Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomic Structure of the Murine Norovirus Protruding Domain and Soluble CD300lf Receptor Complex.

Human noroviruses are the leading cause of acute gastroenteritis in humans. Noroviruses also infect animals, such as cows, mice, cats, and dogs. How noroviruses bind and enter host cells is still incompletely understood. Recently, the type I transmembrane protein CD300lf was identified as the murine norovirus receptor, yet it is unclear how the virus capsid and receptor interact at the molecular level. In this study, we determined the X-ray crystal structure of the soluble CD300lf (sCD300lf) and the murine norovirus capsid protruding domain complex at a 2.05-A resolution. We found that the sCD300lf-binding site is located on the topside of the protruding domain and involves a network of hydrophilic and hydrophobic interactions. sCD300lf locked nicely into a complementary cavity on the protruding domain that is additionally coordinated with a positive surface charge on sCD300lf and a negative surface charge on the protruding domain. Five of six protruding domain residues interacting with sCD300lf were maintained between different murine norovirus strains, suggesting that sCD300lf was capable of binding to a highly conserved pocket. Moreover, a sequence alignment with other CD300 paralogs showed that the sCD300lf-interacting residues were partially conserved in CD300ld but variable in other CD300 family members, consistent with previously reported infection selectivity. Overall, these data provide insights into how a norovirus engages a protein receptor and will be important for a better understanding of selective recognition and norovirus attachment and entry mechanisms.IMPORTANCE Noroviruses exhibit exquisite host range specificity due to species-specific interactions between the norovirus capsid protein and host molecules. Given this strict host range restriction, it has been unclear how the viruses are maintained within a species between relatively sporadic epidemics. While much data demonstrate that noroviruses can interact with carbohydrates, recent work has shown that expression of the protein CD300lf is both necessary and sufficient for murine norovirus infection of mice and binding of the virus to permissive cells. Importantly, the expression of this murine protein by human cells renders them fully permissive for murine norovirus infection, indicating that at least in this case, host range restriction is determined by molecular events that control receptor binding and entry. Defining the atomic-resolution interactions between the norovirus capsid protein and its cognate receptor is essential for a molecular understanding of host-range restriction and norovirus tropism.
The roles of centrins/caltractins at the centrosome and in genome maintenance

The principal microtubule-organising centre in animal cells, the centrosome, contains centrin, a small, highly-conserved calcium-binding protein that can be found throughout eukaryotes. Several centrin isoforms exist and have been implicated in various cellular processes including nuclear export and DNA repair. Although centrins play a major role in ensuring the assembly and appropriate functioning of the ciliary/flagellar basal bodies in protists and lower eukaryotes, their involvement in vertebrate centrosome duplication or centrosomal functions are less clear. Here we use the hyper-recombinogenic chicken DT40 cell line to dissect the roles of the various centrin isoforms. We found that all three centrin isoforms present in chicken, encoded by Cetn4, Cetn2 and Cetn3, are expressed in DT40 cells. We have successfully targeted all three Cetn loci, generating single, double and triple mutants of the centrin genes. RT-PCR, immunoblot and immunofluorescence microscopy have confirmed the absence of the centrins. Unexpectedly, centrin-deficient cells undergo normal cellular division with no significant differences in cell cycle progression. Light and electron microscopy analyses revealed no detectable defects in centrosome composition or ultrastructure in these cells. Additionally, microtubule re-nucleation analysis showed that the centrosomes retain function and cells are able to proceed through mitosis without any delay. Although centrin-deficient DT40 cells had normal survival rates following ionizing radiation (IR), they were highly sensitive to ultraviolet (UV) irradiation, with Cetn3 deficiency exacerbating the sensitivity of Cetn4/Cetn2 double mutants. DNA damage checkpoints were intact, but repair of UV-induced DNA damage was delayed in centrin nulls. To further investigate centrins’ activity in nucleotide excision repair, we performed mutagenic analysis of centrin2. Surprisingly, we found that neither key Mps1, CK2 and Aurora A phosphorylation sites nor the calcium binding ability of centrin2 are required for survival following UV treatment. However, we show that the mutation of all four EF hands impacts centrin2 localisation to the centrosome and dramatically decreases the formation of defined, linear centrosomal structures induced upon cPOC5 overexpression.
Effect of Plant Growth Regulators on Fruit-set and Quality of Guava

Two plant growth regulators: β-NOA (50 and 80 ppm) and GA (200 and 250 ppm) were applied to emasculated flowers at anthesis to set parthenocarpic fruit, while in the control treatment fruit set was achieved by natural pollination. The application of β-NOA found ineffective in setting parthenocarpic guava. No significant differences were observed in the length and diameter of fruit between parthenocarpic and naturally pollinated seeded fruit at different days after anthesis. The mean fruit weight, TSS and ascorbic acid content of parthenocarpic fruit were similar to that of seeded fruit. Significant higher amount of total polyphenol was detected in the seeded fruit than the parthenocarpic fruit. Although 200 ppm GA showed comparatively better response to fruit growth, TSS and ascorbic acid content than 250 ppm GA but not in a statistical level.
Density and population estimates of Rose-bellied Bunting (Passerina rositae), Cinnamon-tailed Sparrow (Peucaea sumichrasti), and Orange-breasted Bunting (Passerina lechlancherii) in the Sierra Tolistoque, Oaxaca, Mexico

ABSTRACT Micro-endemic species are at greater risk of extinction because of their small populations and limited distribution. We conducted a breeding population survey of 3 little-known Mexican endemic bird species: Rose-bellied Bunting (Passerina rositae), Cinnamon-tailed Sparrow (Peucaea sumichrasti), and Orange-breasted Bunting (Passerina lechlancherii) in Sierra Tolistoque, Oaxaca. The purpose of the survey was to (a) determine the population density and size of these 3 species in the Sierra Tolistoque, (b) estimate the relative importance of various landscape features for each species, and (c) provide more rigorous scientific information to aid in the conservation and management of these species. In the case of Rose-bellied Bunting, we aimed to assess whether it prefers ravines over other landscape types during the breeding seasons, as stated in previous studies. Between late May and June 2012, we conducted point counts (n = 209) throughout the southern slope of the Sierra Tolistoque on the Pacific slope of the Isthmus of Tehuantepec, in Oaxaca, Mexico. Overall bird density was 0.98 birds/ha for Rose-bellied Bunting, 0.547 birds/ha for Orange-breasted Bunting, and 0.514 birds/ha for Cinnamon-tailed Sparrow. The estimated population in each landscape category showed that despite the existence of subtle interspecific preferences, hillsides are the major reservoirs for the 3 species. Rose-bellied Bunting did not occur in greater density in ravines compared to hillsides, which comprised more than twice the area of ravines. The importance of the Sierra Tolistoque for the long-term conservation of the 2 micro-endemic species is crucial considering our population estimates suggest that ∼30% of the estimated world population of Rose-bellied Bunting and Cinnamon-tailed Sparrow are found within the range of the Sierra Tolistoque.
Genetic evaluation and selection in Jatropha curcas L.

J. curcas (physic nut) is one of the most promising oilseeds for biofuel production and the knowledge about genetic parameter estimates is important for its breeding. Here, we evaluated 121 families, from 48 to 60 months of age, aiming genetic evaluation and selection. The trial was set up in an 11 x 11 lattice design, with three replications and 4-plant plot. The traits evaluated were fruit yield (FY), grain (GY) and oil yield (OY), fruit husk percentage (FH) and seed oil content (OC). Individual heritabilities were low (0.19 to 0.23), requiring accurate selection and improvement methods. Moderate repeatabilities were observed for FY (0.54), GY (0.52), OC (0.30) and OY (0.51), indicating that the families evaluated maintained relative superiority over the years. With selection of the 20 best individuals, the predicted genotypic gains (66%) were greater than the additive gains (56%), indicating greater possibilities of success from cultivation of clones.
Utilizing gradient simulations for quantifying community‐level resistance and resilience

Resilience is a complex, multidimensional property of ecosystems that describes how ecosystems respond to disturbance and likely results from the interactions of species and their environments across temporal and spatial scales. Due to the complexity in how ecosystems function and respond to disturbance, measuring resilience is a challenge. Gradient analysis provides a familiar, yet somewhat neglected framework for understanding and characterizing resilience. With simulations parameterized on existing biomonitoring data, we used distance-based measures in ordination space to characterize community-level resilience, here defined as a function of resistance and recovery. Our simulations and analyses involved five steps: (1) We generated regional species pools by simulating species distributions across environmental gradients; (2) we sampled from these regional species pools to emulate temporal changes in reference (i.e., minimally disturbed) and impacted communities responding to disturbance; (3) we performed ordinations on observations from both impacted and reference communities to summarize multivariate data; (4) we calculated distance-based measures for individual community trajectories in the ordinations to quantify their relative resistance and resilience; and (5) we compared these distance-based metrics between reference and impacted communities. We conclude with an empirical example demonstrating the lack of resistance of the Harp Lake (Ontario, Canada) zooplankton community to invasion relative to the changes observed among minimally disturbed reference communities. Overall, distance measures on ordinations provide a simple and effective visual framework to quantify the relative resistance and resilience of communities to disturbance, and our simulation approach provides a novel technique to develop and evaluate quantitative metrics related to ecosystem or community-level processes.
A Novel Herpesvirus Associated with Hepatic Necrosis in a San Esteban Chuckwalla, Sauromalus varius

ABSTRACT A San Esteban Chuckwalla, Sauromalus varius, died without previous signs of systemic illness. On necropsy, intranuclear inclusion bodies were seen in the liver. Appearance of viral particles on electron microscopy was consistent with a herpesvirus. Degenerate PCR primers targeting a conserved region of herpesvirus DNA-dependent DNA polymerase gene were used to amplify products from paraffin embedded liver tissue. Nucleotide sequencing of the PCR product showed that the sequence from this lizard was unique. Phylogenetic and comparative sequence analysis suggested that this virus is a novel member of the subfamily alphaherpesvirinae, and is here termed iguanid herpesvirus 2.
Molecular mechanism of the dual regulation of bacterial iron sulfur cluster biogenesis by CyaY and IscX

IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialised and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest that iron-sulfur cluster assembly is an exquisite example of an enzymatic process which requires a double regulation under the control of iron as the effector.
Intracellular BH3 profiling reveals shifts in anti-apoptotic dependency in B-cell maturation and activation

Apoptosis is critical to B-cell maturation, but studies of apoptotic regulation in primary human B cells is lacking. Previously, we found that infecting human B cells with Epstein-Barr virus induces two different survival strategies (Price et al., 2017). Here, we sought to better understand the mechanisms of apoptotic regulation in normal and activated B cells. Using intracellular BH3 profiling (iBH3), we defined the Bcl2-dependency of B-cell subsets from human peripheral blood and tonsillar lymphoid tissue as well as mitogen-activated B cells. We found that naïve and memory B cells were BCL-2 dependent, while germinal center B cells were MCL-1 dependent and plasma cells were BCL-XL dependent. Proliferating B cells activated by CpG or CD40L/IL-4 became more dependent upon MCL-1 and BCL-XL. As B-cell lymphomas often rely on survival mechanisms derived from normal and activated B cells, these findings offer new insight into potential therapeutic strategies for lymphomas.
Physconia labrata, a new species from western North America and Asia

Abstract A new species belonging to the lichen genus Physconia is described from Alaska and the Canadian and American Rocky Mountains and adjacent forested regions. It is also reported from China, Nepal, India and Siberia. The new species, Physconia labrata, is superficially similar to P. perisidiosa, but can be distinguished by having a blackened, corticate lower surface and a paraplectenchymatous upper cortex.
Carotene Thermal Degradation Products and their Effects on the Oxidative Stability of Soybean Oil

Soybean oil used in processed foods is susceptible to lipid oxidation. Carotenes are utilized as colorants in processed foods containing soybean oil. Though carotenes are easily degraded during thermal processing, little is known regarding the effects of thermally degraded carotenes on the oxidative stability of soybean oil. Thermally degraded (3-carotene or lycopene solutions were added to soybean oil samples at concentrations of 0, 25,45, and 50 ppm, respectively. Each sample, as well as controls containing 5, 25, and 50 ppm o f unheated (3-carotene or lycopene, contained 3 ppm of chlorophyll to allow photosensitized singlet oxygen oxidation to occur. The vial containing each sample was sealed airtight and stored either at 25°C in a light box (1650 lumens) or in a dark oven at 60°C. The oxidative stability of each soybean oil sample was determined by measuring (every 4 hours for 24 hours) peroxide value and headspace oxygen depletion by thermal conductivity gas chromatography. Oxidative stability was further identified by first utilizing solid phase microextraction (SPME) fibers to adsorb volatile oxidation products in the headspace of the samples, then quantifying and comparing the volatiles’ total peak area from their respective gas chromatogram. Soybean oil samples containing 50 ppm degraded (3-carotene displayed 11.5% higher peroxide values (under light) as well as higher headspace oxygen depletion values (in the dark) when compared with controls (p<0.01). Lycopene degradation products (50 ppm) in soybean oil decreased peroxide values up to 10.5% under light, and significantly decreased headspace oxygen depletion o f samples in the dark (p<0.05). Over all concentration ranges, headspace oxygen depletion values for samples stored under light containing either P-carotene or lycopene degradation products did not differ significantly from controls. After 30 days of storage in the dark at 60°C, samples containing 50 ppm degraded p-carotene displayed a significantly higher (p<0.05) SPME-GC total volatile peak area when compared with controls containing 50 ppm düLl-trans P-carotene. Under similar conditions, samples containing 50 ppm degraded lycopene displayed a significantly lower (p<0.05) SPME-GC total volatile peak area when compared with controls containing only oil. These results indicate that thermally degraded P-carotene can act as a prooxidant in soybean oil exposed to elevated temperatures, which may cause a decrease in the oxidative stability o f thermally processed foods containing soybean oil. Thermally degraded lycopene, however, may act as an antioxidant in soybean oil exposed to elevated temperatures and therefore may actually increase the oxidative stability o f food systems containing soybean oil.
Two independent modes of chromosome organization are revealed by cohesin removal

The three-dimensional organization of chromosomes is tightly related to their biological function 1. Both imaging and chromosome conformation capture studies have revealed several layers of organization 2-4: segregation into active and inactive compartments at the megabase scale 5, and partitioning into domains (TADs) 6,7 and associated loops 8 at the sub-megabase scale. Yet, it remains unclear how these layers of genome organization form, interact with one another, and contribute to or result from genome activities. TADs seem to have critical roles in regulating gene expression by promoting or preventing interactions between promoters and distant cis-acting regulatory elements 9-14, and different architectural proteins, including cohesin, have been proposed to play central roles in their formation 15,16. However, experimental depletions of these proteins have resulted in marginal changes in chromosome organization 17-19. Here, we show that deletion of the cohesin-loading factor, Nipbl, leads to loss of chromosome-associated cohesin and results in dramatic genome reorganization. TADs and associated loops vanish globally, even in the absence of transcriptional changes. In contrast, segregation into compartments is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the 3D organization of the genome results from the independent action of two distinct mechanisms: 1) cohesin-independent segregation of the genome into fine-scale compartment regions, defined by the underlying chromatin state; and 2) cohes-dependent formation of TADs possibly by the recently proposed loop extrusion mechanism 20,21, enabling long-range and target-specific activity of promiscuous enhancers. The interplay between these mechanisms creates an architecture that is more complex than a simple hierarchy of layers and can be central to guiding normal development.
Study of the susceptibility to antibiotics of cells released from Staphylococcus epidermidis biofilms

s and Posters Gaio V, Acúrcio V, França A, Cerca N. (2016). Preliminary studies on the susceptibility of Staphylococcus epidermidis biofilm-released cells to antibiotics and ability to survive in the presence of human blood. In Biofilms 7. No. P3: 83, Porto, Portugal, June 26-28, 2016 França A, Gaio V, Carvalhais V, Perez-Cabezas B, Correia A, Pier GB, Vilanova M, Cerca, N. (2016). S. epidermidis biofilm-released cells: the final frontier? In 3rd International Conference Pathophysiology of Staphylococci, Tubingen, Germany, September 15-17, 2016
The use of larvae or recruits in coral restoration initiatives: Symbiodinium acquisition does not differ between coral life stages in the wild

Active restoration initiatives are increasingly considered in natural resource management. Laboratory‐reared coral larvae and recruits have been proposed for stock production but it is unknown if their use impacts subsequent symbiosis once transplanted to the reef. We exposed laboratory and field settled aposymbiotic recruits (recently settled <1 month) to Symbiodinium in the wild, then analyzed the acquired communities using ITS‐2 sequencing. There was no significant difference between treatments based on overall community and diversity metrics, or differential abundance of individual taxa. These results suggest that early acquisition is analogous and thus supports the use of either life‐stage as an option for reef restoration.
Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture

This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the order Thermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA of one archaeon is only 91.6% identical to Thermogymnomonas acidicola as most closely related isolate. Hence, this organism is the first member of a new genus. The enrichment culture is dominated by this microorganism and the ARMAN. The third archaeon in the community seems to be present in minor quantities and has a 100% 16S rRNA identity to the recently isolated Cuniculiplasma divulgatum. The enriched ARMAN species is most probably incapable of sugar metabolism because the key genes for sugar catabolism and anabolism could not be identified in the metagenome. Metatranscriptomic analysis suggests that the TCA cycle funneled with amino acids is the main metabolic pathway used by the archaea of the community. Microscopic analysis revealed that growth of the ARMAN is supported by the formation of cell aggregates. These might enable cross feeding by other community members to the ARMAN.
Comparative insights to the transportome of Nosema: a genus of parasitic microsporidians

Nosema, a genus of parasitic microsporidia, causes pebrine disease in arthropods, including economically important silkworms and honeybees. Nosema have gene-poor genomes shaped by loss of the metabolic pathways, as a consequence of continued dependence on host-derived substrates. As an act of counterbalance, they have developed an array of transporter proteins that allow stealing from their hosts. Here, we have identified the core set of twelve transporter families present in Nosema genus, viz. N. apis, N. bombycis, N. ceranae and N. antheraea through in silico pipeline. Transportomes of N. apis, N. bombycis, N. ceranae and N. antheraea have a dominant share of secondary carriers and primary active transporters. The comparatively rich and diverse transportome of N. bombycis indicates the role of transporters in its remarkable capability of host adaptation. The core set of transporter families of Nosema includes ones that have a likely role in osmo-regulation, intra- and extra-cellular pH regulation, energy compensation and self-defence mechanism. This study has also revealed a set of ten species-specific transporter families within the genus. To our knowledge, this is the first ever intra-genus study on microsporidian transporters. Both these datasets constitutes a valuable resource that can aid in development of inhibitor-based Nosema management strategies.