Miracle-dz/UniFAR-FTUs huggingface dataset:
Resistance monitoring of larvae treated with Bt cotton and pesticides in Helicoverpa armigera (Lepidoptera: Noctuidae)

Abstract Transgenic Bt cotton was first introduced into Qiuxian County (Hebei, China) in order to control the cotton bollworm, Helicoverpa armigera, in 1998. Owing to the high selection pressures in this region, monitoring of Bt resistance in H. armigera is critical to verify the efficacy of transgenic cotton and construct the new management strategy. The F2 screen was conducted to detect the resistance allele frequency in the field population of H. armigera in Qiuxian County from 2010 to 2012. The annual values were 0.0389 (95% CI: 0.0064–0.0714), 0.0372 (95% CI: 0.0036–0.0708) and 0.0781 (95% CI: 0.0318–0.1244), respectively. In order to test the optional insecticides to control H. armigera, through leaf-dip bioassay, the resistance of field population from Qiuxian to 6 insecticides were detected. The results showed Qiuxian population was kept high resistance to cyhalothrin (Resistance Ratio = 61.8–95.2) and to beta-cypermethrin (Resistance Ratio = 50.9–82.3), low to moderate resistance to phoxim (Resistance Ratio = 9.1–23.7), and susceptibility to emamectin benzoate, abamectin and spinosad. Emamectin benzoate, abamectin and spinosad are the alternative options for controlling H. armigera in Qiuxian County, if the efficacy of Bt cotton is compromised by Bt resistance in the field.
Mir-132 controls beta cell proliferation and survival in mouse model through the PTEN/AKT/FOXO3 signaling

Aim and hypothesis microRNAs (miRNAs) play an integral role in maintaining beta cell function and identity. However, their diversity as well as the complexity of identifying their endogenous targets and how they are regulated made deciphering their precise role a real challenge. This project was aimed toward the identification of miRNAs and their downstream targets specifically involved in islets beta cells regeneration in mouse model. Methods Using a partially pancreatectomized mouse model to induce beta cell proliferation, we identified several miRNAs that were differentially expressed in relationship to beta cell replication. The further validated by RT-PCR. Transcriptomic analysis and bioinformatic data mining was then performed to identify the downstream target of miR-132 in insulinoma cell line MIN6 cells, which were then further validated at transcriptional and translational levels. Beta cell proliferation was further assessed in pancreatectomized control and miR- 132-/- mice to validate the role of miR-132 in vivo. Results Sequence specific inhibition of miR-132 correlated with reduced cell proliferation as well as increased apoptosis, whereas its overexpression resulted in reduced apoptosis. Increased levels of miR-132 correlated with repression of PTEN and thus increased Akt signaling and downstream activation of the transcription factor FOXO3a. Consistent with these findings we found that proliferation of beta cell in miR-132-/- pancreatectomized mice was significantly reduced compared to wild-type littermates. Conclusions/Interpretations Here we have uncovered an exhaustive list of targets and the signaling pathways by which miR-132 controls beta cell proliferation and survival in pancreatic beta cells. The fact that miR-132 controls beta cell proliferation and survival by regulating PTEN activity, the node of Akt/FOXO3 signaling pathway may represent a suitable target to enhance beta cell mass.
Targeting Hedgehog Signalling as a Drug Therapy in Aggressive Fibromatosis

Aggressive fibromatosis is a benign fibroproliferative tumour that can occur as a sporadic lesion or a manifestation in patients with familial syndromes, such as familial adenomatous polyposis. Tumours are characterized by the stabilization of β-catenin and the activation of β-cateninmediated transcription. Current treatment results are far from ideal, and recurrence rates are high. As a result, there remains a need for more effective therapeutic strategies. In this work, we demonstrate the effect of hedgehog signalling inhibition on aggressive fibromatosis tumour development and β-catenin modulation. We found that hedgehog inhibition decreased cell viability and proliferation as well as total β-catenin levels in human aggressive fibromatosis tumour cells in vitro. Furthermore, following hedgehog inhibition in Apc/Apc aggressive fibromatosis mouse model, the number and volume of the tumours formed was reduced. Together, this work suggests that hedgehog signalling inhibitor agents are potential candidates to effectively manage aggressive fibromatosis.
Antioxidant Properties of Ewe versus Cow Yogurt and Effect of Its Consumption on Cortisol Levels of Adults (Borderline-high Cholesterol Levels)

Antioxidant in vitro markers were used to evaluate the total antioxidant activity of ewe (whole and semi-skimmed) and cow’s set yogurts. Results showed that cow set yogurt had significantly (p≤0.05) total higher antioxidant activity than ewe set yogurt and peptidic fraction had significant higher contribution to the total antioxidant activity compared to lipidic and/or phenolic fraction. However, when lipidic fraction was evaluated, ewe yogurt (whole and skimmed) had higher antioxidant activity than cow probably associated to the high levels of conjugated linoleic acid (CLA) in ewe milk. Although significant differences win cortisol levels were observed in certain groups of population studied (normal risk woman) regarding consume ewe yogurt, it is not possible to conclude a significant lowering effect of ewe yogurt on cortisol levels in general population.
Decadal-scale reduction in forest net ecosystem production following insect defoliation contrasts with short-term impacts of prescribed fires.

Understanding processes underlying forest carbon dynamics is essential for accurately predicting the outcomes of non-stand-replacing disturbance in intermediate-age forests. We quantified net ecosystem production (NEP), aboveground net primary production (ANPP), and the dynamics of major carbon (C) pools before and during the decade following invasive insect defoliation and prescribed fires in oak- and pine-dominated stands in the New Jersey Pinelands National Reserve, USA. Gross ecosystem production (GEP) recovered during the year following defoliation at the oak stand, but tree mortality increased standing dead and coarse woody debris, and ecosystem respiration (Re) accounted for >97% of GEP. As a result, NEP averaged only 22% of pre-disturbance values during the decade following defoliation. At the pine stand, GEP also recovered to pre-disturbance values during the year following understory defoliation by gypsy moth and two prescribed fires, while Re was nearly unaffected. Overall, defoliation and tree mortality at the oak stand drove a decadal-scale reduction in NEP that was twofold greater in magnitude than C losses associated with prescribed fires at the pine stand. Our study documents the outcomes of different non-stand-replacing disturbances, and highlights the importance of detrital dynamics and increased Re in long-term measurements of forest C dynamics following disturbance in intermediate-age forests.
Mixtures are more salient stimuli in olfaction

In their natural environment, animals often encounter complex mixtures of odours. It is an open question whether and how responses to complex mixtures of multi-component odours differ from those to simpler mixtures or single components. To approach this question, we built a full-size model of the early olfactory system of honeybees, which predicts responses to both single odorants and mixtures. The model is designed so that olfactory response patterns conform to the statistics derived from experimental data for a variety of their properties. It also takes into account several biophysical processes at a minimal level, including processes of chemical binding and activation in receptors, and spike generation and transmission in the antennal lobe network. We verify that key findings from other experimental data, not used in building the model, are reproduced in it. In particular, we replicate the strong correlation among receptor neurons and the weaker correlation among projection neurons observed in experimental data and show that this decorrelation is predominantly due to inhibition by interneurons. By simulation and mathematical analysis of our model, we demonstrate that the chemical processes of receptor binding and activation already lead to significant differences between the responses to mixtures and those to single component stimuli. On average, the response latency of olfactory receptor neurons at low stimulus concentrations is reduced and the response patterns become less variable across concentrations as the number of odour components in the stimulus increases. These effects are preserved in the projection neurons. Our results suggest that the early olfactory system of insects may be particularly efficient in processing mixtures, which corresponds well to the observation that chemical signalling in nature predominantly involves mixtures.
Sugars in space, N-glycosylation mutants of the erythrocyte anion exchanger

Scanning N-glycosylation mutagenesis was used to determine the topology of a polytopic membrane protein, the human erythrocyte anion exchanger 1 (AH), using cd-free translation and hansfected cells. N-glycosylation acceptor sites located near the middle of large EC loops were effiaently N-glycosylated. however no N-glycosylation occurred ai sites located within sharply defined regions dose to the adjacent TM segments. To be efficiently N-glycosylated, EC lmps in polytopic membrane proteins must be large, than 25 residues in size, with acceptor sites located greater than 12 residues away from the preceding TM segment and greater than 14 residues away from the foiiowing TM segment. Application of this requirement allowed a significant refinement of the topology of AE1 induding a more accurate mapping of the ends of TM segments. The strict distance dependence for Nglycosylation of loops suggests that TM segments in polytopic membrane proteiw are held quite precisely within the translocation rnachinery during the N-glycosylation process. A novel 12 transmembrane segment mode1 for AE1 was proposed. with a T-loop structure connecting TM segments 9 and 10. Mutations designed to dimpt the folding of T-loop suggest that this loop may be transiently exposed to the lumen of the endoplasmic reticulum during biosynthesis, but normally foi& rapidly, preùuding N-glycosylation. The resuits indicate that the folding of the carboxyl-terminal region of AE1 is more compIex than originaiiy proposed and that this region of the transporter may have a dynamic aspect Calnexin is a lectin-We ER chaperone, considered a dissociable part of the translocon cornplex. The spatial requirements for calnexin interaction with AE1 were characterized. The results show that the interaction of calnexin with the polytopic membrane glycoprotein AEl was dependent on the presence but not the location of the oligosaccharide. Furthemore, calnexin was associated with AE1 after its release &am the translocation A lectin gel-shift assay was developed, whkh aiiowed an enhanced resoiution of glycoproteins by SIX gel electrophoresis. The use of N-linked glycosylation has proven a valuable tool to study the topology of a membrane protein in a fine detaii and the dynamics of early stages of protein folding in the membrane protein biosyithesis.
Analyses of microbial communities at biogeochemical interfaces and their interaction with organic pollutants in soil

To study the responses of soil indigenous microbial communities to persistent organic pollutants, the Eutric Cambisol (60°N, 17°E) and the Luvisol (48°N, 11°E) were spiked with the model polycyclic aromatic hydrocarbons (PAH) substrate phenanthrene and incubated at room temperature. Total community DNA was extracted from samples collected at day 0, 21 and 63 and used for further molecular analysis. Soil type-dependent responses to phenanthrene were revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes using a novel PCR detection system. By GeoChip, phenanthrene spiking of pristine soils was found facilitate the detection of bacterial functional genes. New incP-9 plasmids which might not be involved in PAH degradation was present in both soil samples as uncovered by a novel PCR detection system in conjunction with Southern blot. Diverse, dynamic, common and soil-type specific bacterial responses to phenanthrene spiking in two different pristine soils were illustrated by DGGE and bar coded pyrosequencing analyses of 16S rRNA gene fragments. A novel pipeline was constructed for processing large sequence datasets.
Unpaid extinction debts for endemic plants and invertebrates as a legacy of habitat loss on oceanic islands

The majority of documented extinctions world‐wide in the last four centuries are of species endemic to islands. However, the phenomenon of delayed extinctions as a result of habitat loss has rarely been assessed on oceanic islands. In this study, we tested whether extinction debt (ED), in general, occurs on islands and for which taxonomical groups this phenomenon is most pronounced by assessing ED for multiple endemic taxa and for each of the main altitudinal ecosystems in a well‐studied oceanic archipelago.
Real-time monitoring of T-cell-secreted interferon-γ for the diagnosis of tuberculosis

ABSTRACT In this paper, we report the development of a label-free biosensor, based on surface plasmon resonance, for real-time monitoring of captured human CD4+T-cells, and their dynamic cytokine production upon specific antigen stimulation. Microarrays of CD4+T-cells, and interferon gamma (IFN-γ) specific antibody (Ab) spots were printed side by side onto the poly(OEGMA-co-HEMA) matrix. The placement of CD4+ T-cells near the anti IFN-γ Ab-coated spots ensured a high local concentration of secreted IFN-γ for detection. We have demonstrated that this approach enables the detection of tuberculosis (TB) infection in clinical samples, with an overall sensitivity of 85.5% and an overall specificity of 97.7%.
New record of Trichoglossum rasum from Asia

Trichoglossum rasum, a rare species in the genus Trichoglossum, previously reported only from New Caledonia in 1909, was recently observed in Khasi hills, India. This paper illustrates important distributional record along with first molecular phylogenetic placement of the species. A review of all 19 hitherto accepted species in the genus is also provided.
Hydrolysis of cellobiose by β-glucosidase from Aspergillus niger in the presence of soil solid phases: minerals, biochar, and activated carbon

This study investigates the effects of different soil solid phases on the extracellular enzymatic hydrolysis of cellobiose to glucose. Montmorillonite, kaolinite, goethite and wood char did not adsorb cellobiose whereas they adsorbed 10, 70, 70, 99 % respectively of β-glucosidase from Aspergillus niger . The hydrolysis rate decreased with increasing enzyme adsorption; wood char, for instance, reduced it by 30 %. Activated carbon adsorbed almost 100 % of both cellobiose and β-glucosidase and inhibited hydrolysis completely. Among the immobilization methods for β-glucosidase which are also interesting for industrial applications, only the covalent binding to Eupergit©C particles was sufficiently stable. However, the immobilization caused an activity loss of 76 %.
The function of floral orientation in bluebells: interactions with pollinators and rain in two species of Mertensia (Boraginaceae)

Pollinators are traditionally considered to be the primary agent of selection on floral traits. However, floral traits may also be under selection from abiotic agents (e.g. rain), which makes considering the relative importance of pollinators and abiotic selective agents on floral traits essential. The functional significance of floral orientation is often ascribed to pollinator attraction, but orientation can also protect reproductive structures from rain. Therefore, a study that incorporates both factors will enhance our understanding of the ecological roles of floral orientation in plant fitness. Mertensia brevistyla and M. fusiformis are herbaceous species that differ in their floral orientations. A series of field and laboratory experiments was used to investigate the adaptive function of floral orientation in these species, particularly with respect to pollinators and rain. We measured and compared floral orientation and visitor assemblages between M. brevistyla and M. fusiformis populations in western Colorado, USA. We manipulated floral stems and conducted a choice experiment with floral visitors, and also compared orientations of pollinator-visited stems with those of unvisited stems in a natural setting. We examined pollinator- and rain-mediated selection on floral orientation by manipulating orientation, conducting supplemental pollinations, applying watering treatments and measuring subsequent seed set. We also experimentally tested the likelihood of rain contact with anthers, and the effect of rainwater on pollen germinability. Mertensia brevistyla had a significantly more upright floral orientation than M. fusiformis, and seed set was highest in upright M. brevistyla and in horizontal/pendant M. fusiformis stems, supporting an adaptive function (via female fitness) of the interspecific difference in orientation. However, floral visitor assemblages did not differ significantly between the two species; visitors did not exhibit significant preference for either orientation; and pollinator-mediated selection on orientation was undetectable. Similarly, there was little effect of water on seed set in either species, regardless of floral orientation. However, pollen germinability was reduced in both species by immersion in water; and water was more likely to contact anthers in M. fusiformis than in M. brevistyla, due to interspecific differences in floral morphology. We conclude that pollinators are likely not the primary selective agent driving differences in orientation in these Mertensia species. Instead, the negative effect of rain on pollen germinability helps explain the more pendant orientation of M. fusiformis, while short anthers in more upright M. brevistyla provide an alternative adaptation to rain. The selective agent driving effects of orientation on seed set remains unclear. This study illustrates the necessity of considering male fitness and abiotic agents in interpreting the functional significance of inflorescence traits.
CLONING AND CHARACTERISATION OF ALKALI MYOSIN LIGHT CHAIN GENE (MLC-3) OF CATTLE FILARIAL PARASITE SETARIA DIGITATA

Lymphatic filariasis is a tropical disease caused by filarial parasites including Wuchereria bancrofti. Although bancroftian filariasis causes severe disabling and debilitating clinical conditions in human, very little is known about the molecular biology of the parasite. The paucity of parasitic material is the main reason for this lack of knowledge. Setaria digitata is a cattle filarial parasite, closely resembling W. bancrofti in many aspects. Therefore it can be used as a model organism to study W. bancrofti. In the present study, the genomic library of S. digitata adult parasites was constructed and probed with a 32 P labeled partial mRNA sequence PCR amplified from a previously isolated cDNA clone containing a 661 bp mRNA transcript of S. digitata alkali myosin light chain gene. Isolated positive clones were sequenced and edited by using bioinformatics tools. Though the 5´ flanking region did not reveal any consensus TATA box sequences, a potential CAAT box like sequence, CCAAT and seven possible transcription factor elements were identified. The entire gene had four exons encoding 149 amino acids interrupted by three introns of varying lengths of 87, 295 and 69 bp respectively. Sequences around the splice junctions were fairly conserved and agreed with the general GT-AG splicing rule. The 3´ flanking region consists of three putative polyadenylation signals with the sequence AATAAA. The gene was AT rich with a GC content of 35%. Southern hybridisation studies suggested that this gene is likely to be a single-copy gene. Homology search of amino acid sequences showed more than 80% similarity with Caenorhabditis species and 40-50% with other vertebrate and invertebrate myosin light chains. Analysis of the amino acid sequence with the NCBI conserved domain database for interactive domain family identified the protein as a member of calcium binding protein family as it comprised of two highly conserved EF hand motifs, and may suggest a possible function in Ca 2+ binding.
Metabolic Imaging and Applications in Protein and Lipid Homeostasis

Metabolic Imaging and Applications in Protein and Lipid Homeostasis Yihui Shen Metabolic activity is an important functional parameter of a living cell. Microscopic techniques are demanded to resolve the heterogeneity of metabolic activity from cell to cell and among subcellular compartments. Towards this, work in the Min lab has been dedicated to developing a prevailing metabolic imaging platform that couples chemical imaging by stimulated Raman scattering (SRS) microscopy with small vibrational tags on precursor molecules. This thesis describes efforts along metabolic imaging by SRS microscopy, with focus on visualizing protein and lipid homeostasis. Chapter 1 describes the design principle of metabolic imaging, including selection of vibrational tags and setup of SRS microscopy, and an overview of successful demonstrations of metabolic imaging in protein and lipid metabolism. Chapter 2 describes adoption of such principle to visualize protein turnover with C-phenylalanine metabolic labeling under steady-state condition and various perturbations. The rest of this thesis (Chapters 3-6) switches focus to fatty acid metabolism and cellular lipid homeostasis. As the minimal tagging in vibrational imaging preserves the physicochemical property of lipid molecules to the largest extent, it motivated me to revisit fatty acid metabolism from a biophysical perspective. Bearing the question in mind whether the non-equilibrium metabolic activity could drive phase separation in biological membranes, I thus look into the principle of membrane organization and its implication in biological membranes in Chapter 3. Then in Chapter 4, I describe the discovery and characterization of previously unknown phase separation in endoplasmic reticulum (ER) membrane caused by lipid synthesis. In this case, metabolic imaging by SRS enables identification of solid-like domains formed by saturated fatty acid (SFA) metabolites. This observation further raises the question whether phase separation bears any functional roles in the adverse effects of SFAs (or lipotoxicity). Towards this, Chapter 5 introduces the background of lipotoxicity including its definition and models. Then I review proposed mechanisms for lipotoxicity, which point to the central role of ER in mediating the stress transduction. In Chapter 6, I present our findings that suggest the association of the observed solid-like domains with ER structural remodeling and local autophagic arrest. Together, these efforts demonstrate the valuable capability of SRS imaging to reveal metabolic heterogeneity and how this aids in the investigation of metabolic stress.