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Authors: Pieters, Pascal A., et al
Published: Jan 2021
Authors: Pieters, Pascal A., et al
Published: Jan 2021
Regulatory pathways inside living cells employ feed-forward architectures to fulfill essential signal processing functions that aide in the interpretation of various types of inputs through noise-filtering, fold-change detection and adaptation. Although it has been demonstrated computationally that a coherent feed-forward loop (CFFL) can function as noise filter, a property essential to decoding complex temporal signals, this motif has not been extensively characterized experimentally or integrated into larger networks. Here we use post-transcriptional regulation to implement and characterize a synthetic CFFL in an cell-free transcription-translation system and build larger composite feed-forward architectures. We employ microfluidic flow reactors to probe the response of the CFFL circuit using both persistent and short, noise-like inputs and analyze the influence of different circuit components on the steady-state and dynamics of the output. We demonstrate that our synthetic CFFL implementation can reliably repress background activity compared to a reference circuit, but displays low potential as a temporal filter, and validate these findings using a computational model. Our results offer practical insight into the putative noise-filtering behavior of CFFLs and show that this motif can be used to mitigate leakage and increase the fold-change of the output of synthetic genetic circuits.
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From Paper: A fragment-based protein interface design algorithm for symmetric assemblies
Authors: Joshua Laniado, Kyle Meador, Todd O. Yeates
Published: Jan 2021
From Paper: A fragment-based protein interface design algorithm for symmetric assemblies
Authors: Joshua Laniado, Kyle Meador, Todd O. Yeates
Published: Jan 2021
Theoretical and experimental advances in protein engineering have led to the creation of precisely defined, novel protein assemblies of great size and complexity, with diverse applications. One powerful approach involves designing a new attachment or binding interface between two simpler symmetric oligomeric protein components. The required methods of design, which present both similarities and key differences compared to problems in protein docking, remain challenging, and are not yet routine. With the aim of more fully enabling this emerging area of protein material engineering, we developed a computer program, Nanohedra, to introduce two key advances. First, we encoded in the program the construction rules ( . . the search space parameters) that underlie all possible symmetric material constructions. Second, we developed algorithms for rapidly identifying favorable docking/interface arrangements based on tabulations of empirical patterns of known protein fragment-pair associations. As a result, the candidate poses that Nanohedra generates for subsequent amino acid interface design appear highly native-like (at the protein backbone level), while simultaneously conforming to the exacting requirements for symmetry-based assembly. A retrospective computational analysis of successful vs failed experimental studies supports the expectation that this should improve the success rate for this challenging area of protein engineering.
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Authors: Schmücker, Anna, et al
Published: Jan 2021
Authors: Schmücker, Anna, et al
Published: Jan 2021
Histone variants are distinguished by specific substitutions and motifs that might be subject to post-translational modifications (PTMs). Compared with the high conservation of H3 variants, the N- and C-terminal tails of H2A variants are more divergent and are potential substrates for a more complex array of PTMs, which have remained largely unexplored. We used mass spectrometry to inventory the PTMs of the two heterochromatin-enriched variants H2A.W.6 and H2A.W.7 of , which harbor the C-terminal motif KSPK. This motif is also found in macroH2A variants in animals and confers specific properties to the nucleosome. We showed that H2A.W.6 is phosphorylated by the cell cycle-dependent kinase CDKA specifically at KSPK. In contrast, this modification is absent on H2A.W.7, which also harbors the SQ motif associated with the variant H2A.X. Phosphorylation of the SQ motif is critical for the DNA damage response but is suppressed in H2A.W.7 by phosphorylation of KSPK. To identify factors involved in this suppression mechanism, we performed a synthetic screen in fission yeast expressing a mimic of the H2A.W.7. Among those factors was the BRCT-domain protein Mdb1. We showed that phosphorylation of KSPK prevents binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and as a result hampers response to DNA damage. Hence, cross-talks between motif-specific PTMs interfere with the vital functions of H2A variants. Such interference could be responsible for the mutual exclusion of specific motifs between distinct H2A variants. We conclude that sequence innovations in H2A variants have potentiated the acquisition of many specific PTMs with still unknown functions. These add a layer of complexity to the nucleosome properties and their impact in chromatin regulation.
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Authors: Barry W. Brook, Stephen R. Sleightholme, Cameron R. Campbell, Ivan Jaric, Jessie C. Buettel
Published: Jan 2021
Authors: Barry W. Brook, Stephen R. Sleightholme, Cameron R. Campbell, Ivan Jaric, Jessie C. Buettel
Published: Jan 2021
The Thylacine (Thylacinus cynocephalus), or 'Tasmanian tiger', is an icon of recent extinctions, but the timing of its final demise is shrouded in controversy. Extirpated from mainland Australia in the mid-Holocene, the large island of Tasmania became the species' final stronghold. Following European settlement, the Thylacine was heavily persecuted and pushed to the margins of its range. The last captive animal died in 1936, but numerous sightings were reported thereafter. Here we collate and characterize the type, quality, and uncertainty of over a thousand unique sighting records of Thylacines since 1910. We use this novel and unique curated database to underpin a detailed reconstruction and mapping of the species' spatio-temporal distributional dynamics, to pinpoint refugia of late survival and estimate the bioregional patterns of extirpation. Contrary to expectations, the inferred extinction window is wide and relatively recent, spanning from the 1980s to the present day, with extinction most likely in the late 1990s or early 2000s. While improbable, these aggregate data and modelling suggest some chance of ongoing persistence in the remote wilderness of the island. Although our findings for this iconic species hold intrinsic value, our new spatio-temporal mapping of extirpation patterns is also applicable more generally, to support the conservation prioritization and search efforts for other rare taxa of uncertain status.
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Authors: Seidu, Issah, et al
Published: Jan 2021
Authors: Seidu, Issah, et al
Published: Jan 2021
Local Ecological Knowledge has the potential to improve fishery management by providing new data on the fishing efforts, behavior, and abundance trends of fish and other aquatic animals. Here, we relied on local knowledge of fishers to investigate ecological factors that affect elasmobranch fishers‟ operations and the changes in stock status of sharks and rays from 1980 to 2020 in five coastal communities in Ghana. Data were gathered from fishers using participant observation, interviews, focus group discussions, and participatory rural appraisal techniques. The results revealed fisher‟s understanding of six main ecological variables, which are mostly applied to enhance their fishing operations: season and weather conditions, lunar phase, bait type, presence of seabirds and fish movement, color of seawater, and sea current. These ecological features have been applied over the years to enhance fishing operations as well as maximize fisher catch. Fishers reported a profound decline in shark and ray catch from 1980 to 2020 and attributed the decline in size, number, and composition of their catch to overfishing and Illegal, Unreported and Unregulated (IUU) fishing operations. In general, most shark and ray species were abundant in 1980 but have been severely depleted as of 2020, with the exception of Blue Shark ( and Devil rays ( spp), which were reported to be common by the interviewed fishers. The first species depleted were the Thresher sharks (Alopiidae), Tiger Shark ( ), Blackchin Guitarfish ( ), and Lemon Shark ( ), which were depleted early in the 2000s. The next depletions of Hammerhead sharks (Sphyrnidae), Bull Shark ( ), Sand Tiger Shark ( ), Stingrays ( spp), and Spineback Guitarfish ( ) occurred in the 2010s. We found Local Ecological Knowledge of fishers to be surprisingly consistent with scholarly knowledge and call for their inclusion in research, decision-making and management interventions by biologists and policy makers.
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Authors: Seidu, Issah, et al
Published: Jan 2021
Authors: Seidu, Issah, et al
Published: Jan 2021
Small-scale shark fisheries support a large number of coastal community livelihoods in developing countries. Shark meat comprises a cheap source of protein and is traded locally in many parts in developing countries, while the skins, oil, fins and gill rakers are exported to the international market. This study addresses a gap in literature regarding the importance of elasmobranchs to key shark-fishing communities and the degree to which trade in shark products (meat and fins) vary in time and among fishing communities in Ghana. We interviewed 85 fishers and traders involved in shark fisheries in Axim, Dixcove, and Shama communities using semi-structured questionnaires. Fishing was the primary source of income and accounted for 59.9% of the total household income of respondents. Other important economic activities were fish processing (15.2%), fish retailing (14.8%), and small businesses (2.9%). One-third and often two-thirds of respondents generated between 80-100% of their income from shark fisheries: Axim (n = 65%), Dixcove (68%), and Shama (35%). Shark meat consumption was common among fishers and traders and represents a substantial source of protein in the diet of the study communities. Overexploitation of these species may compromise food security. Hammerhead Sharks (Sphyrna spp) and Bull Shark (Carcharhinus leucas) have the most valuable fins and meat. Further, 75% and 95% of fishers and traders respectively see fishing and trading of shark meat as their last safety-net and, therefore, tend to be satisfied with their jobs. Non-fishing related livelihood streams including small businesses and transportation were the major fallback activities both fishers and traders preferred to rely on if there is a ban on the exploitation of sharks in Ghana. Thus, any shark management strategy must take into consideration the preferred livelihood fallback options outlined by fishers and traders, and implement them to ensure the success of the intervention.
From Paper: Mating pattern, duration and multiple mating in <i>Chondromorpha severini</i> Silvestri (Diplopoda: Polydesmida)
Published: Aug 2020
From Paper: Mating pattern, duration and multiple mating in <i>Chondromorpha severini</i> Silvestri (Diplopoda: Polydesmida)
Published: Aug 2020
- We set up a Caenorhabditis elegans model to extrapolate anthelmintic (AH) effects of commercial polyphenols to related gastrointestinal zoonotic species.
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Authors: Lalande, Lucas D., et al
Published: Dec 2020
Authors: Lalande, Lucas D., et al
Published: Dec 2020
- very informative about the role of aging on body mass of elephants in both males and females
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Published: Jan 2021
Published: Jan 2021
Little is known about the social behavior of pygmy slow lorises, in particular, the social relationships of same sex individuals have rarely been investigated. The Slow Loris Conservation Centre was built at the Japan Monkey Centre to enhance the welfare of confiscated slow lorises, promote their conservation, improve public education and perform scientific research on the species. In the course of improving housing conditions, several same-sex pairs of pygmy slow lorises were formed. We monitored their behaviors and fecal glucocorticoid metabolite (FGM) levels to understand whether male same sex pairings could be a feasible management strategy. The subjects were 10 male and 6 female lorises for comparison, all of whom were over five years old. We successfully formed five pairs of male lorises after eight formation attempts. Male pairs initially showed some aggressive behaviors; however, the rate decreased approximately 10 days after introduction. All of the male pairs eventually exhibited extensive affiliative social behaviors, including allogrooming and social play, during the dark (active) phase, and sleep site sharing during the light (inactive) phase. The rate of sleep site sharing during the light phase was higher than expected, suggesting that the pairs preferred to stay near each other. There was no evidence of increased stress after a long period of male male social housing. Female same sex pairs and male female pairs demonstrated a high level of affiliative behaviors right after introduction. These results highlight the flexibility and high sociability of this species and indicate that such same sex pairings are a feasible option for their social management.
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Authors: Lormant, Flore, et al
Published: Jan 2021
Authors: Lormant, Flore, et al
Published: Jan 2021
It is now well-accepted that memory is a dynamic process, and that stress and training level may influence which memory system an individual engages when solving a task. In this work, we investigated whether and how chronic stress impacts spatial and cue-based memories according to training level. To that aim, control and chronically stressed Japanese quail were trained in a task that could be solved using spatial and cue-based memory and tested for their memory performances after 5 and 15 training days (initial training and overtraining, respectively) and following an emotional challenge (exposure to an open field). While chronic stress negatively impacted spatial memory in chronically stressed birds after initial training, this impact was lowered after overtraining compared to control quail. Interestingly, the emotional challenge reinstated the differences in performance between the two groups, revealing that chronic stress/overtraining did not eliminate spatial memory. Differences caused by previous stressors can re-emerge depending on the more immediate psychological state of the individual. Contrary to spatial memory, cue-based memory was not impaired in any test occasion, confirming that this form of memory is resistant to chronic stress. Altogether these findings reveal a dynamic dialogue between stress, training, and memory systems in birds.
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