Miracle-dz/UniFAR-FTUs huggingface dataset:
The Roles of daf-6 and Cell-Cell Interactions in Sensory Organ Morphogenesis

The roles of daf-6 and cell-cell interactions in sensory organ morphogenesis Elliot A. Perens, PhD. The Rockefeller University 2006 The development of multicellular organs depends on the regulation of cell shape, position, and orientation. The genetic regulation of these morphogenetic processes is poorly understood. As a model for organ morphogenesis, I studied the development of the Caenorhabditis elegans amphid sensory organ. Sensory organs in diverse species are often composed of neuronal sensory endings accommodated in a lumen formed by ensheathing epithelia or glia. The generation of this structure may require cell-autonomous factors that control lumen formation, as well as cell non-autonomous factors that coordinate the morphogenesis of the lumen with the resident neuronal processes. Understanding these processes would provide insight into lumen formation, glia morphogenesis, and cell-cell interactions during development, especially neuronal regulation of glia morphogenesis. In this thesis, I identify and characterize genes required for lumen formation in the amphid sensory organ. First, the gene daf-6 is required cell autonomously during amphid lumen formation. daf-6 encodes a Patched-related protein that is a member of a previously uncharacterized sub-family of sterolsensing domain containing proteins. Interestingly, daf-6 is expressed and required in several tubular structures, such as the excretory system and vulva. Thus, a similar genetic pathway is required for the formation of different lumens. Secondly, I conducted a forward genetic screen and identified and characterized mutations that suppress the lumen formation defects in daf-6 mutants. Finally, by examining mutants defective in sensory neuron process formation, I showed that amphid lumen shape is determined by its resident sensory endings.
Investigations on the Mechanisms of Resistance to Pixantrone in Tumor Cells.

Pixantrone is an aza-anthracenedione currently undergoing Phase 3 clinical trials and has shown significant activity in non-Hodgkin’s lymphoma. Preclinical studies with the aza-anthracenediones demonstrated a remarkable structure activity requirement, i.e., the ring nitrogen must be in the 2 position for anti-tumor activity. More importantly, Pixantrone which lacks hydroxyl groups at either the 1 or 4 positions of the chromophore, lacked any cardiotoxicity in pre-clinical trials. These pre-clinical findings have been substantiated during clinical development of Pixantrone. Given that there is a very real possibility that Pixantrone will progress to broader clinical use, we reasoned that understanding potential mechanisms by which tumor cells may become resistant to the drug were essential. By continuous in vitro exposure of MCF-7 cells to increasing concentrations of Pixantrone, we have developed a cell line (MCF7/aza) 20 fold resistant to the drug. These cells are cross resistant with mitoxantrone, surprisingly to a much great degree of resistance to mitoxantrone than to Pixantrone. Two compounds BBR 3438 and BBR 3576, represent a new class of anticancer drugs- the aza-anthrapyrazoles- have entered clinical trials and both were cross resistant in the MCF 7/aza cells. Using western blotting techniques we have demonstrated that the MCF 7/aza cells express elevated levels of BCRP but not Pgp. Further, resistance to Pixantrone was reversed with fumitremorgin C, a classic BCRP inhibitor that reverses mitoxantrone resistance in BCRP expressing cells. Resistance to Pixantrone was not reversed by verapamil, the classic Pgp inhibitor that reverses mitoxantrone resistance in MDR cells. Microscope evaluation of cells treated with Pixantrone demonstrated a unique intracellular distribution of the drug in MCF 7/aza cells in that the drug was sequestered in cytoplasmic vesicles rather than in the nucleus. More recently wehave completed a microarray analysis of MCF 7/Aza compared to MCF 7 cells and not surprisingly found a large number of genetic alterations in the resistant phenotype. One of the most striking alterations was a greater than 30 fold increase in BCRP. The results of our studies indicate that Pixantrone, a non-cardiotoxic mitoxantrone analogue, induced a resistant phenotype more closely related to that seen with mitoxantrone than the multi-drug resistance seen with many other anti-cancer drugs. It is of interest that an aza-anthracenedione, BBR 2378, was not cross resistant in MCF 7/aza cells. The unique structural feature of BBR 2378 is the presence of tertiary amines at the terminus of both sides arms of the compound in contrast to Pixantrone, BBR 3438, BBR 3576 or mitoxantrone all of which lack tertiary amine side arms. BBR 2378 has been previously been shown to be active in MDR cell linesas well. These results suggest that side arms play a pivotal role in determining activity or resistance in a variety of drug resistance tumor phenotypes.
Combinations of multiple genes controlling endosperm characters in relation to maximum eating quality of vegetable waxy corn.

1Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Maha Sarakham 44150, Thailand 2Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand 3Plant Breeding Research Center for Sustainable Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand *Corresponding author’s email: bsuriharn@gmail.com Co-authors’ email addresses: sakunkan.s@msu.ac. th, kamol9@gmail.com
Muscarinic Lateral Excitation Contributes to Visual Object Segmentation during Collision Avoidance

Visual neurons specialized in tracking objects on a collision course are often finely tuned to their target stimuli as this is critical for survival. The presynaptic neural networks converging on these neurons and their role in tuning them remains poorly understood. We took advantage of well-known characteristics of one such neuron to investigate the properties of its presynaptic input network. We find a structure more complex than hitherto realized. In addition to dynamic lateral inhibition used to filter out background motion, presynaptic circuits include normalizing inhibition and short-range lateral excitatory interactions mediated by muscarinic acetylcholine receptors. These interactions preferentially boost responses to coherently expanding visual stimuli generated by colliding objects, as opposed to spatially incoherent controls, helping implement object segmentation. Hence, in addition to active dendritic conductances within collision detecting neurons, multiple layers of both inhibitory and excitatory presynaptic connections are needed to finely tune neural circuits for collision detection.
The role of altered ciliary muscle morphology in refractive error and accommodative function

The primary theme of this thesis was to investigate in vivo ciliary muscle morphology in refractive error, and how ciliary muscle parameters are linked with accommodative function in a young adult population. Anterior segment optical coherence tomography was utilised for all ciliary muscle image acquisition to examine morphological differences between eyes. High levels of inter-ocular ciliary muscle symmetry were shown in emmetropes and myopes. Whilst the myopic ciliary muscle was longer and thicker than in emmetropes for both eyes, ciliary muscle length and thickness were linked with axial length in both cohorts. In amblyopes and anisometropes, high levels of inter-eye ciliary muscle symmetry were observed. The ciliary muscle in amblyopic eyes appear to grow in accordance with the axial length of the non-amblyopic eye (P = 0.022, r2 = 0.438). The possibility of diurnal variation in accommodative axial elongation and accommodative error was explored in emmetropes and myopes. Daily stability in these accommodative functions were shown, and between groups there was no difference in accommodative axial elongation (P = 0.884) or accommodative error (P = 0.098). It was demonstrated that ciliary muscle morphology is not linked with accommodative function, disputing the theory that the thickened ciliary muscle has reduced contractility, which initiates hyperopic defocus in myopigenesis. In emmetropes, males had significantly longer ciliary muscle lengths (P = 0.031) and axial length (P = 0.001) compared with females. Novel parameters to analyse the ciliary muscle were investigated; both inner apical angle and ciliary muscle cross-sectional area measures were linked to axial length, as were the area and apical angle. Both measures are highly effective ciliary muscle analysis parameters which demonstrated high repeatability. The studies detailed demonstrated normal ciliary muscle growth with ocular development in myopia, and indicated that the ciliary muscle is not a crucial causative myopigenesis factor.
Predictable anthropogenic food subsidies, density‐dependence and socio‐economic factors influence breeding investment in a generalist seabird

Recent European policies on the ban of fishing discards and the closure of open-air landfills are expected to reduce predictable and abundant food resources for generalist seabirds. In order to forecast the consequences of this reduction on seabird breeding investment it is important to understand whether diverse anthropogenic foraging resources act synergistically or not and whether their influence is mediated by density-dependent mechanisms. To assess these effects at large spatio-temporal scale, we measured mean egg volume as a proxy of breeding investment in ca. 5,000 three-egg clutches of the Yellow-legged Gull (Larus michahellis) from 20 colonies of the Western Mediterranean, located both along European and African coasts. In European gull colonies, egg volume increased with the availability of fishing discards and landfills in the vicinity of the colony. However, the landfill effect was weaker than the effect of fishing discards, probably due to the lower quality of waste as food for gulls. In contrast, none of the anthropogenic food subsidies influenced egg volume in African colonies, likely due to socio-economic differences (i.e. a much lower availability and predictability of both discards and waste food. Finally, results showed that the positive association between fishing discards and open-air landfills on egg volume was mediated by negative density-dependent mechanisms probably related to an increase in competition for food. This article is protected by copyright. All rights reserved.
Swine Influenza Viruses – Evolution and Zoonotic Potential

Influenza A virus is a highly contagious disease in pigs and has been endemic in Danish pigs for more than 30 years, with H1N1 and H1N2 being the dominating subtypes. In Denmark, the import of live pigs is very limited and the country can therefore be considered as a closed population, providing the perfect opportunity for studying the evolution of swine influenza viruses. The purpose of this study was to investigate the genetic and antigenic evolution of the avian-like H1N1 and H1N2 subtypes found in Danish pigs during the last 10 years. Viruses from a total of 78 samples were isolated and the hemagglutinin and neuraminidase genes full length sequenced. Genetic analysis of H1 revealed an overall genetic identity of 89-100 %, but no chronological drift was revealed. For N1, the overall genetic identity was 89-99% and phylogeny resembled that of H1. Phylogenetic analysis of the N2 gene revealed an overall genetic identity of 88-100 % with two separate co-circulating clades. Surprisingly, estimation of most recent common ancestor of HA suggested the time of emergence for H1 to be around 1913-1919. Estimated selection pressures indicated that more purifying and less diversifying selection controlled the H1 evolution. For antigenic characterization, 58 of the viruses were tested in hemagglutination inhibition tests (HI) against a panel of representative reference sera. Analysis by antigenic cartography showed that most H1s clustered together, regardless of the subtype and year of isolation, with few outliers. These outliers were mainly within the H1N2 subtype and many of these were found to possess mutations at the receptor binding site 225. In conclusion, this study provides an important contribution to the complex epidemiology of circulating swine influenza viruses.
Ecological niche features override biological traits and taxonomic relatedness as predictors of occupancy and abundance in lake littoral macroinvertebrates

The degree to which species ecological and biological traits determine their distribution and abundance has intrigued ecologists for a long time, and it has seen a revival in recent years. This topic is important because it provides information about the determinants of species rarity and their conservation implications. We examined the effects of niche breadth, niche position, biological traits and taxonomic relatedness on the interspecific occupancy–abundance relationship, as well as on occupancy and abundance, in lake littoral macroinvertebrates. We sampled 48 lakes in a boreal lake district, found altogether 155 species, and calculated regional occupancy (as the proportion of sites occupied) and local abundance (as mean abundance at occupied sites) for each species. We determined niche position and niche breadth for each species using the outlying mean index analysis. Also, we calculated trait vectors and taxonomic vectors describing species trait similarity and taxonomic relatedness, respectively, using principal coordinates analysis. We found a strong positive occupancy–abundance relationship that was mostly explained by among‐species variation in niche position, followed by niche breadth. Instead, trait vectors and taxonomic vectors tended to be less important in affecting occupancy and abundance than the niche features. Our results strongly suggest that niche position, a measure of habitat availability for littoral macroinvertebrates, is the chief determinant of their occupancy and abundance. This finding has important implications for ecology and conservation of species, as species with marginal niche position, a reflection of low habitat availability, are both regionally rare and locally uncommon. Such species may face double jeopardy if environmental conditions change and affect their preferred marginal habitat types.
Optimization of Conditions for Protease Production from Aspergillus niger under Solid State Fermentation

The main objective of this study was to optimize the conditions for protease production by Aspergillus niger under solid state fermentation using locally available agricultural substrates. Fifty one fungal isolates were recovered from different sources. The isolates have shown typical A. niger characteristics and they were screened for the production of protease enzyme. Screening was done qualitatively using the Agar Plate Assay and the isolates that gave the widest hydrolysis zone diameters were quantitatively screened in submerged culture using the shake flask method. A.niger isolate that showed the highest production value in the shake flask assay was tested for protease production potential in solid state fermentation using five different agro-waste substrates moistened either with water or with a salt solution. The culture conditions that affect production capacity were then investigated. Results showed that 30 of the fungal isolates have shown typical A.niger characteristics. Of these, 16 have shown clear zones of casein hydrolysis on skimmed milk agar. The maximum activity of the produced protease (15.42U/ml) was recorded for isolate NAF6ii while the minimum (6.45U/ml) was recorded for isolate NAF7i. Therefore, A.niger isolate NAF6ii has been selected for production of protease by solid state fermentation using the five agro-materials as substrates. NAF6ii recorded the maximum protease activity (12.60U/ml) when Mesquite (Prosopis juliflora) fruit powder has been moisturized either with salt solution or with water (11.46U/ml). Results also showed that the optimum conditions for protease enzyme production were: 3.0% of spores’ inoculum (16.80U/ml), pH 7.0 (18.19U/ml), 5.0% of NH4NO3 as a nitrogen source (13.28U/ml), 3.0% of fructose as a carbon source (11.38U/ml) during 96hrs incubation period. These results indicate the potentiality of this fungus as a source for protease production. In addition, the proteases produced from the treatment of local agro-waste could be used in a variety of industrial applications.
Contribution of the Na/Ca Exchanger to Rapid Ca Release in Cardiomyocytes

ABSTRACT Trigger Ca 21 is considered to be the Ca current through the L-type Ca 21 channel (LTCC) that causes releaseof Ca 21 from the sarcoplasmic reticulum. However, cell contraction also occurs in the absence of the LTCC current ( I Ca ). In thisarticle, we investigate the contribution of the Na 1 /Ca 2 exchanger (NCX) to the trigger Ca . Experimental data from ratcardiomyocytes using confocal microscopy indicating that inhibition of reverse mode Na 1 /Ca 2 exchange delays the Catransient by 3–4 ms served as a basis for the mathematical model. A detailed computational model of the dyadic cleft (fuzzyspace) is presented where the diffusion of both Na 1 and Ca 2 is taken into account. Ionic channels are included at discretelocations, making it possible to study the effect of channel position and colocalization. The simulations indicate that if a Na 1 channel is present in the fuzzy space, the NCX is able to bring enough Ca 21 into the cell to affect the timing of release.However, this critically depends on channel placement and local diffusion properties. With fuzzy space diffusion in the order offour orders of magnitude lower than in water, triggering through LTCC alone was up to 5 ms slower than with the presence ofaNa
ON HOW WE CAN NON-CANONICALLY INCREASE HEREDITARY DROUGHT RESISTANCE IN PLANTS (BY AN EXAMPLE OF CEREALS)

Improvement of hereditary drought resistance in crops is recently being among the main objectives for food security of humanity because of global warming and the growing costs for bakery and forage grain. Analysis of complex properties of drought resistance in cereals (phenotyping) shows the limitations of a canonical genocentric approach and the approaches based on molecular genetics to solve the problem of significant hereditary improvement of drought resistance. The priority epigenetic approach that we propose is based on the theory of eco-genetic organization of quantitative traits (TEGOQT). In TEGOQT seven genetic-physiological systems (GPS) involved in harvest increasing, but not particular traits of productivity, are to be operated with. These GPS are attractions; micro-distribution of attractive plastic substances between grains and chaff in ear; adaptability to drought, cold, frost, heat, salt, etc; horizontal immunity; «payment» by dry biomass for a limitative factor of soil nutrition — N, P, K, etc; tolerance to plant density in phytocenosis; hereditary variability in duration of the phases of ontogenesis). In this paper we discuss drought adaptability as a part of GPS complex. It is shown that phenotyping evaluation is necessary to analyze drought tolerance, the complex property to which no less than 22 component characters contribute. This allows to construct a set of eco-genetic portraits (EGP) of parent plants at different types of drought simulated in an artificial climate control chamber. The EGP are histograms which reflect the values of all components of drought resistance for each parent thus allowing to select pairs complementary in the elements of the EGP. Based on a predictive EGP, it is possible to define, through mathematical models that reflect the contribution of each component to the resulting drought tolerance, the optimum combination of components for ensuring maximum positive additive effect, and thus to manage selection of the parents for hybridization in view to create new drought resistant varieties.
Linking species performance to community structure as affected by UV-B radiation: an attenuation experiment

UV-B radiation is known to affect plant physiology and growth rate in ways that can influence community species composition and structure. Nevertheless, comparatively little is known about how UV-B radiation induced changes in the performance of individual species cascades to affect overall community properties. Because foliage leaves are primarily responsible for photosynthesis and carbon gain and are the major organ that senses and responds to UV-B radiation, we hypothesized that, under reduced UV-B radiation, species with larger leaf areas per plant would manifest higher growth rates and hence tend to improve their community status compared to species with smaller leaf areas per plant in herbaceous plant communities. We tested this hypothesis by examining plant traits (leaf area per plant and plant height), plant growth rate (aboveground biomass per plant and plant biomass per area) and community status (species within-community relative biomass) for 19 common species in a two-year field experiment in an alpine meadow on Tibetan Plateau. Aboveground biomass per plant, as well as per area, progressively increased in a 39% reduced (relative to ambient) UV-B treatment during the experimental period. At the second year, 11 out of 19 species significantly or marginally significantly increased their plant height, leaf area per plant and aboveground biomass per plant. No species was negatively affected by reducing UV-B. As hypothesized, the increase in aboveground biomass per plant increased with increasing leaf area per plant, as indicated by cross-species regression analysis. Moreover, the change in species within-community status increased with increasing leaf area per plant. Our study demonstrates that UV-B radiation has differential effects on plant growth rate across species and hence significantly affects species composition and plant community structure. We suggest that UV-B radiation is an ecological factor structuring plant communities particularly in alpine and polar areas.
Anaphase A: Melting Microtubules Move Chromosomes toward Spindle Poles

The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms. Live cell fluorescence microscopy studies showed that poleward chromosome movement is associated with disassembly, or ‘melting’ of the kinetochore-attached microtubule fibers that link chromosomes to poles. Microtubule-marking techniques established that kinetochore-fiber disassembly often occurs through a ‘pac-man’ mechanism, where tubulin subunits are lost from kinetochore-attached plus ends and the kinetochore appears to consume its microtubule track as it moves poleward. In addition, kinetochore-fiber disassembly in many cells occurs partly through ‘flux’, where the microtubules flow continuously toward the poles and tubulin subunits are lost from minus ends. Molecular mechanistic models for how load-bearing attachments are maintained to disassembling microtubule ends, and how the forces are generated to drive pac-man and flux-based movements, are discussed.
Flora das cangas da Serra dos Carajás, Pará, Brasil: Portulacaceae

We present the floristic treatment for the species of Portulacaceae from the canga of the Serra dos Carajás, state of Pará, Brazil. One genus and two species were recorded: Portulaca oleracea and P. sedoides . Keys, descriptions, illustrations, photos, and comments are also provided.