Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental genetics of Xenopus

AbstractDevelopmental genetics of XenopusbyJessica Burnham LyonsDoctor of Philosophy in Molecular and Cell BiologyUniversity of California, BerkeleyProfessor Richard Harland, ChairThe frog Xenopus laevis has been studied for over 200 years. Its advantages as a robust and easily manipulable model organism have been complemented more recently by genetic and genomic studies in Xenopus tropicalis. My thesis work utilized established and cutting-edge techniques to advance our knowledge of developmental genetics in both Xenopus systems.I used an embryological approach to investigate the roles of the Fgf receptors (Fgfrs) during development. Knockdown and overexpression studies suggested that each Fgfr plays a different role in the specification of mesoderm, and my results are consistent with Fgfr4 playing a role in dampening the Fgf signal. I also showed that X. tropicalis Fgfrs 1-3 are alternatively spliced in D3, the extracellular immunoglobulin domain important for ligand specificity. These isoforms exhibit different temporal and spatial expression patterns, suggesting that control of this alternative splicing plays a role in regulating development.My thesis work has also harnessed the power of the X. tropicalis system to understand development using a forward genetic approach. Tadpoles homozygous for the recessive lethal mutation curly exhibit ventral edema and curled tails. I used classical genetics to map curly to a 1.9 Mb window on X. tropicalis chromosome 4. The pteg gene, which lies in this region, is misspliced in curly embryos. Isabelle Philipp and I used next-generation (nextgen) sequencing technology to identify differences between the curly mutant DNA and that of the reference genome. Focusing on the region around the pteg gene, we are currently evaluating these differences to find the lesion that causes the curly phenotype. The efficient application of genetic techniques requires a high-quality genetic map and reference genome, and those available for X. tropicalis were flawed (Wells et al., 2011) (Hellsten et al., 2010). Thus, I developed a genotyping by sequencing (GBS) technique using reduced-representation multiplex nextgen sequencing, and my collaborators in the Rokhsar lab have generated a high-quality SNP map for X. tropicalis based on my data from 192 F2 individuals. This map is being used to construct an improved X. tropicalis genome assembly. By finding regions of correlation for the pigmentation mutation gray, as well as the X. tropicalis sex locus, we demonstrated that this technique can be used for genetic mapping. I applied my GBS method to X. laevis as well, and the SNP map thus generated will facilitate the assembly of a reference genome for this allotetraploid species.By combining the classical advantages of the Xenopus system with modern techniques, my thesis work has contributed to our understanding of the development, genetics, and genomics of vertebrate biology.
Bahiagrass for the Management of Root-Knot and Cyst Nematodes in Soybean

The effect of rotation with bahiagrass (Paspalum notatum) on soybean (Glycine max) yields and end-of-season (2 weeks before soybean harvest) soil populations of root-knot (Meloidogyne arenaria) and cyst nematode (Heterodera glycines, race 4) was studied in a field in Baldwin county, Alabama. Soybean cvs. Braxton, Centennial, Gordon, Kirby, Leflore, Ransom, and Stonewall were planted in plots that had been planted to 'Pensacola' bahiagrass for the previous 2 years and in others that had been in monoculture with soybean. In each of the two cropping systems each cultivar was planted in plots treated at planting with the 15G formulation of aldicarb (41.4 g a.i./100 m of row in a 20-cm-wide band) and without a nematicide. For all cultivars the nematicide treatment did not increase yield or affect second-stage juvenile populations of either M. arenaria or H. glycines. Yields of all cultivars were higher in the bahiagrass-soybean plots than in those in the soybean monoculture. Yield respons
In vitro Superoxide Anion Radical Scavenging Ability of Honeybush Tea ( Cyclopia )

1 Abstract The superoxide anion radical (O2-) scavenging ability of aqueous extracts from honeybush tea, as affected by species and fermentation, and phenolic compounds from fermented C. intermedia, was evaluated. Unfermented C. sessiliflora showed the strongest O2- scavenging ability. Fermentation significantly (P ≤ 0.05) decreased the O2- scavenging ability of the different species. A strong structure-activity relationship was illustrated by the relative O2- scavenging efficacy of the phenolic compounds. The flavone luteolin and the flavanone eriodictyol showed excellent O2- scavenging activity compared to the flavanones, hesperidin and hesperetin. The isoflavone formononetin and coumestan medicagol were not effective scavengers of this radical.
Programmed Cell Death in Relation to Petal Senescence in Ornamental Plants

Cell death is a common event in all types of plant organisms. Understanding the phenomenon of programmed cell death (PCD) is an important area of research for plant scientists because of its role in senescence and the post-harvest quality of ornamentals, fruits, and vegetables. In the present paper, PCD in relation to petal senescence in ornamental plants is reviewed. Morphological, anatomical, physiological,and biochemical changes that are related to PCD in petals, such as water content, sink-source relationships,hormones, genes, and signal transduction pathways, are discussed. Several approaches to improving the quality of post-harvest ornamentals are reviewed and some prospects for future research are given.
Biochemistry and molecular characterisation of chlorpyrifos resistance in field strains of the white‐backed planthopper Sogatella furcifera (Hemiptera: Delphacidae)

Acetylcholinesterase (AChE) is the molecular target of organophosphate (OP) and carbamate (CB) insecticides. The white‐backed planthopper, Sogatella furcifera (Horváth, 1899), is a notorious rice pest in Asia and exhibits high resistance against a specific OP pesticide known as chlorpyrifos. To date, there has not yet been a study on the molecular mechanisms that confer resistance to this pesticide in S. furcifera. In this study, we cloned the full‐length cDNA of AChE type 1 and type 2 genes from S. furcifera (SfAChE1 and SfAChE2). Both genes appear to be functional and are composed of the classic AChE domains. An analysis of the gene family revealed that SfAChE1 and SfAChE2 cluster into in the insect AChE1 and AChE2 clades, respectively. We first performed qPCR experiments to detect AChE expression patterns in distinct developmental stages and tissues. Our results revealed that SfAChE1 is more highly expressed than SfAChE2. Both genes were most highly expressed during the first instar nymph stage, and then expressed at a decreasing rate until the end of the fifth instar nymph stage. Both SfAChE1 and SfAChE2 were more highly expressed than in other tested tissues. Furthermore, we investigated the association between AChE genes and chlorpyrifos resistance and found that Nanjing (NJ‐R) is a chlorpyrifos‐resistant strain with high frequencies of a Ser298Pro mutation in SfAChE1. Conversely, the chlorpyrifos‐susceptible Guangdong (GD‐S) strain did not carry this mutation.
Development of a cryogenic refrigerator for a compact superconducting cyclotron in a hospital environment

Tieftemperaturkuhlung ist unverzichtbar fur den Betrieb von medizischen Anlagen, die durch die Verwendung von supraleitenden Komponenten ein leistungsfahigeres und kompakteres System erreichen sollen. Obwohl kryogene Refrigeratoren im Handel erhaltlich sind, ist manchmal die Entwicklung masgeschneiderter Losungen aufgrund spezieller Systemanforderungen unvermeidlich. Dies ist der Fall fur AMIT’s Teilchenbeschleuniger; ein hochkompaktes supraleitendes Zyklotron fur die Einzeldosisherstellung von radiopharmazeutischen Substanzen in einer Krankenhausumgebung. Zur Erzeugung des Magnetfeldes verwendet das Zyklotron ein Paar supraleitender Magnete, die eine isotherme Kuhlung bei 4,5 K im Wattbereich und eine warmere nicht isotherme Kuhlung zur thermischen Abschirmung erfordern. Die grosten Herausforderungen bei der Kuhlung ergeben sich aus der begrenzten Platzverfugbarkeit, der schadlichen radioaktiven Umgebung, den strengen Sicherheitsaspekten, und der Anforderung eines kontinuierlichen und unterbrechungsfreien Betriebs. In dieser Dissertation wird ein neues Kuhlsystem vorgestellt, welches einen handelsublichen Kryokuhler als Kaltequelle verwendet, und mittels einer erzwungenen Durchstromung mit kaltem Helium aus der Distanz kuhlen kann. Die Studie untersucht funf Prozessvarianten eines Kaskadenkuhlschemas unterschiedlicher Kuhlleistung und Komplexitat. Die technisch einfachste und thermodynamisch effizienteste Variante wird zum Entwurf und zur Herstellung des Kryo-Versorgungssystems verwendet; ein kleiner kryokuhlerbasierter Refrigerator mit 1,66 W isothermer Kuhlleistung bei 4,5 K, und 24,32 W nicht-isothermer Kuhlleistung von 40 K bis 70 K. Die verbleibenden Varianten sind komplexer und leistungsfahiger, und dienen somit als Grundlage fur zukunftige Designiterationen, die, theoretisch, eine isotherme Kuhlleistung von bis zu 11 W erreichen konnten. Das neue Kuhlsystem wird in einem angrenzenden Raum neben dem Zyklotron aufgestellt, wodurch eine auserst kompakte Bauweise des Zyklotrons ermoglicht wird. Die Fahigkeit, isotherme kryogene Kuhlung aus einem entfernten geschlossenen Kleinrefrigerator bereitzustellen, konnte es einer Vielzahl anderer medizinischer Gerate, wie z. B. MRI Scannern, ermoglichen, eine kleinere Grose zu erreichen.
Diversity of gill raker number and diets among stickleback populations in novel habitats created by the 2011 Tōhoku earthquake and tsunami

Background: Catastrophic disasters often create novel habitats and offer an opportunity to investigate how rapidly phenotypic diversification occurs in nature. On 11 March 2011, a large earthquake and subsequent tsunami struck the downtown area of Otsuchi Town, Iwate Pre-fecture, Japan. This catastrophic event created new spring water-fed ponds that sticklebacks (genus Gasterosteus ) quickly colonized. In 2014, there were 48 newly formed stickleback habitats. Questions: Does trophic morphology and ecology vary among stickleback populations in newly created ponds? Is the morphological variation associated with any ecological or environmental factors in the newly formed habitats? Methods: We sampled sticklebacks from four native and 17 novel habitats in 2014. We counted the number of gill rakers (an important trophic trait in fish) and analysed their stomach contents. We measured salinity, water temperature, pH, dissolved oxygen, and the density of benthos in the habitats and conducted principal component analysis on these environmental factors. Then, we tested whether any environmental factors or environmental principal components are associated with variation in gill raker number. Results: The number of gill rakers varied significantly among the newly formed populations. Fish with fewer gill rakers had a higher proportion of benthos in their stomach, suggesting that gill raker number may contribute to the performance of benthic feeding. Furthermore, we found that sticklebacks in habitats with higher benthos density had fewer gill rakers.
Pathogenic variation of Fusarium udum of Pigeonpea

A study was conducted in the glasshouse and under laboratory conditions to verify diversity in Fusarium udum of pigeonpea in Kenya using several isolates of the fungus collected from both traditional pigeonpea growing areas and new ones. Glasshouse tests using twelve pigeonpea lines gave consistent differences in virulence in these isolates. There were also strong differences in growth traits, such as growth rate (aggressiveness), growth habit and morphology, in these isolates in laboratory tests. Therefore, these isolates are true variants of this pathogen. There are as yet no pigeonpea differentials for Fusarium and so it could not be confirmed whether the isolates are races of F. udum in Kenya or not. Its implication in framing a breeding strategy has been discussed.
Comparison of Human Milk, Cow´s Milk and Infant Formulas for Their Antifungal Effects against Environmental Fungi

Aim: Breast-feeding is generally accepted as the optimal method of feeding infants. The purpose of the present study was to investigate and compare the antifungal effect of human milk with infant formula and cow´s milk. Materials and Methods: Eighty Sabouraud agar petri dishes were separated into eight groups. All petri dish lids were closed and incubated, after 15 minutes uncovered. The first group was used to detect the fungal flora of the environmental air. The second group was rubbed with human milk. The third group was rubbed with 0.9% NaCl solution. Fourth group was rubbed with cow´s milk. Fifth, 6, 7 and 8. groups were rubbed with probiotic formula, prebiotic formula, pro-prebiotic formula and standard infant formula respectively. All statistical analyses were performed using the SPSS. Results: The number of fungal colonies grown in human milk-rubbed dishes was significantly less than the other groups except group 7 (groups 1, 3, 4, 5, 6, 7 and 8) (P 0.05, P < 0.0001, respectively). Conclusions: In vitro antifungal effect of human milk is significantly superior than cow´s milk and formulas tested. Human milk is not only the best food for infants but also it protects infants from fungal infections and fungal allergies by means of antifungal effect. Prebiotic and pre-probiotic formula also have antifungal effect.
Investigating the role of gut hormones in energy and glucose homeostasis

Obesity is associated with type-2 diabetes mellitus. Gut hormones are peptides secreted in response to nutrient intake that act to regulate food intake, energy and glucose homeostasis. Thus, alterations in gut hormone abundance and/or signalling can contribute to the development of the obese and T2DM phenotype. The incretin hormones glucagon-like peptide-1 and glucose-dependent insulinotropic hormone augment glucose-mediated insulin secretion. Peptide YY is released from the gut post-prandially and acts primarily as a satiety signal. Recently studies have highlighted a role for PYY in regulating glucose homeostasis, which to date remains partially understood. Dipeptidyl peptidase-4 is involved in the biological inactivation of the incretins hence; DPP-4 inhibition is used to treat T2DM. DPP-4 also regulates PYY. Thus, DPP-4 inhibition may potentially impact on pancreatic PYY function and signalling and may alter the effects of the PYY system on glucose homeostasis. In addition, gut peptides have been identified as possible contributors to cases of hyperinsulinaemic-hypoglycaemia resulting from bariatric surgery. Therefore, this thesis aimed to (1) determine the contribution of pancreatic PYY deletion to the intra-islet PYY system; glucose homeostasis and body weight phenotype and (2) establish the impact of hyperinsulinism on DPP-4 and its gut hormone substrates. To address the first point, pancreatic-specific Pyy null mice were phenotyped for changes in the pancreatic endocrine system, followed by body weight and glucose metabolism, in vivo. Further investigations measuring gut hormone mRNA suggested the intra-islet system was contributing to the observed reduction in weight gain and hyperinsulinaemia. Finally, patients with congenital forms of HI were evaluated for PYY, the incretins and DPP-4. This study highlighted a role for DPP-4, PYY and GIP in mediating HI. In conclusion, this thesis demonstrates a role for gut hormones in energy and glucose homeostasis. Further work is required to understand the interaction of gut peptides on islet function.
A new species of the genus Candonopsis (Crustacea, Ostracoda) from Western Australia

A new species of stygobiont ostracod, Candonopsis (Abcandonopsis) linnaei sp. nov., is described from subterranean waters of the Murchison region in Western Australia. The new species can be easily distinguished from other representatives of the genus by 6-segmented antennula and incompletely divided penultimate segment of the walking leg. A key to the representatives of the genus Candonopsis in Australia is also provided.
Estimation of some population parameters of red mullet (Mullus barbatus ponticus, Essipov, 1927) caught in the Black Sea.

The aim of the present study was to estimate some population parameters of red mullets caught in Central Black Sea. Average length of the sampling size that is composed of 699 individuals was found to be as 11.75 ± 0.111 and their average weight to be as 17.91 ± 0.507 gr. W = 0.0107 L 2.9717 was used to estimate the length-weight relationships. Asymptotic length (L∞) among the parameters of the growth equation was calculated as 20.15 cm whereas growth coef-ficient (K) was found to be as 0.33. Survival rate (S) was 0.28, real mortality rate (A) was 0.72, natural mortality rate (M) was 0.68, fishery mortality rate (F) was 0.60 and enterprise rate (E) was estimated to be as 0.47.
Growth, fertility, prolificacy and fleece weight of Booroola, Romanov and Finnsheep first cross and backcross with the DLS breed.

Performance of 407 yearlings representing 7 genetic groups born 1n February March and mated at 8-9 months of age was evaluated. Romanov (R) f ir s t cross (FC) and backcross (BC) ewe lambs were the heaviest at birth (3.9 and 4.1 kg) followed by Booroola (B) and Flnnsheep (F) crosses, respectively. They were also the heaviest groups at 50, 100 and 365 days of age followed by F then B crosses. F ert il i t y for R, FC (987.) and BC (94%) was significantly higher than that of F (88 and 78%) and B crosses (51 and 68%), respectively. Prolificacy was highest 1n R, FC. Booroola and F, FCs were similar In lamb production. The same tendency was observed 1n BC. Lamb survival ranged between 93 and 97% at birth and between 85 and 92% between birth and weaning. The heaviest U t te r s at birth were those of R, FC (6.4 kg), for the other groups the weight varied between 5.2 and 5.8 kg. Litter weight at weaning ranged between 25 kg for R, FC and 19 kg for B crosses. In FC, Booroola yearlings produced 3.7 kg of wool compared to 3.2 kg for F and R. In backcross F and R clipped 3.1 kg, 0.3 kg lighter than B.
Carbamate herbicides—new tools for cytological studies

Abstract Not Available – First paragraph follows: Cytology (the branch of biology dealing with studies of cell structure and function under the microscope) is important to both plant and animal scientists, because cytological studies disclose useful information on cell organization and behavior under both normal and artificially induced conditions. Plant physiologists in the Department of Horticultural Science, Riverside, are actively engaged in research on herbicides, with special emphasis on selective elimination of weeds from plantings of crop plants. In some experiments, the effects of herbicides become immediately apparent in either the weeds or the crop plants, or in both. In other experiments, damage to both weeds and crop plants remains concealed for a long time before it becomes evident. Such variable and often unpredictable behavior explains the interest of weed control physiologists in the mode of action of selective herbicides upon the species under study. One of the more promising approaches to mode-of-action studies is the cytological examination of herbicidal effects upon individual cells, especially dividing cells in root tissues.
Cardiovascular magnetic resonance imaging for the investigation of ischaemic heart disease

s: 1. Foley JRJ, Fent GJ, Garg P, Broadbent D, Dobson LE, Chew PG, Brown LAE, Swoboda PP, Plein S, Higgins DM, Greenwood JP. Single breath-hold, 3D MDIXON pulse sequence for late gadolinium enhancement imaging of ischaemic scar: a feasibility study. Heart, May 2018, 104 (Suppl 5) A12; DOI: 10.1136/heartjnl-2018-BCVI.32. Poster presentation at BCVI 2018, Edinburgh, UK May 2018. 2. Foley JRJ, Fent GJ, Garg P, Broadbent DA, Dobson LE, Chew PG, Brown LAE, Dall’Armellina E, Swoboda PP, Plein S, Higgins DM, Greenwood JP. Feasibility Study of a Single Breath-hold, 3D mDIXON Pulse Sequence for Late Gadolinium Enhancement Imaging of Ischaemic Scar. Poster presentation at CMR 2018, Barcelona, Spain January 2018. 3. Foley JRJ, Everett CC, Cairns D, Bijsterveld P, Ripley DP, Plein S, Sharples L, Brown J, Greenwood JP. Development and external validation of a multivariable model of pre-test likelihood of coronary artery disease based on a contemporary UK population, with comparison to existing risk models. Heart Jun 2017, 103 (Suppl 5) A64-A66. Poster presentation at BCS Manchester June 2017. 4. Foley JRJ, Swoboda PP, Fent GJ, Garg P, Ripley DP, McDiarmid AK, Dobson LE, Musa TA, Plein S, Witte KK, Greenwood JP. Differences in myocardial mechanics between ischaemic and non-ischaemic cardiomyopathy assessed by CMR: a sub-group analysis of the VINDICATE trial. Heart Jun 2017, 103 (Suppl 5) A77-A78. Poster presentation at BCS Manchester June 2017. 5. Foley JRJ, Swoboda PP, Fent GJ, McDiarmid AK, Garg P, Ripley DP, Musa TA, Plein S, Witte KK, Greenwood JP. Differences in CMR global strain assessment in ischaemic and non-ischaemic
Persentase Organ Dalam dan Deposisi Lemak Broiler Yang Diberi Pakan Tambahan Tepung Kelopak Bunga Rosella (Hibiscus Sabdariffa Linn)

Penelitian ini bertujuan untuk mengetahui pengaruh pemberian pakan tambahan tepung kelopak bunga rosella (Hibiscus sabdariffa Linn) sebagai feed suplement terhadap persentase organ dalam broiler. Penelitian dilaksanakan mulai bulan April sampai September 2012. Pemeliharaan dilakukan pada bulan Juni sampai Juli 2012 di Zona Pertanian Terpadu Fakultas Pertanian Universitas Bengkulu Medan Baru. Pengukuran variabel bobot organ dalam, lemak abdomen, lemak gizzard, dan fatty liver score bertempat di Laboratorium Jurusan Peternakan Fakultas Pertanian Universitas Bengkulu. Penelitian ini menggunakan Rancangan Acak Lengkap (RAL), dengan uji lanjut Duncans Multiple Range Test (DMRT). Sebanyak 48 ekor ayam broiler ditempatkan secara acak ke dalam 16 buah petak, dengan 4 perlakuan dengan 4 ulangan dan setiap ulangan terdiri 3 ekor ayam. Keempat perlakuan tersebut adalah sebagai berikut: ransum basal tanpa tepung kelopak bunga rosella sebagai kontrol (P0), ransum basal + 0,5 % tepung kelopak bunga rosela (P1), ransum basal + 1 % tepung kelopak bunga rosella (P2), ransum basal + 1,5 % tepung kelopak bunga rosella (P3). Variabel yang diamati dalam penelitian ini adalah berat dan persentase organ dalam broiler, lemak abdomen, lemak gizzard, dan fatty liver score. Hasil penelitian dapat disimpulkan bahwa pemberian tambahan pakan tepung kelopak bunga rosella (TKBR) dalam ransum tidak berpengaruh terhadap persentase berat hati dan limpa, namun memberikan pengaruh terhadap persentase berat usus, jantung, gizzard, dan persentase lemak abdomen, lemak gizzard dan fatty liver score, sehingga mampu menurunkan persentase lemak dan fatty liver score. Kata kunci: Tepung kelopak bunga rosella, persentase organ dalam, broiler.