Miracle-dz/UniFAR-FTUs huggingface dataset:
Pioneer Round of Translation Supplies Peptides for Major Histocompatibility Complex Class I Presentation

Author(s): Chen, Keling | Advisor(s): Shastri, Nilabh | Abstract: Cytotoxic T cells monitor MHC class I complexes on antigen presenting cells for the potential presence of any non-self peptides that could derive from viral infection or cancerous cells. Effective immune surveillance requires that MHC class I molecules display a peptide repertoire on the surface representing all cellular proteins. This ensures that foreign antigens from all sources are presented. How the peptide repertoire can be comprehensive despite the large differences in abundance and stability of individual proteins is not known. The pioneer round of translation is the first round of translation that occurs on newly spliced mRNA. It is associated with nonsense-mediated decay of mRNAs, allowing cells to detect and eliminate the aberrant mRNAs containing premature stop codons. We showed here that the peptide presentation by MHC I molecules was strongly influenced by the pioneer round of translation. Inhibition of the pioneer round of translation by knockdown of CBP80, a nuclear cap-binding protein, reduced peptide presentation by MHC class I molecules on the cell surface without affecting global protein synthesis. On the other hand, introduction of premature stop codons changed mRNA stability without affecting peptide presentation by MHC I on the cell surface. In addition, intronless mRNAs bypassing the pioneer round of translation resulted in reduced MHC I presentation on the cell surface. Furthermore, knockdown of CBP80 led to the deficiency of the cytosolic peptides delivered by the transporter associated with antigen processing (TAP) for the MHC class I pathway. Together, these findings highlight the importance of the pioneer round of translation in deriving peptides to generate a comprehensive display of virtually all endogenous proteins for the immune surveillance
Effect of C-terminus site-directed mutations on the toxicity and sensitivity of Bacillus thuringiensis Vip3Aa11 protein against three lepidopteran pests

ABSTRACT The insecticidal activities and specificities of the Vip3Aa proteins derived from different Bt strains are very different, although the similarities between these proteins are higher than 95%. In this study, we hypothesised that the differences in Vip3Aa11 and Vip3Aa39 C-terminal amino acids determine their differences in insecticidal activity against three Lepidoptera insects. To find the amino acid residues associated with insecticidal activity, nine different amino acid residues of Vip3Aa11 were substituted with the corresponding amino acid residues from Vip3Aa39 by site-directed mutagenesis. The toxicity of each protein was estimated by bioassays, and the results demonstrated that the mutant Y784N lost its insecticidal activity against three insects (Agrotis ipsilon, Helicoverpa armigera, and Spodoptera exigua). The insecticidal activity of S543N, I544L, and S686R against S. exigua increased 5-fold, 2.65-fold, and 8.98-fold, while the toxicity to H. armigera and A. ipsilon slightly decreased compared with that of the Vip3Aa11 protein. These findings indicate that the amino acid residues Ser543, Ile544, Thr685, Ser686, Arg704, Ile780, and Tyr784 may be insecticidal activity-related residues. Additionally, the trypsin activation of the four mutants indicated that all proteins can form a 62-kDa core fragment, except Y784N. A possible association between the insecticidal activity and trypsin sensitivity of Vip3A proteins is suggested.
Effects of Seeding Date and Seed Size on Crassostrea gigas (Thunberg, 1793) Culture in a Subtropical Climate

ABSTRACT Studies that carefully monitor and attempt to explain causes of massive oyster mortalities are urgently needed. The objective of the present study was to assess the effects of seeding dates on the mortality and reproductive cycle of the oyster Crassostrea gigas. Seeds of two sizes (3.5–4 mm and 1.5–2 mm) were planted during three seasons: early summer, early autumn, and late autumn. The experimental period was 6 mo. Mortalities of C. gigas at culture phase nursery lantern-nets, intermediate lantern-nets, and final lantern-nets were recorded. The reproductive cycle of the oysters grown from 3.5 to 4 mm seeds planted in each season was closely monitored (bimonthly) during the experimental period. In addition, seawater parameters [temperature (daily) and salinity (weekly)] were monitored throughout the experimental period. Results of this study demonstrated that the planting season affected C. gigas mortality after the nursery phase. Lower cumulative mortality was observed for 3.5–4 mm seeds than for 1.5–2 mm seeds when the seeds were planted in early (MarL: 0.29 ± 0.02) and late (JunL: 0.22 ± 0.10) autumn, after 6 mo of culture. The reproductive cycle of seeds planted in the summer exhibited an early maturation process, and those planted in the autumn exhibited late reproductive development.
Subtypes of functional brain connectivity as early markers of neurodegeneration in Alzheimer’s disease

Highlights Reliable functional brain network subtypes accompany cognitive impairment in AD Symptom-related subtypes exist in the default-mode, limbic and salience networks A limbic subtype is associated with a familial risk of AD in healthy older adults Limbic subtypes also associate with beta amyloid deposition and ApoE4 In Brief We found reliable subtypes of functional brain connectivity networks in older adults, associated with AD-related clinical symptoms in patients as well as several AD risk factors/biomarkers in asymptomatic individuals. Summary The heterogeneity of brain degeneration has not been investigated yet for functional brain network connectivity, a promising biomarker of Alzheimer’s disease. We coupled cluster analysis with resting-state functional magnetic resonance imaging to discover connectivity subtypes in healthy older adults and patients with cognitive disorders related to Alzheimer’s disease, noting associations between subtypes and cognitive symptoms in the default-mode, limbic and salience networks. In an independent asymptomatic cohort with a family history of Alzheimer’s dementia, the connectivity subtypes had good test-retest reliability across all tested networks. We found that a limbic subtype was overrepresented in these individuals, which was previously associated with symptoms. Other limbic subtypes showed associations with cerebrospinal fluid Aβ1-42 levels and ApoE4 genotype. Our results demonstrate the existence of reliable subtypes of functional brain networks in older adults and support future investigations in limbic connectivity subtypes as early biomarkers of Alzheimer’s degeneration.
Meeting Seed Demand for Landscape-Scale Restoration Sustainably: The Influence of Seed Harvest Intensity and Site Management

ABSTRACT Native seed is often collected en masse from remnant ecosystems to supply landscape-scale restoration. Successful large-scale restoration depends on sustained seed yields but also on donor population persistence. Native plants that reproduce solely by seed are especially sensitive to harvesting practices. We addressed the challenge of procuring sufficient seed from remnant sources to restore landscapes while also maintaining remnant populations of native plants. We evaluated: 1) the sustainability of seed harvest at varying intensities in Rudbeckia hirta, a seedreliant plant; and 2) the contribution of fire in promoting sustainability of seed donor populations. We planted seedlings of R. hirta in a field experiment that manipulated management type (burned or unburned) and harvest intensity (0, 50%, or 100% seed removed), and measured changes in seedling recruitment and seed production among treatments. Moderate intensity harvest and burning did not significantly reduce seedling recruitment, but high intensity harvest with burning reduced recruitment by 95% compared to controls. Seed production nearly doubled in burned treatments. In unburned prairie, recruitment is negligible, and harvest intensity does not have an effect on recruitment. For harvest-sensitive prairie species, a strategy incorporating moderate intensity seed harvest with burning is most likely to provide seed for large-scale restoration sustainably.
Polymorphic Arrangement of 5s DNA Orphons in Xenopus laevis

In Xenopus laevis the major oocyte (Xlo), trace oocyte (Xlt), and somatic (Xls) 5s genes occur as separate multigene families, each organized in large clusters of tandemly repeating units. A repeat consists of a 5s RNA gene plus the spacer sequence characteristic of the particular family. I have discovered additional copies of the 5s RNA genes located at a number of dispersed genomic loci, apart from the major clusters. This was done by "null-digesting" total genomic DNA with restriction enzymes that do not cut within the 5s major repeats. The main clusters remain intact as high molecular weight DNA while the dispersed 5s genes can be resolved on gels as lower molecular weight restriction fragments. Probing these smaller fragments with either a 5s gene-specific, Xlo, Xlt or Xls spacer-specific probe has revealed that the organization of the dispersed genes, or orphons, is quite different from the 5s DNAs of the major clusters. The genes appear to be present in single copies and the majority of the fragments have a polymorphic organization in the population. Four types of orphons have been identified on the basis of their structure and incidence of polymorphism. Most orphons contain the 5s gene plus Xlo spacer, while others contain just the gene region. In both cases some of the elements have organizations that appear to be conserved in the population while others appear
Discrimination and assessment of black walnut (Juglans nigra L.) cultivars using phenology and microsatellite markers (SSRs)

Abstract: Black walnut (Juglans nigra L.), a large tree native throughout the eastern United States, produces a high-quality edible nut. Our goal was to maintain the integrity of black walnut breeding programs by verifying the identity of accessions. We sampled 285 ramets of 78 cultivars from the black walnut nut breeding orchards and clonal repositories at the University of Missouri and Kansas State University. We employed both phenotypic and genotypic methods to identify and differentiate cultivars. Phenotypes were evaluated using seven phenological traits. Cultivars varied for all traits among each of the 4 yr, but the best morphological characteristics for evaluating cultivar identity were bud break date and date of first pistillate bloom. Samples (n = 285) were genotyped using 10 polymorphic microsatellite loci. The simple sequence repeats produced a total of 174 alleles and 17.2 alleles per locus. We detected 47 unique genotypes represented by more than one sample, including 128 instances of identical genotypes with different names (synonyms) and 106 instances of different genotypes with a shared name (homonyms). Our results indicated that multiple errors were committed during the propagation of these important cultivars. It may be difficult to determine which genotype is original to a cultivar name in the absence of a foundation plant materials collection or vouchered specimens. These results will assist black walnut breeders and producers by improving the integrity of breeding collections and by identifying the best phenological traits for rapid assessment of trueness to type.
GPS tracking cattle as a monitoring tool for conservation and management

The emergence of GPS technology has resulted in significant advances in the ease and flexibility of studying animal movement patterns, yet barriers remain to the widespread use of GPS units for animal tracking. Here, we developed a low-cost, logistically simple approach, deploying small and inexpensive GPS units to monitor cattle movements and habitat use and to assess the impact of cattle grazing on vegetation. Cattle were collared with i-gotU loggers to track fine-scale and broad-scale movements within an integrated ecosystem (cattle and wildlife) in Laikipia, central Kenya. At the fine scale, cattle exerted a significant impact on vegetation quantity and quality; increasing grazing intensity showed a negative relationship to grass height, but a positive correlation to green-up after rain. At the broad scale, cattle movement density varied notably by herd type and habitat availability, with acacia woodland and savanna grassland habitats used most predominantly. Overall, these small GPS loggers provided a flexible and relatively cheap method of tracking cattle movements, and demonstrated potential for collaring of cattle as a tool for monitoring ecosystem health and assisting management decisions.
Association of HLA Class-I Antigens with Delusional Disorder

Abstract Delusional Disorder is characterized by monosymptomatic paranoid symptoms. In the field of psychiatry it is the only disease where delusion is recorded as a discrete symptom. Delusional disorder is probably heterogeneous group of illness and occurs in a variety of psychiatric and medical conditions. Although delusions remain one of the basic problems in psychopathology, attempts to understand its pathogenesis have been dominated by unsubstantiated speculation. Etiology and psychopathology of delusional disorder is not known. The main purpose of the present study was to investigate the incidence of HLA Class-I antigens in the patients with delusional disorder. Two psychiatrists conducted the screening process following the criteria of Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) to 60 unrelated patients who visited Department of Psychiatry, North Bengal Medical College and Hospital, Siliguri. In the delusional disorder patients significant increases were found for HLA – A3 antigen. This preliminary study of allelic association of polymorphic HLA allele with delusional disorder may lead to develop future strategies to understand the genetic basis of this disorder.
Global Position Effects on the Epigenetics of Variegated Lentiviral Vector Expression in Embryonic Stem Cells

Lentivirus efficiently transduce stem cells, however are notably silenced in embryonic stem cells (ESC). Provirus can be silent, expressing, or variegated when clonal single copy ESCs spawn daughters that revert expression despite containing identical integration sites (IS) indicating epigenetic regulation. In the silent state, variegated provirus are bound by H1 and MeCP2, where H1 compensates for MeCP2 binding in DNA methylation null ESCs, consistent with a model of heterochromatin formation dependent on concentrations of its constituent components. ESC Variegation was hypothesized to result from spreading of nearby heterochromatin. Global IS analysis indicates Variegated IS favour gene deserts, repeat clusters, and LINEs while Expressers prefer gene density with stable modest expression and SINEs. Chromatin data does not support a role for the spread of heterochromatin possibly a consequence of the dynamic/dispersed nature of ESC heterochromatin. Variegation thus may depend on stochastic chromatin regulation by pluripotency factors at proximal genome organizing repeats.
Bidirectional Cycling Dynamics of Living Neuronal Networks in Vitro

Phenomena of synchronization, rhythmogenesis and coherence found in brain networks are believed to be a dynamical substrate for cognitive functions such as learning and memory. However, it is still debated whether the rhythmic activity emerges from network morphology developed in neurogenesis or as a result of neuronal dynamics realized under certain conditions. In this research we found, that in neural networks formed in mature hippocampal cultures with high cellular density the spiking activity self-organized and converged to long, complex and rhythmically repeated superbursts. The superburst lasted tens of seconds and consisted of hundreds of short (50-100 ms) small bursts with a high spiking rate of 139.0 ± 78.6 Hz that can be associated with high-frequency oscillations in the hippocampus. In turn, the interval between peak burst activities in the range of 100-150 ms can be treated as a theta rhythm (11.2 ± 1.5 Hz). Distribution of spikes within the bursts was non-random, representing a set of well-defined space-time base patterns or motifs. We found that the long superburst can be classified into two types. Each type was associated with a unique direction of spike propagation and, hence, can be encoded by a binary sequence with random switching between the two “functional” states. Such precisely structured bidirectional rhythmic activity developed in self-organizing cultured networks were quite similar to what observed in the in vivo experiments.
Anthropogenic increases of catchment nitrogen and phosphorus loads in New Zealand

ABSTRACT Spatial regression models were used to predict yields (kg ha−1 yr−1) of nitrogen (N) and phosphorus (P) discharged from catchments throughout New Zealand under natural and current conditions. The models were derived using loads (kg yr−1) of TN, NO3-N, TP and DRP calculated for 592 river water quality monitoring sites. Anthropogenic increases in yields above natural levels were associated with the proportions of catchments occupied by the intensive agricultural land cover and were unevenly distributed across regions. Anthropogenic increases in national loads of TN, NO3-N, TP and DRP exported to the ocean were 74%, 159%, 48% and 18%, respectively. Increases in loads exported to the ocean varied considerably at smaller scales, with catchments having significant load increases between 4- and 26-fold for N and 6- to 9-fold for P. Predictions of yields and loads reported here have utility in the development of strategies to manage nutrients.
Improved iron acquisition of Astragalus sinicus under low iron-availability conditions by soil-borne bacteria Burkholderia cepacia

ABSTRACT Soil bacteria can assist plant growth and increase uptake of nutrient elements, the question arises as to whether beneficial soil microbes confer augmented iron (Fe) content of host plants under Fe limited conditions. Herein, a novel strain of Burkholderia cepacia (strain JFW16) was isolated from rhziospheric soils of Astragalus sinicus grown under alkaline conditions. Inoculation of plants with B. cepacia JFW16 displayed increased endogenous Fe content compared with non-inoculated plants. Growth promotion and enhanced photosynthetic capacity were also observed for the inoculated plants. The inoculation with JFW16 significantly increased the rhizospheric acidification, and up-regulated the transcription of some Fe acquisition-associated genes in Astragalus sinicus. Moreover, the metabolic pathways of flavins were remarkably enhanced in the inoculated plants, showing the increased biosynthesis and release of flavins in roots. Collectively, these findings demonstrated the potential of B. cepacia JFW16 to improve Fe assimilation in agricultural crops.
Grapes to wine: the nexus between berry ripening, composition and wine style

Grape ripening is a process driven by the interactions between grapevine genotype and environmental factors. Grape composition is largely responsible for the production and final concentrations of most wine aroma compounds even though many compounds in wines (aromatic and non-aromatic) are substantially transformed during the complex process of fermentation and wine ageing. The aim of this study was to investigate if a common pattern in grape/wine flavour plasticity related to ripening exists irrespective of a grape growing region. A further aim was to identify and highlight compounds present in grapes and wines in which plasticity is directly related to grape ripening and is consistent over several vintages. Irrespective of the region, a clear separation of samples was noted according to the harvest stage based on the grape and wine chemical analyses and wine sensory description. Shiraz wines from the first harvest (H1) were associated with red fruit descriptors and higher acidity. Wines from the third harvest (H3) were correlated with dark fruit characters and a higher perception of alcohol. Later harvest dates resulted in higher concentrations of some amino acids in grapes, higher alcohol acetates and dimethyl sulphide in wines, whereas concentrations of Z-3-hexenol, ethyl isobutyrate and ethyl leucate were lower in these wines compared to earlier harvest dates. Trends described were significant and consistent across two distinct regions and two vintages. Irrespective of the environment, this study demonstrated that for Shiraz, a common evolution of grape flavours exists, influencing the final wine chemical and sensory properties. Furthermore, during the late ripening stage, no direct nexus was observed between sugar concentration and grape and wine flavour evolution.
Recombinant Technology Differential expression of IFN-a subtypes in human PBMC: evaluation of novel real-time PCR assays

Studies of the human IFN-a subtype system have been hampered by the lack of efficient procedures to quantify and differentiate the expression of the highly homologous IFN-a subtypes. Here we evaluate four novel real-time PCR assays for the specific detection and quantification of IFN-a mRNA for the subtypes a2, a6, a8 and a1/13 in a combined assay in human peripheral blood mononuclear cells (PBMC). This included (a) the selection of h-glucuronidase (GUS) as a suitable housekeeping gene for relative quantification; (b) verification of the specificity by using human DNA of different IFN-a subtypes; and (c) comparison of the amplification efficiencies among the different assays. This highly sensitive method allows the detection of low-level, constitutive IFN-a mRNA and shows differences in the composition of constitutive IFN-a subtypes compared to other cell types (HeLa and HEp-2). The in vitro stimulation of PBMC with Newcastle disease virus (NDV), Respiratory syncytial virus (RSV) or an inactivated Herpes simplex (HSV) preparation leads to the transcriptional induction of all IFN-a subtypes investigated but to different expression levels. Among the subtypes detected, IFN-a13/1 and a2 are the major transcripts followed by a8, and finally a6 as a minor transcribed subtype. Time-kinetics of IFN-a transcriptional activation also revealed variations in the course of IFN-a transcription between NDV, RSVor HSV. The data obtained from the real-time PCR assays correlated well with IFN-a2 protein release. In conclusion, we have demonstrated the suitability and reliability of new real-time PCR assays for the rapid and efficient analysis of IFN-a subtype expression. D 2003 Elsevier Science B.V. All rights reserved.
Electrocution risk for the endangered Crowned Solitary Eagle and other birds in semiarid landscapes of central Argentina

Summary High mortality by electrocution has been suggested to be the main factor behind the reduction of several birds of prey populations across the world. Almost nothing is known, however, about the impact of power lines on this group of birds in the Neotropical Region. Here we estimate electrocution rates for birds on power lines covering both arid and semiarid biomes of central Argentina. We conducted six bi-monthly power line and raptor surveys throughout 355 km of lines and roads covering an area of approximately 12,000 km2. We described the structural design of 3,118 surveyed electricity pylons. We found 34 electrocuted individuals of four bird families that constitute an annual bird electrocution rate of 0.011 bird/pylon/year. Bird electrocution occurred mostly on concrete pylons with jumpers above the cross-arm. Larger birds of prey had a higher electrocution rate than smaller species. The Crowned Solitary Eagle Buteogallus coronatus was disproportionately affected by this mortality source when compared with its low population density. Electrocution incidents occurred mostly in a few electric pylon designs that represent only 10.2 % of the power pylons monitored in the study area. Therefore, the change or modification of a small fraction of pylons would almost eliminate bird electrocution incidents in our study area. Our results prove that electrocution is a relevant cause of mortality for Crowned Solitary Eagles and urgent mitigating actions are needed to reduce this mortality factor.