Miracle-dz/UniFAR-FTUs huggingface dataset:
University of São Paulo “Luiz de Queiroz” College of Agriculture Characterization of natural genetic variations affecting tomato cell competence to assume different developmental fates

Characterization of natural genetic variations affecting tomato cell competence to assume different developmental fates The study of natural genetic variations affecting organogenic capacity in tomato (Solanum lycopersicum) is attractive due to the existence of several tomato wild relatives with enhanced organogenic capacity. The characterization of such variations is relevant not only in order to manipulate plant development, but also to understand its ecological and evolutionary significance. The objective of this work was to characterize three tomato loci whose alleles from the wild relative S. pennellii enhance in vitro shoot and root regeneration, and analyze their involvement in the acquisition of competence phase. In the first manuscript, we report the genetic and physiological characterization of the loci Rg3C, Rg7H and Rg8F. The S. pennellii alleles were introgressed into the tomato genetic model cv. Micro-Tom (MT), creating the near isogenic lines (NILs) MT-Rg3C, MT-Rg7H and MT-Rg8F. In the second manuscript we present a comparative analysis between the Near-Isogenic Lines (NILs) MT-Rg3C and MT-Rg1. Since Rg1 was proposed to be a key gene in the acquisition of competence, and was mapped in the chromosome three, it is believed that Rg3C is probably equivalent to the Rg1 allele from S. peruvianum. After the introgression of the loci into the MT background, the NILs presented enhanced regeneration of both roots and shoots, confirming that the loci were successfully introgressed. The analysis of the time for acquisition of competence and induction, together with the molecular characterization of the NILs, indicate that the genes present in the loci Rg3C, Rg7H and Rg8F affect in vitro regeneration by distinct pathways. While Rg3C decreased the time required for both acquisition of competence and induction, the other loci seem to influence only the time of acquisition of competence, in the case of Rg8F, or the time of induction, in the case of Rg7H. Additionally, although MT-Rg3C has an enhanced shoot branching phenotype, MT-Rg7H and MT-Rg8F did not differ from MT in this trait. This indicates that enhanced in vitro shoot formation in tomato is not necessarily related to a deleterious high branching phenotype. Comparative analyses of MT-Rg1 and MT-Rg3C strongly indicate that Rg1 and Rg3C are alleles of a same gene controlling regeneration capacity. Integrating Rg1 and Rg3C mapping information, we were able to narrow the number of candidate genes for Rg1/Rg3C to only 27, which were also analyzed and discussed.
The complex acoustic repertoire of a highly social species, the Noisy Miner, Manorina melanocephala

ABSTRACT Communication is an essential component of social interactions between individuals, particularly in larger group sizes. To gain further insight into the factors that underpin cooperative behaviour, herein we examine the acoustic repertoire of the Noisy Miner, Manorina melanocephala, a cooperative species that lives in large colonies. To determine the structure and composition of the Noisy Miner repertoire, we measured the call rates and major acoustic parameters of common vocalisations from colour-banded individuals located at two discrete colonies. A total of 13 different vocalisation types were identified, of which 3 are newly described, with an additional 10 vocalisations being quantified in a new social context. Importantly, we describe a call given only by females and document both sexes producing some calls that were previously thought to be sex-specific. The putative repertoire identified was supported by statistical assessments confirming differences in their spectral and temporal features. Vocalisations were given across a range of social contexts, including the mobbing of predators, aerial alarm vocalisations, apparent maintenance of group cohesion and advertisement of individual location and/or status. This study quantifies the rich vocal repertoire of this social species, and provides further implications for the link between cooperative breeding and large vocal repertoires.
The chemical composition and antioxidant properties of common dandelion leaves compared with sea buckthorn

The aim of this study was to determine the chemical composition and antioxidant activity of dandelion [Taraxacum officinale (Weber) ex Wigg. ] and sea buckthorn (Hippophae rhamnoides Rousi) leaves grown in Poland (53°20′35″N, 14°58′10″E). Both the leaves of sea buckthorn and common dandelion were found to be a very good source of essential nutrients and elements. The dandelion leaves contained significantly more protein, fat, and crude fibre than those from sea buckthorn. Dandelion leaves also contained more phosphorus, potassium, calcium, iron, and zinc. Although the dandelion leaves were a good source of biologically active substances, sea buckthorn leaves exhibited a significantly higher level of antioxidant activity as measured by ABTS. Dandelion leaves were richer in tocopherols, thiamine, riboflavin, and niacin while the sea buckthorn leaves contained higher levels of l-ascorbic acid.
Chemical composition and biological activity of essential oil of Chenopodium ambrosioides from Yemen

The chemical composition of the hydrodistilled leaf essential oil from Chenopodium ambrosioides L. growing wild in Yemen was determined by GC-MS analysis, and its cytotoxic, and general antioxidant potential were evaluated. Major compounds of C. ambrosioides oil were ascaridole (54.2%), isoascaridole (27.7%) and p-cymene (8.1%). At concentrations of 50 and 25 μg/mL, the essential oil showed cytotoxic activity against HT29 (human colon adenocarcinoma cells), with growth inhibition of 100 and 56% (± 3). The free radical scavenging ability of the oil was assessed by the DPPH assay to show antiradical activity with IC50 of 10.4 μg/mL. TLC-bioautographic assay was used to identify the acetylcholinesterase inhibitory effect, and ascaridole was isolated and characterized (ESIMS, 1H NMR, 13C NMR and HMBC) as the responsible constituent for anticholinesterase activity.
Elevated O-GlcNAcylation Enhances Pro-Inflammatory Th17 Function by Altering the Lipid Microenvironment

Chronic, low-grade inflammation increases the risk of atherosclerosis, cancer, and autoimmunity in diseases like obesity and diabetes. Here, we show that increased levels of the nutrient-responsive, post-translational protein modification, O-GlcNAc (O-linked β-N-acetylglucosamine) are present in naïve CD4+ T cells from a diet-induced obesity murine model, and elevation in O-GlcNAc leads to increased pro-inflammatory IL-17A production. Importantly, CD4+ T helper 17 (Th17) cells, which secrete IL-17A, are increased in obesity and contribute to the inflammatory milieu. We found increased binding of the Th17 master transcription factor, RORγt, at the IL-17 locus and significant alterations in the lipid microenvironment, leading to increased ligands capable of increasing RORγt transcriptional activity. Importantly, the rate-limiting enzyme of fatty acid biosynthesis, acetyl CoA carboxylase 1 (ACC1), is necessary for production of these RORγt activating ligands and is O-GlcNAcylated. Thus, we have identified O-GlcNAc as a critical link between excess nutrients and pathological inflammation.
The regional structure of spawning phenology and the potential consequences for connectivity of coral assemblages across the Eastern Tropical Pacific

The coral reefs of the Eastern Tropical Pacific (ETP) are some of the most geographically isolated of the world. A key to understanding their long-Term persistence and population recovery via dispersal (i.e. population connectivity), is knowing when the corals spawn in the region. To this end, we reviewed and synthesized the literature on the reproductive phenology of corals (month of spawning) and their dispersal-related characteristics to infer the potential impact on the region's functional connectivity. We classified the region into four thermal regimes based on long-Term mean sea surface temperature (SST) data: Tropical Upwelling, Thermally Stable, Equatorial Upwelling, and Seasonal. Each regime's unique spawning seasonality was then explored by quantifying the linear dependence between the number of observed spawning events and SST. Finally, the potential impact of this unique regional mismatch in spawning was illustrated using a biophysical larval dispersal model. We found spawning occurs throughout the year in the Upwelling and Thermally Stable regimes (showing low or no linear dependence with SST); whereas spawning had a strong seasonal signal in the Equatorial Upwelling and Seasonal regimes, occurring primarily in the warm months. Considering the region's mismatch in spawning phenologies, and unique dispersal traits, the simulations of coral larval dispersal across the ETP result in infrequently realized connectivity between ecoregions, low local retention and high self-recruitment, that combined with low recruitment densities in the field indicates more vulnerable populations to disturbance than previously appreciated. The strong relationship between spawning phenology and SST in some regimes suggests a greater susceptibility of these coral assemblages to extreme El Nino and La Nina events and future ocean warming.
The complete mitochondrial genome sequence and phylogenetic position of Sinocyclocheilus wumengshanensis (Cypriniformes: Cyprinidae)

Abstract The complete mitochondrial genome (mitogenome) sequence of Sinocyclocheilus wumengshanensis from Yunnan Province in China was analysed using next-generation sequencing. The complete mitogenome was 16,585 bp in length and consisted of 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one D-loop region. Nucleotide composition of the whole mitogenome was 30.5% A, 25.2% T, 27.0% C, and 17.2% G. The gene arrangement and nucleotide composition of the mitogenome of S. wumengshanensis were similar to those of other Sinocyclocheilus species. Phylogenetic analyses using mitogenomes of 12 species showed that 10 Sinocyclocheilus species clustered as one monophyletic clade with strong supports and S. wumengshanensis was closely related to S. grahami.
A Comparative SEM Study of Red Rice and Several Commerical Rice (Oryza sativa) Varieties

A comparative scanning electron microscopy (SEM) study was performed on the surfaces of seeds and coleoptiles of several conspecific rice (Oryza sativa L.) varieties including the weed red rice and several cultivars: Mochi-Gommi and LA-110 (medium grained); Starbonnet, Labelle, and Bluebelle (long grained). Seed surfaces of red rice, LA-110 and Mochi-Gommi possessed trichomes that were more numerous at the seed apex than on other seed parts. Red rice also exhibited a large central awn extending from the seed apex. This awn had spines along its axis and numerous spines at its apical end. These characteristics were absent in the other varieties. No significant differences were noted in the seed-surface tubercles and in the quantity or structure of wax on the seed surface in all six samples. The coleoptiles of all samples had several similarities: the stomata were arranged in parallel rows on both the adaxial and abaxial surfaces, the epicuticular wax structure on both surfaces was rodlet, prickle hairs were found on the adaxial coleoptile surface (but absent on abaxial), spines were present on the edge of the apical end (older portion) and decreased in number toward the basal end (younger portion), and two types of papillae (based on size and shape) were present on both the adaxial and abaxial surfaces. Although there were varietal differences among developing coleoptiles on a macroscopic scale, significant morphological differences were not discernible at the SEM level.
Attenuation of Doxorubicin-induced Oxidative Stress and Organ Damage in Experimental Rats by Theobroma cacao Stem Bark

Eighty rats, randomly selected, were divided into three (3) treatment groups: pre-, coand posttreatment; consisting of 6 sub-groups each (5 rats per sub-group); baseline, normal saline (2 ml), α-lipoic acid (20 mg/kg body weight), and 200 mg/kg, 400 mg/kg, or 800 mg/kg body weight Theobroma cacao stem bark aqueous extract (TCAE). Animals in the pre-treatment group were intoxicated with a single dose (20 mg/kg) of doxorubicin (DOX) intraperitoneally followed by 7 days oral administration of normal saline, α-lipoic acid or TCAE; co-treatment group were coadministered 2.86 mg/kg body weight of DOX with either normal saline, α-lipoic acid or TCAE orally for 7 days while post-treatment group were administered normal saline, α-lipoic acid or TCAE orally for 7 days and on the 8 day, intoxicated with a single dose of DOX (20 mg/kg intraperitoneally). Original Research Article Kosoko et al.; JOCAMR, 2(3): 1-27, 2017; Article no.JOCAMR. 30604 2 Animals were sacrificed (preand post-treatment groups on the ninth day while the co-treatment group on the 8th day), blood samples collected by retro-orbital plexus, kidneys and spleen samples harvested for biochemical and histopathological investigations. A significant elevation in plasma urea and creatinine concentrations with perturbation in plasma electrolyte (K + , Na + , Cl , HCO3 ) concentrations were observed resulting from DOX intoxication. DOX caused a significant increase in activities of splenic ACP, LDH, γ-GT and ALP activities. A significant increase in renal and splenic concentrations of H2O2 generated, MDA and PC; XO, MPX and NOX activities while the concentrations of GSH, AsA and α-TOC; and the activities of SOD, CAT, GST and GPX were significantly reduced following DOX intoxication. Treatment with TCAE significantly attenuated renal and splenic tissue damage and pro-oxidant markers precipitated by DOX intoxication while restoring normalcy to tissue antioxidant markers. Theobroma cacao stem bark aqueous extract presents a potential candidate in the prevention of renal and splenic injury and dysfunction related to doxorubicin intoxication.
H3S10P, Phosphorylation at Ser10 in Mouse Preimplantation Embryos

Pericentromeric heterochromatin appears to be involved with gene regulation and therefore with the developmental potential of embryos. We hypothesized that an epigenetic modification, H3S10P, could be a new marker to follow pericentromeric heterochromatin in preimplantation mouse embryos. Using immunofluorescence, immunoFISH and high resolution microscopy, we observed that H3S10P shows a different distribution pattern in mouse embryos than in somatic cells. It is detected early in interphase around the Nucleolar-Precursor Bodies from 1- to 4-cell, in co-localization with the DNA probes for pericentromeric heterochromatin, and is seen in the chromosome arms throughout mitosis. In fact, H3S10P shows a similar kinetic as seen in somatic cells only after the 4-cell stage: being solely observed in the chromocenters during late interphase and on the mitotic chromosomes until telophase. This distribution seems related to the absence of Aurora B kinase in the earlier stages. We have also compared H3S10P to other related pericentromeric heterochromatin markers such as H3K9me3, HP1β and the double modification, H3K9me3S10P, and concluded that H3S10P is a better marker for pericentromeric heterochromatin of both parental origins. Finally, as cloned embryos often show abnormal pericentromeric heterochromatin remodelling and impaired development after Somatic Cell Nuclear Transfer (SCNT), H3S10P was used to track down heterochromatin reprogramming after SCNT. Our results show that H3S10P underlines only the portion of heterochromatin which is remodelled when compared with the other related markers and that the unremodelled portion maintains the epigenetic signature of the donor cell.
Diallyl Trisulfide Modulates Notch Pathway Components in Breast Cancer Cells

Kiesel, Violet A. M.S., Purdue University, December 2016. Diallyl Trisulfide Modulates Notch Pathway Components in Breast Cancer Cells. Major Professor: Dr. Silvia D. Stan. Breast cancer affects one in eight women throughout the course of their lifetimes creating an immediate demand for novel prevention strategies against this disease. The Notch signaling pathway is often aberrantly activated in human malignancies including breast cancer. Alpha secretases, including A Disintegrin and Metalloprotease (ADAM)10 and -17, are proteases that play a key role in the cleavage of cell surface molecules and subsequent ligand-mediated activation of Notch signaling pathway. High expression levels of ADAM10 are clinically associated with lower disease-free survival in breast cancer patients. The goal of this study was to determine the effect of diallyl trisulfide (DATS), a bioactive organosulfide found in garlic and other Allium vegetables, on Notch pathway components, specifically alpha secretases, in an in vitro model of breast cancer. Here we report for the first time that DATS inhibits the expression of ADAM10 and ADAM17 in estrogen-independent MDA-MB-231 and estrogen-dependent MCF-7 breast cancer cells, as well as in Harvey-ras (H-Ras) transformed MCF10A-H-Ras breast epithelial cells. We also show that DATS inhibits the Notch ligands Jagged-1 and Jagged-2. Furthermore, we show that DATS treatment reduces overall cell viability in MDA-MB-231, MCF-7 and MCF10A-H-Ras cells, and that DATS treatment reduces
Structural Studies of the Mechanism by Which BCL-2 and Beclin Proteins Regulate Autophagy and Apoptosis

NIH grant R21 AI078198, NIH grant R03 NS090939, NSF grant MCB 1413525, NSF grant HRD-0811239, and P30 GM103332-01 to Dr. Sangita Sinha, and North Dakota EPSCoR doctoral dissertation award for Minfei Su and Dr. Sangita Sinha
Spatial structure of ant‐gardens: vertical distribution on host trees and succession/segregation of associated vascular epiphytes

Questions Ant-gardens (AGs) involve a close association between epiphytes and ants with concurrent mutualistic interactions including protection, dispersal and nutrition; however, little is known about the spatial structure patterns that determine their establishment and formation. Our main questions were: 1) Do the AGs have a particular pattern of vertical distribution on their host trees? 2) Does a process of succession of epiphytes occur during the development of AGs? 3) Are epiphytes segregated in AGs? Location An anthropic landscape in southeastern Mexico. Methods We studied AGs built by Azteca gnava ants. We examined their vertical distribution on host trees as well as the diversity, composition and reproductive status of vascular epiphytes associated with the lower, medium and upper zones of small, medium and large AGs. Results A total of 859 AGs and 10,871 epiphytes, belonging to 26 different species, were recorded. We found that AGs are primarily (75%) located within tree crowns, and that the diversity and composition of epiphytes vary among AG sizes and among AG zones. We infer that the epiphytes that first become established in AGs are the bromeliad Aechmea tillandsioides and the gesneriad Codonanthe uleana, followed by the orchid Epidendrum flexuosum and the cactus Epiphyllum phyllanthus; these species were recorded, either individually or in co-occurrence, in 74% of the AGs examined. The species Ae. tillandsioides, Coryanthes picturata and Epid. flexuosum were most frequent in the upper AG zone, while Epidendrum pachyrachis was most frequent in the medium AG zone. Conclusions Our results show that AGs have distinct vertical distribution patterns on their tree hosts and that the establishment of epiphytes in AGs is successive and segregated, suggesting a spatial and temporal optimization in the establishment and development of these complex mutualistic systems. This article is protected by copyright. All rights reserved.
Propriedades físicas do solo e produtividade de soja em sucessão a plantas de cobertura de inverno

Resumo: As alteracoes das propriedades fisicas dos solos agricolas afetam a produtividade das culturas. Este trabalho objetivou comparar resultados obtidos com plantas de cobertura de inverno, em seu primeiro ciclo de cultivo, nas propriedades fisicas do solo e na produtividade de soja (Glycine Max L.) em sucessao. Foram utilizadas quatro especies de plantas de cobertura de solo: ervilhaca (Vicia sativa L.), nabo forrageiro (Raphanus sativus L.), azevem (Lolium multiflorum Lam.) e aveia preta (Avena strigosa Schreb). Os experimentos foram desenvolvidos em Guarapuava, PR, no Campus CEDETEG da Universidade Estadual do Centro-Oeste (UNICENTRO). Realizou-se o acompanhamento de um ciclo destas culturas no outono/inverno de 2010. Os dados de densidade do solo, microporosidade, macroporosidade e porosidade total do solo, foram determinadas atraves de amostras de solo nao deformadas, em aneis volumetricos, retiradas nas camadas de 0,00 a 0,10 e 0,10 a 0,20 m de profundidade, logo apos a instalacao das culturas de cobertura e no seu periodo de maior desenvolvimento (floracao). Observou-se que a utilizacao de plantas de cobertura, no seu primeiro ciclo de cultivo, nao promoveu alteracoes na densidade do solo, microporosidade, porosidade total. Entretanto, na camada de 0,10 a 0,20 m foram verificados maiores valores de macroporosidade nos tratamentos de aveia e azevem. A produtividade de soja foi semelhante apos o ciclo de todas as plantas de cobertura. Palavras chave : Densidade do solo, Porosidade do solo, Plantas de cobertura.
Regeneration of multiple shoots from the callus cultures of Sauropus androgynous (L.) Merr.

Morphogenetic potential of shoot tip, leaf and nodal explants of Sauropus androgynous was investigated to develop a reliable plant regeneration protocol via indirect organogenesis. Explants were cultured on Murashige and Skoog’s ( MS ) medium and Phillips & Collins ( L2 ) medium supplemented with different concentrations of BAP either alone or in combinations with other auxins such as IAA, NAA, 2,4-D and IBA along with GA 3 . However, L2 medium with hormones was found to be more supportive for induction of profuse callus and subsequent regeneration of shoot buds than the same hormonal composition of MS medium. Maximum number of shoots per culture were differentiated from the organogenic callus raised on L2 + BAP (13.20 µM) + IAA (11.42 µM) + GA 3 (1.44 µM). Thus regenerated shoots were rooted on ½ L2 + IAA (2.85 µM). The plantlets were acclimatized for 3-4 weeks in pearlite before transferring them into pots containing soil, sand and manure in 1:1:1 ratio. Nearly 90% of survival was recorded.
Epiphyte Orchid Establishment on Termite Carton Trails

In the coastal zone of central Veracruz, Mexico, we recorded the abundance of orchid plants growing on termite carton trails or directly on the peeling bark of Bursera fagaroides. Although only 19 percent of the surveyed trees contained termite carton trails, trees with termites hosted 92 percent of all orchid individuals. A disproportionate number of orchid seedlings occurred on termite cartons given the relative availability of carton and bark substrate. Our results show for the first time that orchids can establish on termite trails, and we discuss the potential for termite facilitation of orchid populations.