Miracle-dz/UniFAR-FTUs huggingface dataset:
A kinesin-3 recruitment complex facilitates axonal sorting of enveloped alpha herpesvirus capsids

Axonal sorting, the controlled passage of specific cargoes from the cell soma into the axon compartment, is critical for establishing and maintaining the polarity of mature neurons. To delineate axonal sorting events, we took advantage of two neuroinvasive alpha-herpesviruses. Human herpes simplex virus 1 (HSV-1) and pseudorabies virus of swine (PRV; suid herpesvirus 1) have evolved as robust cargo of axonal sorting and transport mechanisms. For efficient axonal sorting and subsequent egress from axons and presynaptic termini, progeny capsids depend on three viral membrane proteins (Us7 (gI), Us8 (gE), and Us9), which engage axon-directed kinesin motors. We present evidence that Us7-9 of the veterinary pathogen pseudorabies virus (PRV) form a tripartite complex to recruit Kif1a, a kinesin-3 motor. Based on multi-channel super-resolution and live TIRF microscopy, complex formation and motor recruitment occurs at the trans-Golgi network. Subsequently, progeny virus particles enter axons as enveloped capsids in a transport vesicle. Artificial recruitment of Kif1a using a drug-inducible heterodimerization system was sufficient to rescue axonal sorting and anterograde spread of PRV mutants devoid of Us7-9. Importantly, biophysical evidence suggests that Us9 is able to increase the velocity of Kif1a, a previously undescribed phenomenon. In addition to elucidating mechanisms governing axonal sorting, our results provide further insight into the composition of neuronal transport systems used by alpha-herpesviruses, which will be critical for both inhibiting the spread of infection and the safety of herpesvirus-based oncolytic therapies. Author Summary Alpha-herpesviruses represent a group of large, enveloped DNA viruses that are capable to establish a quiescent (also called latent) but reactivatable form of infection in the peripheral nervous system of their hosts. Following reactivation of latent genomes, virus progeny are formed in the soma of neuronal cells and depend on sorting into the axon for anterograde spread of infection to mucosal sites and potentially new host. We studied two alpha-herpesviruses (the veterinary pathogen pseudorabies virus (PRV) and human herpes simplex virus 1 (HSV-1)) and found viral membrane proteins Us7, Us8, and Us9 to form a complex, which is able to recruit kinsin-3 motors. Motor recruitment facilitates axonal sorting and subsequent transport to distal egress sites. Complex formation occurs at the trans-Golgi network and mediates efficiency of axonal sorting and motility characteristics of egressing capsids. We also used an artificial kinesin-3 recruitment system, which allows controlled induction of axonal sorting and transport for virus mutants lacking Us7, Us8, and Us9. Overall, these data contribute to our understanding of anterograde alpha-herpesvirus spread and kinesin-mediated sorting of vesicular axonal cargoes.
Investigation on presence of major gene for body weight, feed intake and feed efficiency using a segregation analyses in a mice populationyesian segregation analyses in a mice population

Recent developments in molecular genetics and statistics have allowed the identification and use of major genes to explain the genetic variation. In this context, segregation analysis is a fast, reliable and inexpensive method that uses only phenotype and pedigree information. The aim of this study was to examine whether body weight, feed intake, and feed efficiency in a mouse population are directed by major gene in addition to polygenic and major gene effects by segregation analysis. For this purpose, previously collected dataset was used (n= 661). In this study, genetic variance, error variance, major gene variance, additive and dominant gene effects were estimated by segregation analyses. Dominant variance (1.04) was found to be smaller than the additive genetic variance (7.32) for body weight. Polygenic and major gene heritability predicted as 0.29 (± 0.63) and 0.81 (± 0.98) for body weight, 0.35 (± 0.63) and 0.96 (± 0.98) for feed intake and 0.52 (± 0.63) and 0.81 (± 0.98) for feed efficiency respectively. Existence of major gene was determined by examining the highest probability density regions. Although the major gene has been identified for body weight and feed intake, this result is not confirmed by the Mendelian transmission probabilities.
A comparative assessment of the performance of a stay-green sorghum (Sorghum bicolor (L) Moench) introgression line developed by marker-assisted selection and its parental lines

A glasshouse experiment was conducted to compare the performance of a stay-green QTL introgression line (RSG 03123) and its parental lines (B35, a stay-green and R16, a high yielding cultivar with rapid senescence) after flowering, when water-limited (WL) or well-watered (WW). Flowering time and plant height were similar in RSG 03123 and the recurrent parent, R16. Under WW conditions, retention of green leaf area (GLA) and chlorophyll was similar in RSG 03123 and R16, whereas under WL conditions RSG 03123 retained significantly (P<0.05) more GLA. The rate of senescence was also lower in RSG 03123 as compared to R16 under WL conditions. B35 displayed a delayed onset of senescence under both WW and WL conditions while both R16 and RSG 01323 displayed an earlier onset of senescence under WL conditions. Photochemical efficiency of photosystem II (ΦPSII), gas exchange characteristics, and total soluble carbohydrates contents, in both leaf and stem, were higher in RSG 03123 than in R16 under WL conditions. These parameters were enhanced in RSG 03123 due to higher retention of chloroplast proteins, such as light-harvesting chlorophyll binding protein complex of PSII (LHCPII), oxygen-evolving complex 33 kDa (OEC33), phosphoenolpyruvate carboxylase (PEPC) and the large subunit of ribulose bisphosphate carboxylase-oxygenase (Rubisco). The stay-green characteristics of RSG 03123 were intermediate between R16 and B35; nonetheless, the results show that stay-green QTL are functional during senescence and improve tolerance to water limitation after flowering. Key words: Stay-green QTL, introgression, drought, photosynthesis.
High-density genetic linkage map construction and white rot resistance QTL mapping for Vitis based on restriction site-associated DNA sequencing

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. The present study aimed to provide a foundation to improve future grape white rot resistance breeding. To this end, interspecific hybridization was conducted between a white rot resistance cultivar ‘Zhuosexiang’ (Vitus vinifera L. × Vitus labrusca L.), and a susceptible cultivar ‘Victoria’ (Vitus vinifera L.), using 177 hybrid offspring and two parents for restriction site-associated DNA sequencing (RAD-seq) and high-density genetic linkage mapping. Female, male, and integrated map marker numbers were 2501, 4110, and 6249, respectively. The average genetic distance of adjacent markers was 1.25 cM, 0.77 cM, and 0.50 cM. White rot resistance identification of the two parents and 177 individuals was conducted in July and August of 2017 and 2018. Additionally, white rot resistance quantitative trait locus (QTL) mapping was conducted. In total, nine QTLs were detected and located on linkage groups LG1, LG4, LG7, LG12, LG14, and LG15, with overlapping QTLs on LG7 and LG15. Further, three candidate genes that may be responsible for grape white rot resistance were screened. The results will provide an important theoretical reference for future grape white rot resistance breeding.
Global profiling of myristoylation in Toxoplasma gondii reveals key roles for lipidation in CDPK1 and MIC7 function

N-myristoylation is a ubiquitous class of protein lipidation across eukaryotes and N-myristoyl transferase has been proposed as an attractive drug target in several pathogens. Functionally the myristate often primes for subsequent palmitoylation and stable membrane attachment, however, growing evidence also suggests additional regulatory roles for myristoylation on proteins. Here we describe the first global chemoproteomic screening of protein myristoylation in Toxoplasma gondii. Through quantitative mass spectrometry coupled with validated chemoproteomic tools, we identify 65 myristoylated proteins. We report functionally important myristoylation on the key signalling protein CDPK1 and, surprisingly, myristoylation of the microneme protein 7 (MIC7), a predicted type-I-transmembrane protein. We demonstrate that myristoylation of MIC7 is not important for the trafficking to micronemes, but appears to play a role in host cell invasion. This dataset represents a large fraction of the parasite’s myristoylated proteome and a prerequisite to investigate this modification in Toxoplasma.
Medicago truncatula possesses a single Shaker outward K+ channel: functional characterization and roles in planta

The model legume Medicago truncatula possesses a single outward Shaker K+ channel, while Arabidopsis thaliana possesses two channels of this type, named SKOR and GORK, the former having been shown to play a major role in K+ secretion into the xylem sap in the root vasculature and the latter to mediate the efflux of K+ across the guard cell membrane upon stomatal closure. Here we show that the expression pattern of the single M. truncatula outward Shaker channel, which has been named MtGORK, includes the root vasculature, guard cells and root hairs. As shown by patch-clamp experiments on root hair protoplasts, besides the Shaker-type slowly-activating outwardly-rectifying K+ conductance encoded by MtGORK, a second K+-permeable conductance, displaying fast activation and weak rectification, can be expressed by M. truncatula. A KO mutation resulting in absence of MtGORK activity is shown to weakly reduce K+ translocation to shoots, and only in plants engaged in rhizobial symbiosis, but to strongly affect the control of stomatal aperture and transpitational water loss. In legumes, the early electrical signaling pathway triggered by Nod Factor perception is known to comprise a short transient depolarization of the root hair plasma membrane. In absence of MtGORK functional expression, while the rate of the membrane repolarization is shown to be decreased by about 3 times, this defect is without any consequence on infection thread development and nodule production, indicating that the plant capacity to engage rhizobial symbiosis does not require integrity of the early electrical signaling events.
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
Development and evaluation of diverse promising rapeseed (Brassica napus L.) mutants using physical and chemical mutagens

Genetic variability is a prerequisite for any plant breeding program, and mutagenesis is a proven way of creating new variation within a crop germplasm. Novel genetic variability in rapeseed was induced by gamma rays, Ethyl Methane Sulphonate (EMS) and combined mutagen treatment, using various doses and concentrations. The objective was to evaluate and compare the obtained M2 mutants for important quantitative traits in two contrasted environments. Data on phenological, morphological and agronomic parameters were recorded. A large variability was observed and mutagenic treatments had a significant effect on all traits studied. Compared to control plants, mutant genotypes derived from seeds treated with low EMS concentrations during moderate time were earlier and characterized by a higher number of pods per plant. For high concentration of EMS during long time and for combinations of physical and chemical mutagens, a significant decrease in plant height and stature was noticed, as compared to control. Besides, plants derived from gamma rays-treated seeds exhibited the highest 1000-seed weight. The novel induced variability may be integrated in rapeseed breeding program as a new germplasm with improved agronomic traits. Particularly, EMS1-7-stable mutant may be exploited to develop efficiently and quickly a new rapeseed cultivar with some desirable traits. The present study highlights once more the possibility to bring novel genetic diversity for rapeseed desirable traits improvement through mutation breeding.
Cryptococcus neoformans Recovered From Olive Trees (Olea europaea) in Turkey Reveal Allopatry With African and South American Lineages

Cryptococcus species are life-threatening human fungal pathogens that cause cryptococcal meningoencephalitis in both immunocompromised and healthy hosts. The natural environmental niches of Cryptococcus include pigeon (Columba livia) guano, soil, and a variety of tree species such as Eucalyptus camaldulensis, Ceratonia siliqua, Platanus orientalis, and Pinus spp. Genetic and genomic studies of extensive sample collections have provided insights into the population distribution and composition of different Cryptococcus species in geographic regions around the world. However, few such studies examined Cryptococcus in Turkey. We sampled 388 Olea europaea (olive) and 132 E. camaldulensis trees from 7 locations in coastal and inland areas of the Aegean region of Anatolian Turkey in September 2016 to investigate the distribution and genetic diversity present in the natural Cryptococcus population. We isolated 84 Cryptococcus neoformans strains (83 MATα and 1 MATa) and 3 Cryptococcus deneoformans strains (all MATa) from 87 (22.4% of surveyed) O. europaea trees; a total of 32 C. neoformans strains were isolated from 32 (24.2%) of the E. camaldulensis trees, all of which were MATα. A statistically significant difference was observed in the frequency of C. neoformans isolation between coastal and inland areas (P < 0.05). Thus, O. europaea trees could represent a novel niche for C. neoformans. Interestingly, the MATa C. neoformans isolate was fertile in laboratory crosses with VNI and VNB MATα tester strains and produced robust hyphae, basidia, and basidiospores, thus suggesting potential sexual reproduction in the natural population. Sequencing analyses of the URA5 gene identified at least 5 different genotypes among the isolates. Population genetics and genomic analyses revealed that most of the isolates in Turkey belong to the VNBII lineage of C. neoformans, which is predominantly found in southern Africa; these isolates are part of a distinct minor clade within VNBII that includes several isolates from Zambia and Brazil. Our study provides insights into the geographic distribution of different C. neoformans lineages in the Mediterranean region and highlights the need for wider geographic sampling to gain a better understanding of the natural habitats, migration, epidemiology, and evolution of this important human fungal pathogen.
Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica

With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. We have previously shown that in obligate mutualisms the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners, setting the community antibiotic tolerance at that of the ‘weakest link’ species. In this study, we extended that hypothesis to test whether obligate cross-feeding would limit the extent and mechanisms of antibiotic resistance evolution. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities. Significance statement Little is known about how ecological interactions between bacteria influence the evolution of antibiotic resistance. We tested the impact of metabolic interactions on resistance evolution in an engineered two-species bacterial community. Through experimental and modeling work, we found that obligate metabolic interdependency slows the rate of resistance acquisition, and can change the type and magnitude of resistance mutations that evolve. This work suggests that resistance evolution may be slowed by targeting both a pathogen and its metabolic partners with antibiotics. Additionally, we showed that community context can generate novel trajectories through which antibiotic resistance evolves.
An Eye Tracking Study to Investigate the Influence of Language and Text Direction on Multimedia

AN EYE TRACKING STUDY TO INVESTIGATE THE INFLUENCE OF LANGUAGE AND TEXT DIRECTION ON MULTIMEDIA Arwa Abdulwahab Mashat Old Dominion University, 2017 Director: Dr. Ginger Watson This study investigated how native language orientation influences spatial bias, first visual fixation on screen, first visual fixation on pictures, learning outcomes, and mental effort of learners. Previous studies supported the effect of native language writing or reading direction on spatial bias, examining written text and images created by the participants (Barrett et al., 2002; Boroditsky, 2001; Chatterjee, Southwood & Basiko, 1999; Spalek & Hammad, 2005). However, no study investigated writing direction in multimedia presentations using eye tracking. This study addresses this gap. A total of 84 participants completed the study forming four groups. The first group (NativeLeft_InstrEng) consisted of individuals whose native language is written from left to right and who have never experienced a right to left language. They received the material in English. The second group (NativeRight_InstrAra), whose native language is written from right to left, received the material in Arabic. The third group (NativeLeft_LrnRight_InstrEng) consists of individuals whose native language is written from left to right and who are learning or have learned a language written from right to left. They received the material in English. The fourth group (NativeRight_InstrEng), whose native language is written from right to left, received the material in English. Participants were asked to complete a survey that consisted of eight sections: demographic questions, self-estimate prior knowledge test, the instructional unit, mental effort rating, sentence forming questions, recalling questions, sequence question and finally, post-test
Japan's nationwide long‐term monitoring survey of seaweed communities known as the “Monitoring Sites 1000”: Ten‐year overview and future perspectives

“Monitoring Sites 1000” – Japan's long‐term monitoring survey was established in 2003, based on the Japanese Government policy for the conservation of biodiversity. Ecological surveys have been conducted on various types of ecosystems at approximately 1000 sites in Japan for 15 years now and are planned to be carried out for 100 years. Since 2008, seaweed communities had been monitored at six sites, featuring the kelp (e.g. Saccharina and Ecklonia; Laminariales) and Sargassum (Fucales) communities in the subarctic and temperate regions of Japan. Annual surveys were carried out during the season when these canopy‐forming seaweeds are most abundant. A non‐destructive quadrat sampling method, with permanent quadrats placed along transects perpendicular to the shoreline, was used to determine species composition, coverage, and vertical distribution of seaweeds at these sites; while destructive sampling was done every 5 years to determine biomass. The occurrence of canopy‐forming species Saccharina japonica (var. japonica) and Ecklonia cava have appeared to be stable at the Muroran (southwestern part of Hokkaido Island) and Shimoda (Pacific coast of middle Honshu Island) sites, respectively; whereas the coverage of Ecklonia radicosa (= Eckloniopsis radicosa) at the Satsuma‐Nagashima site in southern part of Kyushu Island was highly variable until its sudden disappearance from the habitat in 2016. Thalli of E. radicosa lost most of their blades through browsing by herbivorous fish, and thus, this may be one of the causes of the decline. A shift in the community structure related to environmental changes had also been observed at some other sites. Pre‐ and post‐disaster data revealed the impact of the 2011 earthquake and tsunami disasters, including a shift in the vertical distribution of Ecklonia bicyclis (= Eisenia bicyclis) to shallower depths at the Shizugawa site in the Pacific coast of northern Honshu Island, due to seafloor subsidence.
Do New World pitvipers “scale‐down” at high elevations? Macroecological patterns of scale characters and body size

Abstract Bergmann's rule describes the macroecological pattern of increasing body size in response to higher latitudes and elevations. This pattern is extensively documented in endothermic vertebrates, within and among species; however, studies involving ectotherms are less common and suggest no consistent pattern for amphibians and reptiles. Moreover, adaptive traits, such as epidermal features like scales, have not been widely examined in conjunction with Bergmann's rule, even though these traits affect physiological processes, such as thermoregulation, which are hypothesized as underlying mechanisms for the pattern. Here, we investigate how scale characters correlate with elevation among 122 New World pitviper species, representing 15 genera. We found a contra‐Bergmann's pattern, where body size is smaller at higher elevations. This pattern was mainly driven by the presence of small‐bodied clades at high elevations and large‐bodied clades at low elevations, emphasizing the importance of taxonomic scope in studying macroecological patterns. Within a subset of speciose clades, we found that only Crotalus demonstrated a significant negative relationship between body size and elevation, perhaps because of its wide elevational range. In addition, we found a positive correlation between scale counts and body size but no independent effect of elevation on scale numbers. Our study increases our knowledge of Bergmann's rule in reptiles by specifically examining characters of squamation and suggests a need to reexamine macroecological patterns for this group.