Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotyping USDA Rice Mini-Core Collection With Functional Markers for Important Agronomic Traits

The USDA rice mini-core collection was established to capture the diversity of an entire collection of over 18,700 accessions of global origins for efficient germplasm evaluation and exploration. Previous studies have investigated its genetic diversity and population structure using genome-wide SSR markers. Many important agronomic traits that are fundamental to rice breeding programs, however, remain to be explored. Functional markers can be developed based on polymorphic sites within genes affecting phenotypic variation in, e.g., starch physicochemical properties, nutritional qualities and biotic resistance. These markers can be used for genotyping and hence differentiating phenotypes among rice accessions. In this study, we employed 12 pairs of functional markers (SNP and Indel) to genotype all 217 accessions constituting the USDA rice mini-core. These markers are highly associated with starch physicochemical properties (intron 1 G/C SNP, 23bp duplication in exon 2, exon 6 C/A SNP, exon 10 C/T SNP of Waxy gene, GC/TT SNPs of SSIIa gene, G/C SNP of SBE3 gene), glutelin content (3.5 kb deletion in Lgc1 gene), grain length (C/A SNP in GS3 gene), brown planthopper resistance (InDel in Bph 14 gene) and rice blast resistance (InDel in Pi54 and Pit gene). Using these functional markers, all the 217 accessions of the mini-core are characterized for aforementioned agronomic traits associated alleles/genes. The results of this study will help breeders select parental materials with desirable allele/gene combinations and phenotypes among mini-core accessions for rice breeding programs.
ERBB2 as a driver of an invasive phenotype of cells grown in 3D culture and an important regulator of oncogenic miRNAs' expression in breast cancer

Breast cancer is often associated with deregulated activity of two receptor tyrosine kinases (RTKs) from the ERBB family: EGFR and ERBB2 (HER2/Neu). Whereas the EGF receptor is often mutated in breast cancer, ERBB2 is up-regulated in up to 20% of invasive breast tumors and plays a triggering role in cell proliferation, invasion and metastasis. Patients overexpressing ERBB2 are treated with targeted therapies and in particular with the monoclonal antibody trastuzumab, which binds an extracellular domain of the receptor and abrogates receptor-kinase activation. However, ERBB2-positive breast cancer patients overexpress ERBB2 to different extent. The expression range is very wide, raising the question whether the tumors expressing moderate, high and very high ERBB2 levels have different outcome and patients carrying them can be treated as one entity or not. To better understand the impact of different ERBB2 levels I developed stable cell line pools overexpressing ERBB2 at different levels. I observed that in 3D culture as well as in matrigel-based invasion assays, cells expressing very high ERBB2 levels showed more invasive properties than those expressing moderate ERBB2 levels, even in the absence of EGF. This was accompanied by disruption of cell polarity in 3D-grown spheroids and anchorage-independent growth which occured only when ERBB2 expression was very high. These phenotypes could be at least partially explained by ERBB2-dose dependent epithelial-mesenchymal transition (EMT), an increase in HB-EGF transcription and constitutive ERK and AKT signaling pathway activation at the very high ERBB2 levels. As recently several miRNAs have been reported to regulate EMT-related processes and because their expression is frequently deregulated in cancer, I also hypothesized that their expression would change with the ERBB2 expression level in 3D culture. To verify my hypothesis, I performed small RNA sequencing from stable cell line pools grown in matrigel. This identified several miRNAs which are ERBB2-level dependent. I focused then on the functional characterization of miR-301b and miR-130b whose expressions were ERBB2-dependent in 3D, but not in 2D culture. Overexpression of these miRNAs phenocopied ERBB2 effects on cell invasion and proliferation as well as induction of EMT, as did overexpression of the related miR-301a.
Morphological Selection of Gametes and Embryos: 2PN/Zygote

The pronuclear (PN)-stage embryo is the first stage of live where the genetic material of both female and male is visible as pronuclei and when fertilization is initiated. Although it is possible to judge the morphology of the oocyte and the spermatozoa by itself, the PN stage is the first event that allows for morphology rating of the new live by various small details that are indicative for the future of the embryo.
Microfibrillar Proteins of Wool: Partial Specific Volumes and Molecular Weights in Denaturing Solvents

The molecular weights of the reduced and S-carboxymethylated microfibrillar protein components of wool have been investigated by sedimentation equilibrium in 6 M guanidine hydrochloride and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The microfibrillar proteins have molecular weights of 57000 (component 5), 58000 (component 7c); 50000 (component 8c-l) with a range of values for the other component 8 polypeptide chains of 45 000--50 000. The proteins migrate anomalously in polyacrylamide gels in the presence of sodium dodecyl sulfate as seen from a comparison of the free mobilities and retardation coefficients of standard proteins with those of the wool proteins. More reliable molecular weights were obtained by plotting the retardation coefficients against molecular weights (Ferguson plot). The partial specific volumes of the microfibrillar proteins have been measured in dilute aqueous buffer solutions, 8 M urea and 6 M guanidine hydrochloride. The values are compared to those calculated from the amino acid compositions.
Detección de Gen CYP4 en el Genoma de Cryptolaemus montrouzieri1 en Base a Secuencias Ortólogas y Uso de Codones

Resumen. En este estudio se detectó el gen CYP4 de Cryptolaemus montrouzieri Mulsant (Coleoptera: Coccinellidae) mediante el diseño de oligonucleótidos obtenidos a partir de la selección de siete secuencias proteicas parciales de Anopheles gambiae Giles (Diptera: Culicidae) asociadas al gen CYP4 y analizados mediante una tabla de uso de codones elaborada en función de ocho genes de Harmonia axyridis Pallas (Coleoptera: Coccinellidae) que es un insecto emparentado a C. montrouzieri. Las secuencias aminoacídicas ortólogas fueron alineadas para determinar las zonas de homología y se elaboró una tabla de uso de codones para H. axyridis. Las secuencias nucleotídicas obtenidas se analizaron con el programa GCUA para determinar los codones más utilizados, reducir la degeneración y tener mejor amplificación. Los productos amplificados se clonaron y se secuenciaron. El número efectivo de codones para H. axyridis fue de 2996. Se observa un mayor uso relativo de codones predominantes con AT. Los oligonucleótidos diseñados 5´GAAGUUGAUACHUUUAUGUUUG3´ y 3´AAARTTTTCWGGRTTTGGAWA 5′, amplificaron un fragmento de 569 pb con alineamiento significativo a una secuencia parcial del citocromo P450 en Aedes aegypti Linnaeus (Diptera: Culicidae) y Tribolium castaneum Herbst (Coleoptera: Tenebrionidae). El uso de secuencias ortólogas y su análisis mediante el uso de codones es útil para la identificación molecular de genes de interés.
Chlorogenic Acid Isomers from Sorbus commixta of Ulleung Island Origin and Their Inhibitory Effects against Advanced Glycation End Product (AGE) Formation and Radical Scavenging Activity

Advanced glycation end product (AGE) formation and reactive oxygen species are potential therapeutic targets for the prevention of diabetic nephropathy and other pathogenic complications. Activity-guided isolation of an ethylacetate-soluble portion of 80% methanolic extract from fruits of Sorbus commixta of the Ulleung Island origin using AGE formation inhibition assay led to the isolation and identification of three caffeoylquinic acid derivatives of a previously known structure, 3-O-caffeoylquinic acid (neochlorogenic acid; 1), 4-O-caffeoylquinic acid (cryptochlorogenic acid; 2), and 5-O-caffeoylquinic acid (chlorogenic acid; 3). The structures of these compounds were confirmed by interpretation of nuclear magnetic resonance and mass spectrometry data. Among the isolates, the major metabolite, neochlorogenic acid (1) showed the most potent inhibitory effect against AGE formation with an IC50 value of 167.5±3.5 μM. Furthermore, all isolated chlorogenic acid isomers were evaluated for their radical scavenging activity against peroxynitrite, and structurally related isomers 1, 2, and 3 exhibited potent inhibitory effects in this radical scavenging assay. This result suggests that the monocaffeoyl quinic acid derivatives isolated from S. commixta might be beneficial for the regulation of diabetic complications and related diseases.
Nitrogen and Rubisco contents in eucalypt canopies as affected by Acacia neighbourhood

In saplings of Eucalyptus pauciflora ssp. pauciflora Sieb. ex Spreng. (snow gum) and E. delegatensis R.T. Baker (alpine ash), growing in their natural communities, nitrogen, protein and Rubisco contents remained remarkably stable for most of the leaves' life spans once the leaves were mature until shortly before leaf shed. Despite its capability to fix nitrogen, Acacia melanoxylon R. Br. growing close to E. pauciflora, had a slightly negative effect on nitrogen contents of the eucalypt leaves (P≤0.10) but a strongly negative effect on protein and Rubisco contents (P<0.0005). On the other hand, there was a clearly positive effect of the nitrogen fixing Acacia dealbata Link on nitrogen contents of neighbouring E. delegatensis saplings (P<0.0005), but only a slightly positive effect on protein or Rubisco contents (not significant and P≤0.05, respectively). These relations are discussed as being consequences of the acacias' successional positions : A. dealbata, a pioneer that disappears later during succession, apparently enhances N availability to its neighbours, whereas A. melanoxylon usually occurs in later successional stages and does not enhance N availability to neighbours, probably because of stronger competitive ability. It is concluded that different acacias can have entirely different potentials as nurse trees to support leaf functions of neighbouring eucalypts, but what is reflected at the leaf level may still be altered at the canopy level due to species-specific differences in dry matter allocation into leaf turn-over.
Optimization of mammalian reovirus T3D growth in L929 cells

Although the demand for high scale production of mammalian orthoreoviruses (T3D in particular) is mounting to advance the research studies and clinical trials associated with their oncolytic capacity, very few reported studies have tried to understand the factors that affect the its production and subsequently optimize them to maximize the virus yield in cell culture systems. For this study, we manipulated several growth parameters (multiplicity of infection, cell density, cell feeding, media pH, and flask size) sequentially to select optimal conditions. Manipulation of cell density, whether cells were fed or not, and flask size all led to moderate changes in progeny virus titer. Altered media pH led to dramatic (more than 100 fold) virus replication changes. We conclude that cell physiological status has a key impact on infection progression and virus production. Optimal parameters consisted of infection at MOI of 0.1, cell density at infection of 95%, media re-feeding, media pH 7.0-8.5, and the smaller the flask size the better.
Evaluation of the ISO 10273 method for isolation of Yersinia enterocolitica 4/0:3 in food samples

Yersinia enterocolitica is the most frequent Yersinia species associated with human yersiniosis in European countries. Bioserotype 4/0:3 is the most common bioserotype isolated from human yersiniosis in many European countries, including Germany. The primary route of human infection is probably ingestion of contaminated food. However, pathogenic strains of Y. enterocolitica are difficult to isolate from food samples. The low isolation rate can be due to the low sensitivity of the culture methods available, especially when the contamination level is low and the background flora is high. In this study, the ISO 10273 method for isolation of pathogenic Y. enterocolitica in food was evaluated using spiked food samples and additionally, the ISO method was compared with a real-time PCR method based on SYBRGreen. Four different food samples (raw pork, ham, lettuce and bean sprouts) inoculated with ca. 10 2 and 10 4 pYV-positive Y. enterocolitica 4/0:3 bacteria per 10 g sample were studied in duplicate. ISO method was shown to be a suitable method for isolation of Y. enterocolitica 4/0:3 only in highly contaminated meat samples. This pathogen could be isolated from the meat samples by direct culturing on CIN agar plates and after selective enrichment in ITC and plating on CIN and SSDC agar plates when the contamination level was high enough (> 10 4 ). Real-time PCR method based on SYBRGreen was shown to be a valuable screening method to detect the samples contaminated with pathogenic Y. enterocolitica. Most (12/16) of the positive samples could be detected by PCR, which targets the ail gene in the chromosome of pathogenic Y. enterocolitica while only 7 out of 16 samples were positive with culturing.
Functional analysis of the escherichia coli hemolysin signal sequence by random oligonucleotide mutagenesis

The E. coli hemolysin is an RTX toxin that is secreted by an ATP-binding cassette transporter complex consisting of HlyB, HlyD, and TolC. Translocation of this protein is dependent on a C-terminal signal sequence located within the last 60 amino acids. Previous studies demonstrated that the signal sequence of a similar toxin, P. haemolytica leukotoxin, could replace that of hemolysin and was efficiently transported. While the two signal sequences share little primary sequence similarities, circular dichroism and 1 5 N nuclear magnetic resonance revealed a conserved helix-strand-helix motif, leading to the hypothesis that this motif is important for efficient secretion. A previous study using helical variants generated by a combinatorial approach suggested that any one of a large number of sequences that yielded a predicted amphiphilic helix in the upstream helical region is sufficient for transport (Morden, 1998). To further elucidate structural requirements of the signal sequence, the helix-strandhelix motif was divided into three regions (al-linker-a2) and each was subjected to random oligonucleotide mutagenesis analysis. The last 16 residues of the extreme Cterminus was also analyzed using two contiguous random libraries (Cterml and Cterm2). This approach replaced the target region with a random sequence, and the presence or absence of any critical element(s) within each region was deduced by measuring the level of secretion of the mutant population. Based on the results from the five random libraries and the al helical library, a twodomain functional model of the hemolysin signal sequence was proposed. The first domain consists of the al and the linker regions. An amphiphilic helical structure in the al region appears to be both sufficient and required for transport. The second domain involves the last 8 residues of the signal sequence, and hydrophobicity in this region appears to be a major determinant of efficient transport. Connecting the two is a stretch of 19 residues, with no specific requirements. This is a surprise since this stretch of amino acids contains the second helix of the helix-strand-helix motif. Nevertheless, this study supports the model that the important features of the signal sequences are secondary structure (i.e. amphiphilic helix) and general biophysical property (i.e. hydrophobicity) rather than primary sequence.
Uso del suelo y grado de cobertura vegetal en una cuenca del centro de la provincia de Buenos Aires

El uso del suelo y el grado de cobertura vegetal son parámetros importantes para estimar la potencialidad deescurrimiento superficial y erosión en una cuenca, y además para evaluar el desarrollo de cultivos,producción, etc. En este trabajo se evalúa la variación del uso del suelo y de la cobertura vegetal porcentual alo largo de un año (abril de 2005 hasta marzo de 2006) en una cuenca agrícola ganadera del centro de laprovincia de Buenos Aires, Argentina. Este ciclo anual, mientras no se produzcan modificaciones deestructura productiva de la zona, puede ser válido para muchos años más. Para lograr el objetivo buscado, serecurre a técnicas de procesamiento digital de imágenes satelitales y de sistemas de información geográfica. Así se determina el uso del suelo por medio de clasificación no supervisada de las imágenes. A cada usoluego se le asigna su cobertura porcentual estimada de manera conjunta según mediciones a campo y deacuerdo al estado fenológico, si se trata de cultivos. Se obtuvieron 12 categorías de uso a lo largo del año, alas que se agregan lagunas, afloramientos rocosos y montes. Los resultados muestran menores grados decobertura en invierno, y presentan un mínimo del 66 % en septiembre, para luego crecer hasta alcanzar unmáximo del 92 % en febrero y marzo, en el apogeo de los cultivos de soja y maíz.
Estimation of postmortem interval using the blowfly Phaenicia (Lucilia) sericata (Diptera: Calliphoridae) in Kaduna, Northern Nigeria -

Background: The period of insect activity (PIA) was experimentally estimated for a carcass of Cavia porcellus (guinea pig) using the blowfly Phaenicia sericata in Kaduna, northern Nigeria. Methods: Cavia porcellus (guinea pig) was killed and the carcass placed inside in a wire cage measuring 81x53x45 cm to prevent larger animals and birds from scavenging and allowed to decompose under ambient conditions and an average of 12hour light and darkness. Results: Six second-instar larvae of blowflies were collected from the decomposing carcass from which four adult flies emerged and identified (two each of P. sericata and P. infernalis ). Using P. sericata , the period of insect activity (PIA) was estimated as the difference between the total development time of the species and the time it required to become adult in the laboratory. The estimated minimum post mortem interval was 13.8 days with the probable day of oviposition between 9 th and 10 th January, 2016, coinciding with the actual period the animal was killed Conclusions: Estimated time between death and discovery of corpse (PMI) based on the period of insect activity (PIA) may be a better alternative in some situations because it eliminate taking multiple temperature measurements at the crime scene, at the carcass as well in the maggot masses on the cadaver.
Identifying Resistance in Corn to Southwestern Corn Borer (Lepidoptera: Crambidae), Fall Armyworm (Lepidoptera: Noctuidae), and Corn Earworm (Lepidoptera: Noctuidae) 1

Southwestern corn borer, Diatraea grandiosella Dyar (Lepi- doptera: Crambidae); fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae); and corn earworm, Helicoverpa zea Boddie (Lepi- doptera: Noctuidae), are major insect pests of corn, Zea mays L. , in the south- ern United States. Corn hybrids produced from resistant germplasm were evaluated together with Bt and nonBt commercial hybrids in field tests and laboratory bioassays for resistance to leaf and ear damage by southwestern corn borer, fall armyworm, and corn earworm. The Bt hybrids, Mp496 × Mp716 and Mp704 × Mp716, exhibited resistance to leaf feeding damage by south- western corn borer and fall armyworm. The Bt hybrids sustained significantly less southwestern corn borer ear damage than their nonBt versions. Those genotypes expressing resistance to leaf feeding also showed resistance, as in- dicated by reduced larval growth or survival in laboratory bioassays base do n lyophilized leaf tissue, to southwestern corn borer, fall armyworm, and corn earworm. Only the Bt hybrids expressed resistance when larval growth was evaluated in bioassays based on lyophilized husk tissues. Using both field tests and laboratory bioassays to assess resistance to these insects will enhance efforts to identify useful germplasm and determine factors contributing to resistance.
Compound structure versus bitter taste

Relation entre la structure et le gout amer pour les acides amines, amines aliphatiques, amides, lactames et derives, heterocycles azotes, uree et derives, esters et lactones, carbonyls et derives, terpenoides, derives de glucides et flavonones glycosides notamment
Behaviour, growth performance, foot pad quality, bone density, and carcass traits of broiler chickens reared with barrier perches and fed different dietary crude protein levels

Abstract Perches serve as a behavioural enrichment and may yield benefits on broiler foot health and growth performance. The benefit may be greater for birds fed high crude protein (HCP) diets, which results in poorer litter conditions. This study investigated the effect of two perch configurations (I shaped vs. X shaped, compared with no perch) and dietary crude protein (CP) level (standard vs. high) on behaviour, foot pad health, bone density, growth performance, and carcass traits of broilers raised to 35 d of age. Perch configuration did not affect body weight (BW) at day 35 or overall average daily gain (ADG), average daily feed intake (ADFI), and gain-to-feed ratio (G:F). Likewise, there was no effect of perch provision independent of CP level for any carcass variable. Feeding standard CP (SCP) level resulted in greater bone density, carcass weight, and dressing percentage but lower breast, wing, and total edible meat yield. We confirmed that greater litter moisture (16%) related to excess dietary CP (13%) caused footpad dermatitis in broilers trending from 3 wk old to significant at 27 and 35 d of age. Provision of barrier perches did not reprieve from litter contact (perching), although more focal birds were observed resting against them and did not affect growth performance, bone density, or carcass traits.
Coastal upwelling areas as safe havens during climate warming

Seaweeds have long been recognized as “ecosystem engineers” and carbon sinks in coastal marine ecosystems. However, recent ocean warming has had drastic eco-physiological impacts on seaweed assemblages and hence coastal community structure (Wernberg et al., 2011, 2013). Seaweeds, particularly species that prefer lower water temperatures, are facing imminent threat and will experience strong population-size reductions at low-latitude range limits (Wernberg et al., 2011, 2013).