Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical composition of fruit juices from different sour cherry cultivars

Sour cherry juices were produced from 5 different cultivars with classic processing technology. Regarding primary juice parameters, high results for dry mass (13.7-1X.8 °Brix), sugar-free extract (57.5-80 g/L), total acidity (15.8-23.7 g/L), sorbitol (12.1-21.6 g/L) and minerals were found. Secondary plant metabolites were present in high amounts as well. In the sum, 651-1693 mg/L of polyphenols were found by means of HPLC/PDA. Neochlorogcnic acid, 3-coumaroyl-quinic acid, chlorogenic acid, and epicatechin were the predominant polyphenols. The quercetin glycosides ranged from 31-109 mg/L. Anthocyanins were identified as cyanidin-3-(2 G -glucosylrutinoside), cyanidin-3-(2G-xylosylrutinoside), cyanidin-3-glucoside, cyanidin-3-rutinoside, and peonidin-3-rutinoside. A significant decline of the anthocyanin concentrations could be observed during a 6 months storage, which reduced the red colour of the juices drastically. The high polyphenol concentrations were responsible for the high antioxidative capacities of the juices.
Understanding the Dlx-mediated effects on cell proliferation

UNDERSTANDING DLX-MEDIATED EFFECTS ON CELL PROLIFERATION Rachel K MacKenzie Advisor: University of Guelph, 2014 Dr. Andrew J Bendall Dlx5 and Dlx6 are members of the Distal-less homeobox (Dlx) gene family and encode transcription factors essential for craniofacial patterning and differentiation of mineralizing cell types in the skeleton during development. Forced expression of Dlx5 or Dlx6 in progenitor cells promotes their differentiation and suppresses proliferation in vitro and in vivo. Conversely, studies involving cancer cell lines have shown that Dlx5 can promote proliferation, perhaps via direct transcriptional activation of cell cycle regulatory genes like c-Myc. We have shown that Dlx5 and Dlx6 inhibit cell growth in multipotent progenitor cells and primary limb bud cells and modestly upregulate c-Myc reporter transcription in such cells. Cumulative EdU-incorporation assays indicate that Dlx5 and Dlx6 decrease the proportion of actively cycling cells in a population and may increase the length of the cell cycle. Flow cytometry results suggest a higher proportion of cells in G1 compared to controls.
The genomic formation of First American ancestors in East and Northeast Asia

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000–18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia. One Sentence Summary Ancient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.
Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse

Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene‐loci in a circum‐Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene‐loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
A highly efficient hybrid peptide ameliorates intestinal inflammation and mucosal barrier damage by neutralizing lipopolysaccharides and antagonizing the lipopolysaccharide‐receptor interaction

Intestinal inflammatory disorders, such as inflammatory bowel disease, are major contributors to mortality and morbidity in humans and animals worldwide. While some native peptides have great potential as therapeutic agents against intestinal inflammation, potential cytotoxicity, anti‐inciting action, and suppression of anti‐inflammatory activity may limit their development as anti‐inflammatory agents. Peptide hybridization is an effective approach for the design and engineering of novel functional peptides because hybrid peptides combine the advantages and benefits of various native peptides. In the present study, a novel hybrid anti‐inflammatory peptide that combines the active center of Cecropin A (C) and the core functional region of LL‐37 (L) was designed [C‐L peptide; C (1‐8)‐L (17‐30)] through in silico analysis to reduce cytotoxicity and improve the anti‐inflammatory activity of the parental peptides. The resulting C‐L peptide exhibited lower cytotoxicity than either C or L peptides alone. C‐L also exerted a protective effect against lipopolysaccharide (LPS)‐induced inflammatory responses in RAW264.7 macrophages and in the intestines of a mouse model. The hybrid peptide exhibited increased anti‐inflammatory activity compared to the parental peptides. C‐L plays a role in protecting intestinal tissue from damage, LPS‐induced weight loss, and leukocyte infiltration. In addition, C‐L reduces the expression levels of tumor necrosis factor‐alpha (TNF‐α), interleukin‐6 (IL‐6), IL‐1β, and interferon‐gamma (IFN‐γ), as well as reduces cell apoptosis. It also reduced mucosal barrier damage caused by LPS. The anti‐inflammatory effects of the hybrid peptide were mainly attributed to its LPS‐neutralizing activity and antagonizing the activation of LPS‐induced Toll‐like receptor 4‐myeloid differentiation factor 2 (TLR4/MD2). The peptide also affected the TLR4‐(nuclear factor κB) signaling pathway, modulating the inflammatory response upon LPS stimulation. Collectively, these findings suggest that the newly designed peptide, C‐L, could be developed into a novel anti‐inflammatory agent for animals or humans.
Conservation Leverage: Ecological Design Culverts also Return Fiscal Benefits

Traditional hydraulically designed culverts impede ecological connectivity and degrade aquatic ecosystems. This problem is compounded by their ubiquity in the built environment. To overcome these limitations, alternative designs have been created to facilitate natural conditions and restore ecological connectivity. However, these “ecological design” culverts have perceived fiscal limitations that have prevented widespread implementation and consequently hampered conservation and remediation of stream ecosystems important for myriad fish species and aquatic organisms. We addressed these perceived fiscal limitations using cost–benefit analysis to estimate the lifetime fiscal net benefits of ecological design culverts over hydraulic culverts. We found that in nearly half of all cases remediation with ecological design culverts was more cost effective than maintaining hydraulic culverts and that it is most cost effective on small streams compared to larger ones. We also found that higher upfront replacement c.
FUNCTIONAL AND ULTRASTRUCTURAL CHANGES OF THE PHOTOSYNTHETIC APPARATUS IN RESPONSE TO CD AND ZN IN VICIA FABA L. LEAVES

Heavy metal as Cd can antagonise uptake and transport of other metal elements such as Mn, Zn, and Fe in leaves of Vicia faba L. concentrations of Cd or Zn up to 100 ÂµM remarkably decreased chlorophyll content compared to control. The degradation in Chl. b under such stress was slower than that of Chl. a. and Cd had more inhibitory effect on both pigments than Zn even under low concentration (50 ÂµM). The results cleared that Zn can strongly antagonise this toxic effect of Cd especially with high Zn concentrations and where full protection and restoration of chlorophyll levels was recorded. Measurements of Na, Mg, P, K, Ca, Cu, Al, Mn, and Zn bounded to the cell membrane, revealed a significant decrease of Ca, K and Mg in the presence of Cd or Zn, also the disappearance of Fe peak was observed at 100 ÂµM Cd. This could be due to Cd ions interaction with the manganese cluster which is present in the evolving complex on the donor side of PSΠ. The effect of metal toxicity for Zn and or Cd, in this study, could be observed in many damages to the cell organelle ultrastructure. Changes in chloroplast ultrastructure and lipid composition of the thylakoid membranes alter the operability of the photosynthetic electron transport chain. The chloroplast treated with 100 ÂµM Cd has a reduced number of intact grana, as well as reduced chloroplast size. Combined treatment of cadmium and zinc led to more changes in the shape of cellular components, such as, the shape of chloroplasts was almost spherical, the grana were completely damaged and a large part of chloroplast appeared with disturbed envelopes. Increasing Zn over Cd concentration treatment acquired beneficial effect as it can successfully antagonize the harmful effect of Cd.
Is the human genome nearly identical to chimpanzee?—a reassessment of the literature

A review of the available literature related to the common claim that few genetic differences exist between chimpanzees and humans was undertaken. While taking the published information at face value, we show that significant reported differences exist in regards to, not only genomic sequence, but gene regulation, regulatory genomic regions, microRNA code, and gene splicing. We conclude that multiple facets of differences in DNA sequences and genetic mechanisms as reported in the standard scientific literature, suggest that clear unbridgeable genetic differences exist between humans and chimpanzees.
Innovative Transcriptomics Approaches for Large Scale Identification of Genes Involved In Plant Secondary Metabolism

Plants synthesize an impressive number of different secondary metabolites involved directly in the interaction with other organisms and with environment or indirectly in the regulation of plant responses [1,2]. Moreover many secondary metabolites hold beneficial effects on human health and are used as bioactive components of drugs [3]. Plant nutraceuticals, natural plant food and use of nutritional therapies and phytotherapies have become progressively popular to improve health and to prevent and treat diseases. Improving the traits related to plant secondary metabolism (i.e. defense responses, fitness, stress tolerance, nutraceutical value, etc.) has become a main target of plant breeding and biotechnology industry [4].
Thermodynamic and mechanistic insights into coupled binding and unwinding of collagen by matrix metalloproteinase 1

Local unwinding of the collagen triple helix is a necessary step for initiating the collagen degradation cascade in extracellular matrices. A few matrix metalloproteinases (MMPs) are known to support this key process, but its energetic aspects remain unknown. Here, we captured the thermodynamics of the triple helix unwinding by monitoring interactions between a collagen peptide and MMP-1(E200A) – an active-site mutant of an archetypal vertebrate collagenase – at increasing temperatures, using isothermal titration calorimetry (ITC). Coupled binding and unwinding manifests as a curved relationship between the total enthalpy change and temperature of the reaction, producing increasingly negative heat capacity change (ΔΔCp ≈ −36.3 kcal/molK2). A specially designed solid-phase binding and cleavage assay (SPBCA) reported strain in the catalytically relevant unwound state, suggesting that this state is distinct from the horizon of sampled conformations of the collagenase-susceptible site. MMP-1 appears to blend selected fit with induced fit mechanisms to catalyse collagen unwinding prior to cleavage of individual collagen chains. Graphical Abstract Highlights The unwinding of the collagen triple helix by matrix metalloproteinases (MMPs) is critical for collagen catabolism, but how MMPs harness bioavailable energy for this energetically expensive process is enigmatic Rising temperature causes linear increases of the negative heat capacity change associated with the interaction of MMP-1 with a collagenase-susceptible triple-helical peptide, indicating enrichment of hydrophobic contacts during the triple helix unwinding The complex of MMP-1 with locally unwound collagen holds considerable structural strain, which becomes relieved upon cleavage of the unwound collagen strand(s) MMP-1 consumes heat to drive specific (structurally distinct) collagen unwinding by increasing entropy associated with evolving hydrophobic anchor points between the enzyme and the substrate The prototypic collagenase MMP-1 appears to blend conformational selection with induced fit, shedding light on the thermodynamic principles by which MMPs trigger collagen breakdown and supporting general mechanistic conclusions concerning conformational changes coupled to protein-protein binding
Phenolic compounds and antioxidant activities of grape canes extracts from vineyards

Grape canes are the main agro-wastes from vineyards. This work studied the antioxidant activities of the defatted methanolic extracts (ME) of canes from 11 genotypes: 5 Vitis vinifera widely known cultivars and 6 Chinese wild varieties from three species ( V. amurensis , V. davidii , and V. pentagona ) and the antioxidant activities of the ME’s chloroform fractions (CF), ethyl acetate fractions (EAF) and water fractions (WF). Among ME and its three fractions, EAF’s total phenolic contents (TPC) and total flavonoid contents (TFC) were the highest, at 586 mg/g of gallic acid equivalent and 320 mg/g of quercetin equivalent, respectively. The antioxidant power of the fractions/extracts was in the order EAF > ME > WF > CF, based on the DPPH radical-scavenging power and ferric-reducing antioxidant activity, while the order was EAF > CF > WF >ME based on the β -carotene-linoleic acid bleaching activity. Methanolic extracts demonstrated the strongest Fe 2+ -chelating activity. The antioxidant activities of the extracts/fractions generally correlated with the TPC and TFC in all assays, except with the Fe 2+ -chelating test. Grape canes from V. davidii had the highest TPC, TFC and antioxidant activities compared with those from other grape species. Catechin, epicatechin and trans- resveratrol were the predominant phenolic components of fractions/extracts. In light of these valuable bioactivities, grape canes from annual pruning practice considered as waste material have good commercial potential for utilization as a promising natural antioxidant in the food, pharmaceutical and cosmetic industries, given its low cost and availability in large amounts.
Taxonomic status of the Neotropical salamanders Bolitoglossa altamazonica and Bolitoglossa peruviana (Amphibia: Caudata: Plethodontidae), with the description of a new species from Northern Peru.

We examine the phylogenetic relationships among salamanders of the genus Bolitoglossa (Eladinea) distributed in the Amazonian basin of northern Peru and southern Ecuador and assess species diversity based on morphological and phylogenetic analyses. We infer a molecular phylogeny using sequences from two mitochondrial (Cytb, 16S) and two nuclear genes (RAG-1, POMC). We find two well-supported subclades, one including [B. altamazonica + B. peruviana] + B. awajun sp. n. , and the other including Bolitoglossa sp. Ituxi + Bolitoglossa sp. Jurúa. Ecuadorian lineages form divergent clades from the Peruvian lineages. Accordingly, Ecuadorian populations previously assigned to Bolitoglossa peruviana sensu lato are treated as members of a Bolitoglossa equatoriana species complex. A newly defined Bolitoglossa altamazonica species complex contains only populations from the Amazonian rainforest of Peru. Maximum likelihood and Bayesian Inference analyses confirm the phylogenetic placement of B. altamazonica and B. peruviana, and support recognition of a related new species of Bolitoglossa. The uncorrected genetic distances between the new species and B. altamazonica are 6.5% for Cytb and 4.9% for 16S; and the uncorrected genetic distances between the new species and B. peruviana are 8.0% for Cytb and 3.9% for 16S. Additionally, analyses of nuclear gene sequences show no haplotype sharing between the new species and closely related species. The new species is distinguished from its congeners by a combination of the following morphological characters: (1) Standard length mean 37.7 mm in males (range 32.0-42.2; n=5) and 41.4 mm in females (range 34.9-48.2; n=6); (2) in life, dorsal coloration uniformly brown with a dark brown triangular marking between the eyes or some irregular light cream spots or patches on the head, back and flanks; (3) iris pale golden; (4) in preservative, dark brown venter with cream mottlings or moderate-sized blotches on the gular region, belly, cloacal region and tail; (5) tips of third finger and third toe protuberant and pointed with nearly complete webbing on the hands and feet; (6) 11-26 maxillary teeth and 8-24 vomerine teeth. Given that the syntypes of B. altamazonica are lost, we designate a neotype for B. altamazonica from Allpahuayo Mishana National Reserve, Loreto department, Peru. Newly collected specimens from ~30 km NE from Moyobamba (type locality of B. peruviana) provide a better understanding of B. peruviana and enable us to show that it is the sister taxon of B. altamazonica. The new species is known from pre-montane forests in Cordillera Escalera Regional Conservation Area, Cordillera Azul National Park and Shucshuyacu, San Martin department, Peru at 485-1311 m elevation, ~75 km SE from Moyobamba. Bolitoglossa awajun sp. n. is the fourth endemic species of salamander from Peru.
A descriptive guide for absolute quantification of produced shRNA pseudotyped lentiviral particles by real-time PCR

Gene silencing techniques, including RNA interference methodologies, are widely used in reverse genetics to study the role of specific genes in biological processes. RNA interference has become easier to implement thanks to the RNAi Consortium (TRC), which has developed libraries of short hairpin RNA (shRNA) sequences in pseudotyped lentiviral particles capable of targeting most genes in the human and mouse genomes. However, a problem is the lack of a simple method to titrate the homemade lentiviral particle product, making it difficult to optimize and standardize shRNA experiments. Here we provide a guide describing a quick, non-laborious and reliable method for the titration of TRC pseudotyped lentiviral particles that is based on the detection and measurement of viral RNA using quantitative PCR. Our data demonstrate that purified linearized shRNA plasmids represent more suitable standards than circular or unpurified linearized plasmids. We also show that for precise absolute quantification, it is important to determine suitable plasmid and viral cDNA concentrations in order to find the linear range for quantification, as well as to reduce inhibition and primer dimer amplification. Finally, we show that the lentivirus concentration impacts the level of knockdown in transduced cells. Primers utilized in this non-functional titration can potentially be applied to functional titration of proviral DNA copies or transgene expression, overcoming problems arising from the absence of fluorescent reporter genes in TRC plasmids.
Current Trends in Natural Products Research from the CBNP10 Symposium at Warwick

Natural products are compounds that are produced by living organisms. They have numerous applications in our everyday life, from antibiotics to herbicides. They possess great chemical and structural diversity, which gives them a leading position as a source of new drugs. Many institutions worldwide are focusing more and more on natural product research, with microorganisms and plants being the most common source for discovery of new compounds. On the 30 th June and 1 st July 2016, early-career scientists working in the field of natural products gathered at the University of Warwick for the 10 th edition of the Chemistry and Biology of Natural Products Symposium (CBNP10). This critical reflection reviews, in the context of the current research in the field, the major considerations that arose from this meeting.
The BWConverter Toolchain: An Incomplete Way to Convert SAT Problems into Directed Graphs

In our previous works we showed, how to convert a directed graph into a SAT problem. We showed that if the directed graph is strongly connected, then the converted SAT problem is Black-and-White. A SAT problem is Black-and-White if it has exactly two solutions, the black assignment, where each variable is false, and the white one, where each variable is true. In this paper, we study the other way: How to convert a SAT problem into a directed graph. This direction seems to be very difficult, so we introduce the BWConverter toolchain which helps us to create Black-and-White SAT instances, and convert them to directed graphs using different strategies. The toolchain consist of two tools: the BWConverter and the NPP tool. As a first step, one has to use the BWConverter tool, which creates a Black-and-White SAT problem from any UNSAT problems. The resulting SAT problem is Black-and-White if the input was UNSAT . As a second step, we generate a directed graph using our NPP tool. This tool generates edges from clauses which contain either exactly one positive literal, or exactly one negative one using the observations of our previous models.
TECHNIQUES FOR EXTRACTION OF ARBUSCULAR MYCORRHIZAL FUNGI SPORES

Arbuscular mycorrhizal fungi (AMF) spores are normally isolated by wet sieving and decanting method. In my present study AMF spores were isolated by capillary rise method. The rise in the capillary is due to the result of surface tension of liquid. Gerdemann and Nicolson, 1963 were developed wet sieving and decanting method to isolate different size of spores. Sucrose density gradient centrifugation (Daniel and Skipper, 1982), New plate counting method (Mosse and Bowen, 1968) and Adhesion floatation technique (Sutton and Barron, 1972) are also useful for extraction of spores and our research article will help the researchers to pick out the suitable method to extract AMF spores from soil.