Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybridisation between cherry tomato (small fry) and Petomech for shortened fruit maturation, size and earliness

Tomato ( Lycopersicon esculentum var. cerasiforme) is among the most important vegetable crops grown world wide providing good nutritional requirements and boost incomes, especially in sub-Saharan Africa. The objective of this study was to determin the heritability of shortened fruit maturation (SFM) period in a hybrid from a cross between cherry (Small fry) tomato and Petomech. A field experiment was carried out at the Crops Research Institute (CRI), Kwadaso. A cross was made between Petomech and Small fry. Fruit maturation period (FMP) (days from anthesis to the breaker stage of fruit Colour) was 42 days for Small fry and 52 days for Petomech. Parental, F 1 , F 2 , and backcross generations differed in FMP, yield, estimates of broad- and narrow-sense SFM heritabilities of 61.4 and 38.8%, respectively, on a single-plant basis. A test for midparent heterosis also showed significance (P<0.05). Genetic control of SFM was quantitative in nature, and highly dominant. The F 1 and F 2 generations had FMP of 47.2 and 49.5 days, respectively. F 1 , F 2 , and backcross generations all differed in number of fruits per plant, giving broad- and narrow-sense heritabilities of 69.73 and 55.67%, respectively. With a mean per fruit weight of 150.1 g Petomech recorded the highest fruit weight, while Small Fry recorded the lightest fruit weight of 81.4 g. Estimated broad-and narrow sense heritability for fruit weight was 71.76 and 41.68%, respectively. There was a significant difference between Small Fry and Petomech, as well as the BC 1 and BC 2 in terms of fruit size. The highest heterotic effect was found in number of fruits per plant (27.6%) over mid-parent. The highest yield was recorded by Petomech (18.9 t ha -1 ), while Small Fry recorded the lowest value of (14.3 t ha -1 ). Keywords: Genetics, heterosis, heritability, Lycopersicon esculentum
A toolkit to study seabird–fishery interactions

A toolkit to study seabird–fishery interactions Tangi Le Bot*, Amélie Lescroël, and David Grémillet Centre d’Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS—Université de Montpellier—Université Paul-Valéry Montpellier EPHE, Montpellier, France Point Blue Conservation Science, 3820 Cypress Drive, Suite 11, Petaluma, CA 94954, USA Percy FitzPatrick Institute and DST-NRF Centre of Excellence at the University of Cape Town, Rondebosch 7701, South Africa *Corresponding author: tel: þ33 (0) 467 613 309; e-mail: tangi.lebot@cefe.cnrs. fr. Le Bot, T. , Lescroël, A. , and Grémillet, D. A toolkit to study seabird–fishery interactions. – ICES Journal of Marine Science, 75: 1513– 1525.
Patterns of microsatellite distribution reflect the evolution of biological complexity

Microsatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been non-exhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.
Effects of mercury on axonal growth with implications for Alzheimer’s Disease.

Effects of mercury cause severe brain damage in young children, adults and elderly people. Mercury comes in different forms; there is organic mercury (Hg2Cl2), inorganic mercury that are found as salts and elemental mercury is found as a liquid or quicksilver (Hock, 1997). Each form of mercury is found in a different place: organic mercury (methylmercury) is found in fish that consumed mercury by eating algae or by eating smaller fish that consumed algae; the methylmercury concentration increases has it goes up the food chain. The inorganic form of mercury is found in batteries or laboratories whereas the elemental form of mercury is found in glass thermometers and dental fillings (Hock, 1997). Different forms of mercury affect different parts of the neuron. It has been suggested that organic mercury affects the structure of the microtubules and inorganic mercury affects the surface membrane structure of the neuron (Miura, 2000). The addition of mercury to a healthy live neuron will affect the neuron immediately, affecting the growth of the axon (Miura, 2000). Axonal growth is extremely important to normal development and it requires many mechanisms to obtain the axonal elongation (Goldberg, 2003). The main cytoskeletal elements that are needed for axonal growth are microtubules and actin filaments (Goldberg, 2003). These properties hold the plasma membrane of the axon, so blebbing of the plasma membrane does not occur. Axonal growth takes place at the growth cone where lamellipodia and filopodia occur; growing the axon to its designated target or targets (Goldberg, 2003). As the microtubules are polymerizing, there are also neuronal growth factors in the peptide family called neurotrophins, which act as a signal to induce the axonal growth development (Goldberg, 2003).
Elm genetic diversity and hybridization in the presence of Dutch elm disease

The impact of Dutch elm disease (DED) on the genetic diversity of slippery elm (Ulmus rubra) is summarized and its potential impact on the genetic diversity of other North American native elms, American elm (U. americana), rock elm (U. thomasii), winged elm (U. alata), cedar elm (U. crassifolia), and September elm (U. serotina), is discussed. The potential for hybridization between the introduced Siberian elm U. pumila and the native North American elms is considered given previous findings with U. rubra. We do not expect DED to reduce the genetic diversity of these native elms. The only exception may be U. serotina if its restricted range leads to genetic discontinuities among populations. We do not expect hybridization between U. americana and U. pumila due to incompatibility barriers, but hybridization between U. pumila and other native elms appears more likely and could have negative effects on the long term conservation of these species. This information is timely given the current efforts to restore American elm across the U.S. landscape.
Prevalence and microbial ecology of Enterobacteriaceae on Texas produce and the survival of Salmonella on parsley as affected by processing and storage

Prevalence and Microbial Ecology of Enterobacteriaceae on Texas Produce and the Survival of Salmonella on Parsley as Affected by Processing and Storage. (August 2004) Elizabeth Anne Duffy B.S., California Polytechnic State University, San Luis Obispo; M.S., Colorado State University Chair of Advisory Committee: Dr. Gary R. Acuff To assess the risk factors involved in the contamination of fresh produce with human pathogenic organisms, a total of 1,257 samples were collected from cantaloupe, oranges, and parsley in the field and after processing, and the environment. Samples were collected twice in a season from two farms with operating packing sheds per commodity and analyzed for the presence of Salmonella. Sixteen, 6, and 3 isolates were obtained from irrigation water, packing shed equipment, and washed cantaloupe, respectively. Salmonella was not detected on oranges or parsley. Serotyping, pulsedfield gel electrophoresis, and repetitive sequence-based polymerase chain reaction assays were applied to Salmonella isolates to evaluate their genetic diversity and to determine if there are relationships between sources of contamination. Using PFGE, all Salmonella isolates obtained from irrigation water and equipment were determined to be different from cantaloupe isolates. Only one equipment isolate was related to isolates from
Proteolytic activity of the rat and guinea pig blastocyst in vitro.

Experiments were performed to determine whether a proteolytic enzyme is present in the rat and guinea pig trophoblast its nature if so and whether live trophoblast tissue in culture is able to digest a gelatin membrane. Hypoosmotic shock at acid pH on Days 8 9 and 10 of development produced high proteolytic activity in the guinea pig trophoblast but not in the rat trophoblast. High proteolytic activity was observed in the yolk sac visceral layer of both the rat and guinea pig trophoblast following hypoosmotic shock at low pH on Days 8 9 10 13 and 14. When the trophoblast and yolk sac of the 8-day-old guinea pig embryo were grown on a fixed gelatin membrane proteolytic activity was barely evident. It is concluded that the enzyme is intracellular in location is an endopeptidase acts at acidic pH and may be cathespin.
Qualitative and Quantitative Estimation of Crown Gall Inhibitory Activity of Curcumin, Hydroalcoholic Extract of Curcuma aromatica Salisb and Curcuma zedoaria (Christm.) Roscoe

Based on folklore and anecdotal information about traditional medicines paved the way for the production of new antitumor and antibiotic drugs. Huge amounts and the long period of research is required for the development of pharmaceuticals of ethnobotanical anecdotal or folkloric origin. Biological assays and ultimate clinical testing are required for the verification of claimed biological activity. Information about the biological activity of plant extract could be obtained by bioassays which could also be used to identify the active components by direct fractionation of herbal extract. In assessing the antitumor activity of plant extracts bioassay is used over many years. Vincristine, Vinblastine, International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 01 (2018) Journal homepage: http://www.ijcmas. com
Phylogenetic analysis of wood-inhabiting molds and assessment of soft-rot wood deterioration. Part 5. Genus Aureobasidium

Abstract The genus Aureobasidium is wellknown as a wood-staining mold and as a black yeast-like fungi, which produces mainly dark spores or pigmented hyphae within the wood cell lumens. Nevertheless, few studies are dedicated to wood-colonizing Aureobasidium species and little is known about the wood degradation patterns of this genus. In the present study, four Aureobasidium species, including Aureobasidium melanogenum, Aureobasidium leucospermi, Aureobasidium pullulans, and an unknown Aureobasidium sp. , were isolated and identified based on phylogenetic analysis. A. melanogenum and A. leucospermi were observed for the first time in Korea. The degradation pattern of Douglas-fir by Aureobasidium was observed for the first time by scanning electron microscopy (SEM). All tested Aureobasidium species except an unknown Aureobasidium sp. revealed soft-rot Type ΙΙ (erosion) in sapwood pine.
Diversity of wasps (Hymenoptera: Vespidae) in conventional and organic guarana (Paullinia cupana var. sorbilis) crops in the Brazilian Amazon

Diversity of wasps (Hymenoptera: Vespidae) in conventional and organic guarana ( Paullinia cupana var. sorbilis ) crops in the Brazilian Amazon. The present study aimed to determine the diversity of wasp species associated with the guarana crop and the difference in composition of species associated to organic and conventional crops, as well as among environments established in each management (adjacent forest, crop edge and guarana crop). We collected 977 individuals and 59 species, in 23 genera of Vespidae, sixteen of Polistinae (52 species) and seven Eumeninae (seven species). Polybia was the most abundant and rich genus with 553 specimens and 15 species, followed by Agelaia (139, nine) and Protopolybia (103, five). In organic management crop, 686 individuals allocated in 18 genera and 47 species were collected, whereas in conventional management crop 291 individuals allocated in 18 genera and 41 species were collected. According to the three sampling points, in both management types, the edge of the crop field shows the highest abundance of wasps with a total of 519 individuals allocated in 19 genera and 45 species. Given the intense use of both environments (forest and crop) by the wasps, it is important to grow crops in regions near native forests, where the chances of social wasp colonies to be founded are increased.
Association Mapping Identifies Markers Linked with Yield Traits in an Oil Palm Breeding Population

Abstract Oil palm ( Elaeis guineensis ) is an important oil crop for human consumption worldwide. Oil production is an interested trait to get more value of palm oil. Oil yield traits in an oil palm breeding program is difficult as oil palm is a highly heterozygous out-crossing crop with a long life cycle and large size. This research aims to identify Single Nucleotide Polymorphism (SNP) markers linked with oil palm yield traits. Total 40 candidate SNP markers were tested with 499 individual palms from an unrelated set of 32 families using association testing for quantitative traits. 9 SSR markers were used to estimate population structure and kinship relationships. The results indicated that the genotypes at 36 markers associated with oil yield traits (BN, ABW, FFB and PH combined) at significant statistical P-value, corrected for multiple testing. Eg_Pairs05 and SSCP0020 were highly significant associated with traits that might be high potential markers for oil palm breeding in the future. Keywords: GWAS; SNP marker; marker assisted selection (MAS)
Biogeography and ecology of the genus Turbinicarpus (Cactaceae): environmental controls of taxa richness and morphology

The biogeography and the ecology of the genus Turbinicarpus are scarcely known and the taxonomic segregation of the genus Rapicactus from Turbinicarpus has been debated. The present study aims to (i) evaluate the distribution of all taxa of Turbinicarpus in the full distributional range of the genus (NE Mexico); (ii) investigate the potential ecological divergence between Rapicactus and Turbinicarpus; and (iii) analyse the influence of environmental variables on plant morphology. The distribution pattern of all taxa belonging to the genus Turbinicarpus s.l. (Turbinicarpus + Rapicactus) was mapped using information from 12 herbaria, as well as unpublished databases. The study area was divided into cells of 25 km × 25 km. The relationships between taxa richness, sampling effort and environmental variables were tested by using grid data, via spatially explicit models. The elevational distribution of populations and the effects of climate, latitude and elevation on the mean steam diameter of the populations were separately investigated for Turbinicarpus and Rapicactus. Turbinicarpus s.l. taxa richness is highest within 100°W and 101°W longitude, about 2500 km north of the equator, with maximum diversity in areas with a mean annual temperature of 17–19 °C and a mean annual rainfall of 550–650 mm. A significant relationship was observed between taxa richness and sampling effort, and between taxa richness and longitude, mean annual rainfall and calcium-rich substrate. Rapicactus taxa were found to grow at higher elevations compared with Turbinicarpus. Body size of the plants showed a negative relationship with latitude and elevation in Turbinicarpus, and a positive one with latitude in Rapicactus. The results showed that the genus Turbinicarpus s.l. presents diversity hotspots in the floristic regions of Chihuahuan Desert and Sierra Madre Oriental. The responses of Rapicactus and Turbinicarpus to latitudinal and elevational gradients were different, supporting the segregation of Rapicactus from Turbinicarpus.
Screening of methanol & acetone extract for antimicrobial activity of some medicinal plants species of Indian folklore

In search for new and safe antibacterial agent medicinal plants have been continuously investigated. The methanol and acetone extract of Alstonia scholaris (stem bark), Achyranthus aspera (whole plant) Moringa oleifera (leaves), Tinospora cordifolia (stem), and Enicostema hyssopifolium (stem) were screened for their antibacterial activity using the agar diffusion method. The susceptibility of the microorganisms to the extracts of these plants was compared with each other and with selected standard antibiotics. The antimicrobial activities of these plants were discussed according to their phytochemical components. Finding of current research was suggest A. scholaris and M. oleifera can be explored as a new source of antibacterial compound, for Enterobacter aerogens (ATCC13048), Staphylococcus aureus (ATCC9144), and Micrococcus luteus (ATCC4698).
Lagoon nurseries make a major contribution to adult populations of a highly prized coastal fish

This study investigated the contributions of five putative nursery areas, namely four coastal lagoons and the marine coastal zone, to the local offshore fishery of the gilthead sea bream Sparus aurata, in the Gulf of Lion (NW Mediterranean). A detailed database of multi‐elemental lagoon and marine otolith signatures was developed, based upon analysis of multiple sequential spots across growth bands of the otoliths of juveniles (n = 142) sampled from the habitats over a 5‐yr interval. Adults of 10 annual cohorts (n = 114), fished throughout the Gulf, were then submitted to a similar microchemical analysis of the growth band of their otoliths that was formed after nursery settlement in their first year. Using the juvenile signature database and Random Forest classification algorithms, adults were re‐assigned to the lagoons or marine coastal zone as a nursery. More than 80% of adults derived from lagoons, being ≥ 85.0% for five consecutive cohorts. Therefore, the marine coastal zone apparently contributed few adults, especially as a function of surface area. The four lagoons differed, however, in their contribution to the S. aurata fishery. Two lagoons qualified as “Effective Juvenile Habitats” that contributed more than 20% of the adults fished. Two shallow brackish lagoons were “Nursery‐Role Habitats” that contributed almost twice as many adults, per unit surface area, as the overall average. Such information can support strategies for sustainable management of multiple coastal lagoon habitats, and of valuable fisheries that depend upon them.
Combination of Doxorubicin and Areca Ethanolic Extract Induces Apoptosis by Increasing Caspase-3 Level on Breast Cancer (T47D) Cells

Despite causing many side effects, doxorubicin (Dox) is still one of breast cancer drug of choice. Thus, combination of chemotherapy is developed in order to decrease doxorubicin regimen dose. The aim of this research is to examine the combination effect of doxorubicin (dox) and areca extract (AE) on T47D human breast cancer cells. The cytotoxic activity was determined using MTT assay. The combination index (CI) of the combination treatment was calculated to determine the effects (synergistic, additive or antagonistic). The combination application of dox (6-22nM) and AE (8-30µg/ml) on T47D cells showed synergistic (CI<0.9) or additive effect (CI=0.9-1.1). The effective combination of dox-AE was 6 nM - 8 µg/ml on CI<0.5. Apoptosis induction of AE solely and its combination with dox was then observed using double staining method. Moreover, expression of Bax and caspase-3 protein which mediated apoptosis, were observed using immunocytochemistry. Combination of AE and Dox increased expression of Caspase-3 but did not increase expression of Bax. This result showed AE increase the effectiveness of doxorubicin against T47D cells. Keywords : Breast cancer, doxorubicin, areca extract, T47D cells
Characterisation of the zebrafish cerebellar efferent system

The efferent system of the cerebellum is formed by the neurons of the deep cerebellar nuclei. Using morphology and expression analysis together with axon tracing I have identified and characterised this cell population, the Eurydendroid cells (ECs), in the zebrafish. With the help of transgenic lines expressing fluorescent proteins and in vivo time lapse analysis I have revealed the developmental period, their differentiation behaviour and their integration into the layered cerebellar cortex. Finally nmyc expression and its regulation were identified as a potential key factor in EC proliferation or specification. These results significantly expand our knowledge of cerebellar development in teleosts and their use as informative disease models.
Reverse Association of Single Cells to Rheumatoid Arthritis Accounting for Mixed Effects Identifies an Expanded CD27- HLA-DR+ Effector Memory CD4+ T Cell Population

Defining disease associated cellular subsets from single cell assays can be confounded by technical variation and inter-individual differences in subset frequencies. We present Mixed effects modeling of Associations of Single Cells (MASC), a novel reverse single cell association strategy that tests whether case-control status influences the membership of single cells in any of multiple cellular subsets. MASC is able to account for random technical artifacts that confound clustering and person-to-person biological variation. After demonstrating appropriate type I error, we applied this method to mass cytometry data collected from 52 cases and controls to identify CD4+ memory T cells altered in the circulation of rheumatoid arthritis (RA) patients. MASC identified a population of effector memory T cells expanded in RA patients compared to non-inflammatory controls (OR = 1.7; p = 1.1 × 10−3). This population was characterized by absence of CD27 and expression of HLA-DR and constituted 1.7% of the total resting CD4+ memory T cells in controls and 3.1% in cases. We replicated the expansion of CD27- HLA-DR+ T cells in an independent cohort of 39 RA patients (p = 0.011), and find that effective RA treatment reduces the frequency of these cells in circulation. Further, we find that CD27- HLA-DR+ cells infiltrate the joints of RA patients and produce abundant effector cytokines upon stimulation. We propose that MASC is a broadly applicable method to identify disease-associated cell populations in high-dimensional single cell data.
A Systematic Study on Genus Mystus from Paschim Medinipur, West Bengal, India

Present study reveals the existence of four species under genus Mystus from freshwater aquatic systems of Paschim Medinipur. It is the first time study on the group from the study area. Taxonomy of the species and their geographical distribution is the prime interest of the present work. A comprehensive zoogeography of the species in different blocks has been recorded in details.