IL-23–driven diseases, improve upon current approaches to treating IMIDs with IL-23 inhibition, and ultimately facilitate optimal identification of patients and, thereby, outcomes

Timing and conditions of peak metamorphism and cooling across the Zimithang Thrust, Arunachal Pradesh, India

The Zimithang Thrust juxtaposes two lithotectonic units of the Greater Himalayan Sequence in Arunachal Pradesh, NE India. Monazite U–Pb, muscovite 40Ar/39Ar and thermobarometric data from rocks in the hanging and footwall constrain the timing and conditions of their juxtaposition across the structure, and their subsequent cooling. Monazite grains in biotite–sillimanite gneiss in the hanging wall yield LA-ICP-MS U–Pb ages of 16 ± 0.2 to 12.7 ± 0.4 Ma. A schistose gneiss within the high strain zone yields overlapping-to-younger monazite ages of 14.9 ± 0.3 to 11.5 ± 0.3 Ma. Garnet–staurolite–mica schists in the immediate footwall yield older monazite ages of 27.3 ± 0.6 to 17.1 ± 0.2 Ma. Temperature estimates from Ti-in-biotite and garnet–biotite thermometry suggest similar peak temperatures were achieved in the hanging and footwalls (~ 525–650 °C). Elevated temperatures of ~ 700 °C appear to have been reached in the high strain zone itself and in the footwall further from the thrust. Single grain fusion 40Ar/39Ar muscovite data from samples either side of the thrust yield ages of ~ 7 Ma, suggesting that movement along the thrust juxtaposed the two units by the time the closure temperature of Ar diffusion in muscovite had been reached. These data confirm previous suggestions that major orogen-parallel out-of-sequence structures disrupt the Greater Himalayan Sequence at different times during Himalayan evolution, and highlight an eastwards-younging trend in 40Ar/39Ar muscovite cooling ages at equivalent structural levels along Himalayan strike

Association between enthesitis/dactylitis resolution and patient-reported outcomes in guselkumab-treated patients with psoriatic arthritis

Objectives To evaluate the association between enthesitis resolution (ER) and dactylitis resolution (DR) and meaningful improvements in patient-reported outcomes (PROs) among biologic-naïve patients with PsA receiving guselkumab in the DISCOVER-2 study. Methods Enthesitis and dactylitis, characteristic lesions of PsA, were evaluated by independent assessors using the Leeds Enthesitis Index (range, 0–6) and Dactylitis Severity Score (range, 0–60). Proportions of patients with ER or DR (score = 0) among those with score > 0 at baseline were determined at weeks 24, 52, and 100. PROs included: fatigue (Functional Assessment of Chronic Illness Therapy-Fatigue [FACIT-Fatigue]), pain (0–100 visual analog scale), physical function (Health Assessment Questionnaire-Disability Index [HAQ-DI]), and health-related quality of life (36-item Short-Form Health Survey physical/mental component summary [SF-36 PCS/MCS]). Meaningful responses were defined as: improvements of ≥ 4 for FACIT-Fatigue, ≥ 0.35 for HAQ-DI, and ≥ 5 for SF-36 PCS/MCS and absolute scores of ≤ 15 for minimal pain and ≤ 0.5 for normalized HAQ-DI. Associations between ER/DR status and PRO response status were tested using a Chi-square test. Results Guselkumab-treated patients with ER were more likely than those without ER to achieve minimal pain (p < 0.001), normalized HAQ-DI (p < 0.001), and PCS response (p < 0.05) at weeks 24, 52, and 100. Patients with DR were more likely than those without DR to achieve FACIT-Fatigue response at week 24 and week 52 (both p ≤ 0.01) and minimal pain at week 24 and normalized HAQ-DI at week 52 (both p ≤ 0.03). Conclusion In biologic-naïve patients with active PsA treated with guselkumab, achieving ER or DR was associated with durable improvements in selected PROs, including those of high importance to patients

IL-23 past, present, and future: a roadmap to advancing IL-23 science and therapy

Interleukin (IL)-23, an IL-12 cytokine family member, is a hierarchically dominant regulatory cytokine in a cluster of immune-mediated inflammatory diseases (IMIDs), including psoriasis, psoriatic arthritis, and inflammatory bowel disease. We review IL-23 biology, IL-23 signaling in IMIDs, and the effect of IL-23 inhibition in treating these diseases. We propose studies to advance IL-23 biology and unravel differences in response to anti-IL-23 therapy. Experimental evidence generated from these investigations could establish a novel molecular ontology centered around IL-23-driven diseases, improve upon current approaches to treating IMIDs with IL-23 inhibition, and ultimately facilitate optimal identification of patients and, thereby, outcomes

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible evolutionary trajectories of adaptation. However, little is known about the actual shape of fitness landscapes, including whether valleys of low fitness create local fitness optima, acting as barriers to adaptive change. Here we provide evidence of a rugged molecular fitness landscape arising during an evolution experiment in an asexual population of Saccharomyces cerevisiae. We identify the mutations that arose during the evolution using whole-genome sequencing and use competitive fitness assays to describe the mutations individually responsible for adaptation. In addition, we find that a fitness valley between two adaptive mutations in the genes MTH1 and HXT6/HXT7 is caused by reciprocal sign epistasis, where the fitness cost of the double mutant prohibits the two mutations from being selected in the same genetic background. The constraint enforced by reciprocal sign epistasis causes the mutations to remain mutually exclusive during the experiment, even though adaptive mutations in these two genes occur several times in independent lineages during the experiment. Our results show that epistasis plays a key role during adaptation and that inter-genic interactions can act as barriers between adaptive solutions. These results also provide a new interpretation on the classic Dobzhansky-Muller model of reproductive isolation and display some surprising parallels with mutations in genes often associated with tumors