Miracle-dz/UniFAR-FTUs huggingface dataset:
Rub1/NEDD8, a ubiquitin-like modifier, is also a ubiquitin modifier

Of all ubiquitin-like small protein modifiers, Rub1/NEDD8 is the closest kin of ubiquitin in sequence and in structure. Despite their profound similarities, prevalence of ubiquitin and of Rub1 is starkly different: targets of ubiquitin modification reach into the thousands, whereas unique targets of Rub1/NEDD8 appear limited to one family of proteins, Cullins. This distinction is likely due to dedicated E1 activating enzymes that select either one or the other and relay the modifier until it is covalently attached to a target. To convert typical neddylation targets for modification by ubiquitin, and vice versa, we designed reciprocal substitutions at position 72 of Rub1 and of ubiquitin to render them substrates for activation by their non-cognate E1 activating enzymes. We found that this single amino acid is sufficient to distinguish between Ub and Rub1 in living cells, and determine their targets. Thus, modification of Cullins by UbR72T could compensate for loss of Rub1, even as it maintained its ability to polymerize and direct conjugates for degradation. Conversely, Rub1T72R activated by ubiquitin-activating enzyme entered into the ubiquitination cascade, however was not efficiently polymerized, essentially capping polyubiquitin chains. Upon shortage of free ubiquitin under stress, even native Rub1 spilled-over into the ubiquitinome suppressing polyubiquitination. By contrast, the need to maintain monomeric modifications on unique targets is a likely explanation for why the Rub1-activating enzyme strictly discriminates against ubiquitin. Swapping Rub1 and ubiquitin signals uncovered a reason for maintaining two separate pathways across eukaryotic kingdom.
The genomics of trait combinations and their influence on adaptive divergence

Understanding rapid adaptation requires quantifying natural selection on traits and elucidating the genotype-phenotype relationship for those traits. However, recent studies have often failed to predict the direction of adaptive allelic variation in natural populations from laboratory studies. Here, we test for genomic signatures of genetic correlations to illustrate how multifarious, correlational selection may drive counterintuitive patterns of population divergence in the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Apple-infesting populations with relatively early emerging adults have recently evolved from hawthorn-infesting populations consisting of relatively later emerging adults. Multiple studies have reported a paradoxical relationship between population differentiation and seasonal timing, as determined by the timing of diapause termination; alleles associated with late termination occur at higher frequencies in the earlier emerging apple-infesting populations compared to hawthorn-infesting populations. We present evidence that historical selection on diapause termination and another trait, initial diapause intensity, over geographic gradients generated genetic correlations between the traits in a direction antagonistic to contemporary selection on apple-infesting populations. Single nucleotide polymorphism in genomic regions of high linkage disequilibrium associated strongly with diapause termination and intensity, population divergence, geography, and evolutionary responses in laboratory selection experiments. These associations were consistent with geographically variable selection and with correlated evolutionary responses driving higher frequencies of late-associated alleles in the early emerging apple race. In contrast, loci associated only with diapause termination showed the expected pattern (more early-associated alleles in the apple race) in half of the population pairs. Our results suggest that selection on loci demonstrating antagonistic pleiotropy may often shape genomic footprints of rapid adaptation.
A Fork-Tailed Coelacanth, Rebellatrix divaricerca, gen. et sp. nov. (Actinistia, Rebellatricidae, fam. nov.), from the Lower Triassic of Western Canada

ABSTRACT An unusual fork-tailed coelacanth from the Lower Triassic Sulphur Mountain Formation of British Columbia, Canada, marks the first considerable departure in actinistian body form since the Mississippian Period. Rebellatrix divaricerca, gen. et sp. nov., is unique among coelacanths in its possession of a bifurcated caudal fin, reduced segmentation of fin rays, and fusion of caudal fin elements. Parsimony analysis of a character-taxon matrix of 109 characters and 29 taxa recovered R. divaricerca as sister taxon to Latimerioidei. The family Rebellatricidae is erected to include only R. divaricerca. This novel body shape of the new coelacanth raises questions about the idea that coelacanths were morphologically static following the Mississippian. Rebellatrix divaricerca also emphasizes the morphological diversity of coelacanths during the Early Triassic, a time when species diversity of coelacanths was also highest. The slender, fork-tailed body form suggests fast swimming and an active lifestyle, unique among known fossil and extant coelacanths.
Adolescent Intermittent Ethanol Exposure Effects on Kappa Opioid Receptor Mediated Dopamine Transmission: Sex and Age of Exposure Matter

Underage alcohol drinking increases the risk of developing alcohol use disorder (AUD). In rodents, adolescent ethanol exposure augments ethanol consumption and anxiety-like behavior while reducing social interaction. However, the underlying mechanisms driving these adaptations are not understood. The dopamine and kappa opioid receptor (KOR) systems in the nucleus accumbens (NAc) are implicated in affective disorders and AUD, with studies showing augmented KOR function and reduced dopamine transmission in ethanol-dependent adult animals. Thus, this study, we examined the impact of adolescent intermittent ethanol (AIE) exposure on dopamine transmission and KOR function. Rats were exposed to water or ethanol (4 g/kg, intragastrically) every-other-day during early (PD25–45) or late (PD45–65) adolescence. While AIE exposure during early-mid adolescence (early AIE) did not alter dopamine release in male and female rats, AIE exposure during late adolescence (late AIE) resulted in greater dopamine release in males and lower dopamine release in females. To determine the impact of AIE exposure on KOR function, we bath applied cumulative concentrations of KOR agonist, U50,488 (0.01–1.0 μM), and measured its effect on dopamine release. Early AIE exposure potentiated KOR-mediated inhibition of dopamine release in female rats, while late AIE exposure attenuated this effect in male rats. Together these data suggest that AIE-exposure impact on neural processes is dependent on sex and exposure timing. These differences likely arise from differential developmental timing in males and females. This is the first study to show changes in KOR function following AIE exposure.
SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients

SARS-CoV-2, the causative agent of COVID-19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over 450,000 deaths, and overwhelmed healthcare systems worldwide. Like SARS-CoV, which emerged in 2002 and caused a similar disease, SARS-CoV-2 is a betacoronavirus. Both viruses use human angiotensin-converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS-CoV-2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low passage (P) strains of SARS-CoV-2 (Wash1: P4 and Munich: P1) were cultured twice in Vero-E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1: P6 and minor variants in the Munich: P3 strain. Cleavage of the S glycoprotein in SARS-CoV-2-infected Vero-E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies we investigated the development of neutralizing antibody titers in serial serum samples obtained from COVID-19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies.
Short-lived plants have stronger demographic responses to climate

To mitigate and adapt to climate change, there is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data, combined with our understanding of plant physiology and life history theory provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesized time series of structured population models from 165 populations from 62 plants around the globe to link plant population growth rates to precipitation and temperature drivers. We expected: (1) more pronounced demographic responses to precipitation than temperature, especially in arid biomes; (2) a higher climate sensitivity in short-lived rather than long-lived species; and (3) a stronger response to climate by species that reproduce more frequently. We found that precipitation anomalies have a nearly three-fold larger effect on λ than temperature. Precipitation has substantially more pronounced effects in more arid sites, but large noise makes this relationship non-significant. Species with shorter generation time have much stronger absolute responses to climate anomalies, while the degree of iteroparity does not correlate with population responses to climate. We conclude that key species-level traits can predict plant population responses to climate, and discuss the relevance of this generalization for conservation planning and evolutionary theory.
Social media reveals consistently disproportionate tourism pressure on a threatened marine vertebrate

Establishing how wildlife viewing pressure is distributed across individual animals within a population can inform the management of this activity, and ensure targeted individuals or groups are sufficiently protected. Here, we used social media data to quantify whether tourism pressure varies in a loggerhead sea turtle (Caretta caretta) population and elucidate potential implications. Laganas Bay (Zakynthos, Greece) supports both breeding (migratory, and hence transient) and foraging (resident) turtles, with turtle viewing representing a major component of the tourism industry. Social media entries spanning two seasons (April to November, 2018 and 2019) were evaluated, and turtles were identified via photo-identification. For both years, 1684 and 2105 entries of 139 and 122 unique turtles were obtained from viewings, respectively (boats and underwater combined). However, while residents represented less than one-third of uniquely identified turtles, they represented 81.9% and 87.9% of all entries. Even when the seasonal breeding population was present (May to July), residents represented more than 60% entries. Of note, the same small number of resident turtles (<10), mostly males, were consistently viewed in both years; however, different individuals were targeted by boats versus underwater. Thus, turtles appear to use and remain in the area despite high viewing intensity, possibly indicating low disturbance. However, photo-identification records revealed a high risk of propeller and boat strike to residents (30%) leading to trauma and mortality. To reduce this threat and ease viewing pressure, we recommend the compulsory use of propeller guards for all boats and the creation of temporary “refuge” zones for resident animals at viewing hotspots, with these suggestions likely being relevant for other wildlife with similar population dynamics. In conclusion, social media represents a useful tool for monitoring individuals at a population scale, evaluating the pressure under which they are placed, and providing sufficient data to refine wildlife viewing guidelines and/or zoning.
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses

Viruses commonly use specifically folded RNA elements that interact with both host and viral proteins to perform functions important for diverse viral processes. Examples are found at the 3′ termini of certain positive-sense ssRNA virus genomes where they partially mimic tRNAs, including being aminoacylated by host cell enzymes. Valine-accepting tRNA-like structures (TLSVal) are an example that share some clear homology to canonical tRNAs but have several important structural differences. Although many examples of TLSVal have been identified, we lacked a full understanding of their structural diversity and phylogenetic distribution. To address this, we undertook an in-depth bioinformatic and biochemical investigation of these RNAs, guided by recent high-resolution structures of a TLSVal. We cataloged many new examples in plant-infecting viruses but also in unrelated insect-specific viruses. Using biochemical and structural approaches, we verified the secondary structure of representative TLSVal substrates and tested their ability to be valylated, finding structural heterogeneity within this class. In a few cases, large stem-loop structures are inserted within distinct variable regions located in an area of the TLS distal to known host cell factor binding sites. In addition, we identified one virus whose TLS has switched its anticodon away from valine; the implications of this remain unclear. These results refine our understanding of the structural and functional mechanistic details of tRNA mimicry and how this may be used in viral infection.
Diametric Property of Rotational and Spiral Doppler Effect in Human Heart Atrial Fibrillation

Compass mapping of moving rotors during atrial fibrillation unveiled unique properties of a different form of Doppler phenomenon. New rotational (RDE) and spiral Doppler effect (SDE) equations are derived and explain the diverging frequency changes (increasing and decreasing) that occur simultaneously on either side of passing rotor. These equations confirm that regions of maximal frequency are shifted 90° compared to moving sources that exhibit classical doppler effects. The new SDE equation predicts sequence reversal, side-dependent frequency changes, and an unpaired strong-side wave front strike previously observed in patients with persistent atrial fibrillation. Conclusion: The diametric property of SDE is a mechanism behind dysynchrony of atrial fibrillation when a spinning source of wave fronts moves between two stationary electrodes. The diametric property of SDE in other fields of science are discussed. Statement of Significance Spinning sources of periodic wave fronts during atrial fibrillation do NOT exhibit classical Doppler effects when they approach and pass between 2 adjacent equidistant electrodes. The wave front is a spinning single spiral arm and frequency of wave front strikes is not only dependent upon distance between successive WF crests, but it is also dependent upon changes in rotation. Rotational and spiral math were developed and to derive new rotational and spiral wave front Doppler effect equations in two dimensions. These equations predict the unique and profound diametric property that have been observed clinically in which the strong side electrodes record an approaching increasing frequency while the weak side electrodes record an approaching decreasing frequency. The solution opens up many new avenues of research, not only into atrial fibrillation, but at all levels of nature, into objects that spin.
Mapping cell structure across scales by fusing protein images and interactions

The eukaryotic cell is a multi-scale structure with modular organization across at least four orders of magnitude1,2. Two central approaches for mapping this structure – protein fluorescent imaging and protein biophysical association – each generate extensive datasets but of distinct qualities and resolutions that are typically treated separately3,4. Here, we integrate immunofluorescent images in the Human Protein Atlas5 with ongoing affinity purification experiments from the BioPlex resource6 to create a unified hierarchical map of eukaryotic cell architecture. Integration involves configuring each approach to produce a general measure of protein distance, then calibrating the two measures using machine learning. The evolving map, called the Multi-Scale Integrated Cell (MuSIC 1.0), currently resolves 69 subcellular systems of which approximately half are undocumented. Based on these findings we perform 134 additional affinity purifications, validating close subunit associations for the majority of systems. The map elucidates roles for poorly characterized proteins, such as the appearance of FAM120C in chromatin; identifies new protein assemblies in ribosomal biogenesis, RNA splicing, nuclear speckles, and ion transport; and reveals crosstalk between cytoplasmic and mitochondrial ribosomal proteins. By integration across scales, MuSIC substantially increases the mapping resolution obtained from imaging while giving protein interactions a spatial dimension, paving the way to incorporate many molecular data types in proteome-wide maps of cells.
Effect of salt and acid stress on Triticum aestivum inoculated with Glomus fasciculatum

Microbiology Laboratory, P. G. Department of Botany, Karnatak University Dharwad-580003, India Bheemareddy, V.S. and Lakshman, H.C. (2011). Effect of salt and acid stress on Triticum aestivum inoculated with Glomus fasciculatum. Journal of Agricultural Technology 7(4): 945-956. Arbuscular mycorrhizal (AM) symbiosis increased resistance to various abiotic stresses, such as drought, acid and salt stresses. The effect of salt and acid stress on Triticum aestivum L. varieties was studied with and without mycorrhizal inoculation. Four T. aestivum L. varieties were subjected to salt stress by supplementing 1N NaCl and acid stress by 1N HCl under control and inoculated conditions. Plant growth was reduced in control plants under salt and acid stress. AM inoculation helped the plants to withstand acid and salt stress. An inoculated plant showed better growth under salt and acid stress than control plants. Acid and salt treatments were found to be inhibitory for growth and development of Triticum aestivum L. varieties. Acid stress was found to be more inhibited than salt stress. Less growth was noticed in plants subjected to acid stress. Key words: Arbuscular mycorrhizal fungi, Triticum aestivum L. varieties, HCL and NaCl
Efficacy of bioresorbable plates in the osteosynthesis of linear mandibular fractures

Background and Objectives: There are limited evidences available about the performance of biodegradable system in the treatment of linear mandibular fractures without the aid of postoperative maxillomandibular fixation (MMF). Hence, the present study was planned to evaluate the treatment outcomes in mandibular fractures, using 2.5 mm bioresorbable plates and screws without postoperative MMF. Methodology: This cohort study compares both prospective and retrospective data. The prospective study treated 20 adult patients with linear mandibular fracture using bioresorbable plates and screws, without using postoperative MMF (Group 1). Retrospective data were collected from a previous published study in which patients were treated with bioresorbable plates and screws with 2 weeks postoperative MMF (Group 2) and those treated with metal plates and screws without postoperative MMF (Group 3). Group 1 patients were followed up at 2 and 4 months to evaluate the functional outcomes in terms of fracture mobility, malocclusion, pain, and soft-tissue deformity and compared with its preoperative findings. Further, the treatment outcomes of Group 1, Group 2, and Group 3 were compared among themselves at 2-month follow-up. Results: Group 1 patients showed a significant improvement in the treatment outcomes at 2 and 4-month follow-up. In addition, when 2 months postoperative outcomes were compared among the three groups, no statistically significant difference was observed in the treatment outcomes. Conclusion: Endpoint osteosynthesis can be achieved with the bioresorbable fixation system when used in the treatment of un-displaced linear mandibular fractures, without postoperative MMF. A minor modification of using a lower size osteotomy drill can prevent screw loosening.
Continual Relation Learning via Episodic Memory Activation and Reconsolidation

Continual relation learning aims to continually train a model on new data to learn incessantly emerging novel relations while avoiding catastrophically forgetting old relations. Some pioneering work has proved that storing a handful of historical relation examples in episodic memory and replaying them in subsequent training is an effective solution for such a challenging problem. However, these memory-based methods usually suffer from overfitting the few memorized examples of old relations, which may gradually cause inevitable confusion among existing relations. Inspired by the mechanism in human long-term memory formation, we introduce episodic memory activation and reconsolidation (EMAR) to continual relation learning. Every time neural models are activated to learn both new and memorized data, EMAR utilizes relation prototypes for memory reconsolidation exercise to keep a stable understanding of old relations. The experimental results show that EMAR could get rid of catastrophically forgetting old relations and outperform the state-of-the-art continual learning models.
Changing Dynamics Of Gendered Livelihoods Practices In Post Crises Of Swat Northwest Pakistan

This research attempts to focus on the changing dynamics of livelihoods practices among gender, and how conflict and flood crises (2005-2010) effected the various needs of livelihoods of the social classes in Swat valley of northwest Pakistan. Qualitative methods; formal/informal interviews, focus groups discussion, key informant interviews and participant observation, were used to explore the dynamics of changes in occupations, household dependency and those factors which influenced the changes accessing livelihood resources. The paper revealed that those households depending agriculture, small business and labour in market have been highly affected during conflict and flood crises in comparison to those households who were depending on remittances, public and private jobs and skilled works. The study found that the livelihood dependency of the households in all villages was based on agricultural and natural resources, which has changed to market and jobs based oriented resources. The factors like economic development, migration, conflict and displacement, and post conflict development have created diverse opportunities of livelihood resources for men and women, which brought social and cultural changes in the livelihood practices between genders at household level. The research emphasizes on the long-term livelihoods strategies and gendered equal opportunity policies by government and NGOs after the crises, which may improve the social statuses of the men and women.