Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Therapies for Spinal Muscular Atrophy Using Gene Therapy and Nanotechnology

Spinal muscular atrophy (SMA) is a genetic disease which is characterized by muscle weakness and atrophy. The disease arises from mutations in the survival motor neuron 1 (SMN1) gene causing degeneration of spinal cord motor neurons. No effective treatment is currently available for SMA however it may be possible to treat the disease using gene therapy. The aim of this project is to develop potential therapies for SMA by investigating different viral and non-viral gene therapy vectors and assessing the effect of potential disease modifying genes. The data collected are described under four chapters as follows: 1: The aim here was to develop a novel approach based on polymer nanoparticles (polymersomes) for gene delivery. Encapsulation of DNA by polymersomes was optimised and polymersomes were used to restore SMN levels into a fibroblast cell line isolated from a child with severe SMA. 2: The ability of adeno-associated virus serotype 5 (AAV5) vectors expressing GFP to transduce the central nervous system (CNS) following intravenous injection was tested in neonatal wild-type mice. Overall transduction efficiency of AAV5-GFP in the brain was low and very few lumbar spinal cord neurons were found to be transduced, suggesting that AAV5 is not an appropriate vector to treat diseases such as SMA. 3: AAV6 was used to overexpress hnRNP R in an in vivo model of SMA. hnRNP R is a candidate disease modifying gene for SMA due to its interaction with SMN and β-actin. However this strategy had only a very marginal effect on the phenotype and life-span of this SMA mouse model. 4: Finally AAV9 was used to silence phosphatase and tensin homolog (PTEN) in an in vivo model of SMA. PTEN is a negative regulator of growth which acts on the PI3K/Akt pathway. AAV9-mediated PTEN silencing resulted in a significant increase in the lifespan of a SMA mouse model coupled with an improved phenotype. In conclusion this work highlights two major findings: i) polymersomes can be used to deliver SMN plasmid DNA to restore SMN mRNA and protein levels in an in vitro model of SMA; ii) AAV9-mediated silencing of PTEN can improve the phenotype and increase lifespan of a SMA mouse model.
Boat harbour design can exacerbate hull fouling

Hull fouling is a major cost for owners of small vessels and an important pathway for the spread of non-indigenous aquatic species. The extent of fouling depends on a hull's susceptibility to recruitment by aquatic organisms and the local availability of competent planktonic propagules (‘propagule pressure’). Management strategies have typically been concerned with increasing resistance of the hull to recruitment through the use of toxic paints. Here we tested the hypothesis that fouling is influenced by the design of the harbour in which the boat is moored. We compared recruitment of sessile invertebrates to available surfaces in two types of recreational boat harbours: marinas that were partially enclosed by a permanent breakwall, and marinas that lacked breakwalls. Recruitment in the marinas was compared to coastal reference sites that were not used for mooring. At each location, recruitment tiles were deployed for 4 weeks on four separate occasions over a period of 2 years. Measurements of current velocities and spatial patterns of water flow at each location showed that permanent breakwalls created complex patterns of circulation that retained water within the marina basin for up to 12 h d−1. Despite large regional and temporal variability in fouling over time, most organisms recruited in greatest numbers to surfaces in partially enclosed marinas, and were often several orders of magnitude more abundant in the enclosed marinas than in unenclosed marinas or coastal reference locations. Harbour design has an important influence on the rate at which fouling organisms recruit to available surfaces within marinas. Entrainment of water in enclosed marinas may limit the dispersal of planktonic propagules by advective currents but effectively increases propagule pressure to available surfaces, including resident boat hulls. This is likely to accelerate the development of hull-fouling assemblages and increase the chances of transport of non-indigenous species that establish populations in the harbour basin.
DENSITIES OF HELIOTHIS VIRESCENS AND HELICOVERPA ZEA (LEPIDOPTERA: NOCTUIDAE) IN THREE PLANT HOSTS

Large numbers of field-collected tobacco budworms Heliothis virescens L. , and/or bollworms Helicoverpa zea (Boddie) (heliothines) might be difficult to obtain depending upon host plants available to the insects. Of the >95 cultivated and wild plants that have been identified as their hosts, some are highly attractive to these insects, some are also widely available and of those, some could be used to collect large numbers of both insect species. However, the reliability of these plants in space and time in providing abundant samples of larvae and/or moths is not well understood. We studied naturally-occurring heliothine populations over a 3-year period in 2 different geographic locations in plots of garbanzo bean ( Cicer arietinum L.), upland cotton ( Gossipium hirsutum L.), and velvetleaf ( Abutilon theophrasti Medikus) finding that garbanzo bean produced significantly higher numbers of tobacco budworm and bollworm larvae and adults as compared to the other 2 plant species. Tobacco budworm larvae were found in at least 1 host plant (primarily garbanzo) all the years in both locations while bollworm larvae were not. Field moth emergence represented ≤ 10% of its larval densities and abiotic factors made a difference on moth emergence between years. When large numbers of both insects are needed for field or laboratory studies, garbanzo bean offers a clear advantage over cotton or velvetleaf to obtain collections of heliothines.
Thermal ecology and physiology of an intertidal predator-prey system: Pisaster ochraceus and Mytilus californianus

We present a Dynamic Energy Budget (DEB) model for the quintessential keystone predator, the rocky-intertidal sea star Pisaster ochraceus. Based on first principles, DEB theory is used to illuminate underlying physiologic al processes (maintenance, growth, development, and reproduction), thus providing a fr amework to predict individual-level responses to environmental change. We parameterize d the model for P. ochraceus using both data from the literature and experiments condu cted specifically for the DEB framework. We devoted special attention to the mod el’s capacity to (1) describe growth trajectories at different life-stages, including pe lagic larval and post-metamorphic phases, (2) simulate shrinkage when prey availability is in ufficient to meet maintenance requirements, and (3) deal with the combined effect s of changing body temperature and food supply. We further validated the model using a independent growth data set. Using standard statistics to compare model outputs with real data (e.g. Mean Absolute Percent Error, MAPE) we demonstrated that the model is capable of tracking P. ochraceus’ growth in length at different life-stages (larvae : MAPE=12.27%; post_____________ 3 Monaco, CJ, Wethey, DS, and Helmuth. 2013. PLoS ONE. 9(8): e104658. Reprinted here with permission of publisher.
Phylogenetic relationships between isolated populations of the limestone‐dwelling microsnail Gyliotrachela hungerfordiana (Gastropoda: Vertiginidae)

The vertiginid species Gyliotrachela hungerfordiana, an obligate limestone-dwelling microsnail, is relatively widespread and is found on a large number of isolated limestone hills in Peninsular Malaysia. To elucidate the pattern of colonization of these hills, we conducted a molecular phylogenetic analysis on G. hungerfordiana subpopulations from 15 separate limestone outcrops. As outgroups, we also included five related Peninsular Malaysian Vertiginidae (Gyliotrachela frequens, Gyliotrachela transitans, Gyliotrachela salpinx, Gyliotrachela depressispira and Paraboysidia tarutao), one population each. A combined analysis of nuclear (internal transcribed spacer 1) and mitochondrial (cytochrome c oxidase 1) sequences showed that (1) G. hungerfordiana is monophyletic; (2) there is a clear geographical pattern in the phylogenetic relationships between G. hungerfordiana populations, with genetic distances increasing with geographic distance; (3) this pattern is disturbed by a few long-distance (north-west to south-east and north to south) colonizations. Resumen La especie Gyliotrachela hungerfordiana de la familia Vertiginidae, un micromolusco que vive obligatoriamente en piedras calizas, tiene una distribucion relativamente amplia y puede ser hallada en un gran numero de colinas de piedra caliza aisladas en la peninsula de Malasia. Para dilucidar el patron de colonizacion de la especie en estas colinas, realizamos un analisis filogenetico molecular de 15 sub-poblaciones de G. hungerfordiana separadas por afloramientos de piedra caliza. Como grupos externos, tambien incluimos una poblacion para cada una de las cinco especies (G. frequens, G. transitans, G. salpinx, G. depressispira y Paraboysidia tarutao) de la familia Vertiginidae de la peninsula de Malasia relacionados con G. hungerfordiana. El analisis combinado de secuencias nucleares (Internal Transcribed Spacer 1; ITS-1) y mitocondriales (Cytochrome C Oxidase 1; COI) mostro lo siguiente: (1) G. hungerfordiana es monofiletica; (2) existe un patron geografico claro de las relaciones filogeneticas entre las poblaciones de G. hungerfordiana, con un incremento de las distancias geneticas a mayor distancia geografica; (3) el patron anterior es interrumpido por algunas colonizaciones de larga distancia (noroeste a sureste y de norte a sur).
Artificial insemination and early embryonic development of the mangrove crab Perisesarma bidens (De Haan) (Crustacea: Brachyura).

The aim of this study was to explore a technique of artificial insemination and document the early embryonic development of the mangrove sesarmid crab Perisesarma bidens (De Haan). Observations were made on fertilization of the eggs of this crab by artificial insemination up to hatching under laboratory conditions. The female extruded the eggs into the abdominal cavity 24-48 h after copulation. Unfertilized eggs were collected from the pleopods of the female immediately after laying and were stored in 80% filtered sea water (FSW). Sperm were removed from the spermatheca of the same female and diluted in 80% FSW. The unfertilized eggs and sperm were shaken well in a glass beaker for artificial insemination. The eggs were rinsed 3-5 times with 80% FSW after 5 min of mixing of sperm with ova. Eggs were incubated in 100 ml flat cylindrical culture bottles containing 70 ml of 80% FSW at 25°C in a water bath. The fertilization membrane was observed 3-5 min after insemination. The other 2 outer layers of fertilized eggs were also observed 8-10 min after insemination. The internal yolk of the egg is the major source of nutrition for developing embryos. An average of 65% of fertilized eggs hatched as 1st zoeae after 17 d of incubation. It is therefore feasible to produce embryos by artificial insemination during the peak breeding season from May to Sept. This is the first report of early embryonic development from fertilization to larval hatching of P bidens by artificial insemination.
Allergénicité des Granules Cytoplasmiques de Pollen

Le pollen des Graminees est l'un des principaux vecteurs d'allergenes. Il contribue a l'apparition des allergies respiratoires comme l'asthme et la rhinite allergique. En contact avec l'eau de pluie ou des polluants atmospheriques, le pollen peut liberer des microparticules (<5 ! m) dites granules cytoplasmiques de pollen. A cause de leur taille, ces granules peuvent penetrer plus profondement dans l'appareil respiratoire que le pollen entier et induire ainsi des reactions allergiques. L'objectif de ce travail est de caracteriser l'allergenicite de ces granules selon 3 volets : epidemiologique, experimental et analytique. Les resultats de l'etude epidemiologique mettent evidence un effet eventuel des granules dans la survenue des allergies respiratoires, et plus particulierement de l'asthme. Dans la partie experimentale, les resultats obtenus permettent de montrer que les granules induisent des reactions allergiques, humorales et cellulaires ainsi que des reponses inflammatoires, comparables au pollen entier, chez le rat Brown Norway, le modele animal d'allergie ici utilise. Enfin, la partie analytique permet de conclure que l'allergenicite des granules depend a la fois de leur contenu en allergenes hydrosolubles et non-hydrosolubles.
Identification of Distinct Regions of 5′ Flanking DNA That Mediate Constitutive, IFN-γ, STAT1, and TGF-β-Regulated Expression of the Class II Transactivator Gene

Class II transactivator (CIITA) is a master regulator required for constitutive and IFN-γ-inducible expression of class II MHC genes. Although the role of CIITA is greatly appreciated, the mechanisms underlying constitutive and IFN-γ-induced expression of CIITA are not understood. The study of CIITA induction is extremely important, but has been fraught with difficulty. This study describes for the first time a large (7-kb) fragment of 5′ flanking sequences that mediates the B cell-specific, IFN-γ-induced, and TGF-β-suppressed expression of CIITA. This pattern of expression matches the authentic expression of the endogenous gene. Within the 7-kb fragment, sequences that lie between nucleotides −545 and −113 relative to the transcriptional start site are critical for constitutive promoter expression in B cells. In contrast, inducible activation of CIITA by IFN-γ requires sequences contained in an additional 4 kb of upstream DNA. This region mediates an IFN-γ response when linked to either the endogenous CIITA promoter or a heterologous promoter. A role for STAT1 in regulation of the CIITA promoter is shown by the rescue of IFN-γ induction by expression of STAT1 in STAT1-defective U3A cells. TGF-β significantly inhibits IFN-γ-mediated induction of the CIITA promoter in 2fTGH fibroblasts, which indicates that the promoter is a target for TGF-β. This inhibition is achieved by suppression of the basal promoter. This study provides a focal point for understanding the mechanism of B cell-specific, IFN-γ-induced, and TGF-β-suppressed expression of CIITA.
La cabra Blanca de Rasquera: caracterización morfológica y faneróptica

espanolEl objetivo de este trabajo fue caracterizar morfologicamente la Cabra Blanca de Rasquera, un caprino autoctono del sur de Catalunya. Para ello se utilizaron un total de 242 animales (173 hembras y 69 machos) distribuidos entre las 12 ultimas explotaciones de este caprino. Se analizaron 14 variables cualitativas, 26 variables cuantitativas y 7 indices derivados. La Cabra Blanca de Rasquera es de tipo mediolineo, eumetrico (alzada a la cruz en hembras de 71,92 ± 3,70 cm), de perfil fronto-nasal recto a subconvexo y de capa mayoritariamente policromada en negro sobre fondo blanco (79,7% en machos y 64% en hembras) o blanca uniforme (11,6% en machos y 18,6% en hembras). Tambien es caracteristica una gran variabilidad en la forma de los cuernos, destacando el tipo prisca (21,7% en machos y 45% en hembras) y el tipo en rueda (28,1% en machos y 63,3% en hembras). Presenta un marcado dimorfismo sexual, observandose gran variabilidad morfologica intra-sexo. No obstante, tanto en machos como en hembras se confirmo la existencia de 3 subpoblaciones morfometricamente diferen-ciables en funcion de los principales territorios de pastoreo EnglishThis work was aimed to characterize phenotipically the Blanca de Rasquera goat, an autochthonous breed located in the southern area of Catalonia. For this purpose, 242 animals (173 females and 69 males) from the last 12 remaining exploitations of this breed were used, monitoring 14 qualitative and 26 quantitative variables, as well as 7 derived indexes. The Blanca de Rasquera goat breed is medium-lined, middle-sized (71.92 ± 3.70 cm of height at withers on females), mainly straight-profiled and with dominance of black-spotted on a white background (79.7% on males and 64% on females) or solid white (11.6% on males and 18.6% on females) coat types. The horn shape is also characteristic, being the prisca type (21.7% on males and 45% on females) and the "wheel-shaped" type (28.1% on males and 63.3% on females) the most frequent ones. This goat breed also shows a strong sexual dimorphism, as well as remarkable morphostructural variability within genders. Nevertheless, the existence of 3 differentiated subpopulations has been confirmed according to the 3 main grazing areas
Potential protective effect of Nigella sativa crude oils towards fatty liver in rats

The main purpose of the present research was to study the protective effect of Nigella sativa crude oils (NCO) extracted from plain and g-irradiated seeds towards inflammatory fatty liver (steatohepatitis). The protective effect of the oils was tested during induction of inflammatory fatty liver in rats through feeding high fructose diet. Biochemical analyses including plasma lipids, tumor necrosis factor-a (TNF-a) and malondialdehyde (MDA) levels and liver fat and liver function tests were carried out to determine the efficiency of the oils. Results showed that fatty liver control group exhibited significant dyslipidemia, high plasma TNF-a and MDA along with significant high liver triglycerides and cholesterol and liver dysfunction compared to control normal. Oral administration of NCO produced significant improvement of all parameters. No significant change in all biochemical parameters was noticed when the group given g-irradiated NCO was compared with that given the plain oil. Lipid analysis by GC showed that linoleic and oleic where the most abundant fatty acids constituting NCO. Volatile oils’ contents were 0.1 wt% of NCO; p-cymene and thymoquinone being the major constituents. Administration of NCO from plain or g-irradiated seeds produced similar and significant, but not complete, prevention of inflammatory fatty liver. Practical applications: This investigation revealed that the crude oil of Nigella sativa seed may potentially be used as dietary supplement for prevention of inflammatory fatty liver. The study also showed thechemicalcomposition ofthefixedand volatileoilfractions oftheEgyptianN.sativaseedsthat may be useful for further studies.
INFLUENCE OF WATER MOVEMENT AND ROOT GROWTH ON THE DOWNWARD DISPERSION OF ROTYLENCHULUS RENIFORMIS

Moore, S. R. , K. S. Lawrence, F. J. Arriaga, C. H. Burmester, and E. van Santen. 2011. Influence of Water Movement and Root Growth on the Downward Dispersion of Rotylenchulus reniformis. Nematropica 41:75-81. The presence of Rotylenchulus reniformis below the plow layer can have negative effects on cotton production by restricting the uptake of water and nutrients by roots in the lower soil horizons. Two trials were established in 7.62-cm diameter by 75-cm deep soil cores to determine 1) the effect of water movement on vertical translocation of R. reniformis, and 2) the role of root growth in the downward migration of R. reniformis. The water movement study consisted of three treatments of simulated rainfall amounts, 25-mm, 76-mm, and 127-mm, and no rainfall. Water movement minimally affected the movement of R. reniformis through the soil profile. Nematodes were observed to a depth of 30-cm after the 25-mm rain event. Rotylenchulus reniformis was detected to a depth of 45-cm following 76-mm of rainfall and to the maximum sampling depth of 75-cm following 127-mm of rainfall. Cotton roots reached the maximum depth of 75-cm at 60 days after planting (DAP). Vermiform life stages reached 75-cm at 45 DAP. Females colonized roots to a depth of 62-cm at 90 DAP. Cotton roots were observed to exhibit less growth when the numbers of females embedded in the roots was the highest Moore, S. R. , K. S. Lawrence, F. J. Arriaga, C. H. Burmester, and E. van Santen. 2011. Influencia del movimiento del agua y el crecimiento de las raices sobre la dispersion vertical de Rotylenchulus reniformis. Nematropica 41:75-81. La presencia de Rotylenchulus reniformis por debajo de la capa arable puede tener consecuencias negativas sobre la produccion de algodon, al restringir la toma de agua y nutrientes en los horizontes inferiores del suelo. Se establecieron dos experimentos en secciones de suelo de 7.62 cm de diametro y 75 cm de profundidad para deteminar 1) el efecto del movimiento del agua sobre la translocacion vertical de R. reniformis, y 2) el papel del crecimiento de las raices en la migracion vertical de R. reniformis. El estudio del movimiento del agua consistio de tres tratamientos de cantidad de lluvia simulada, 25-mm, 76-mm, y 127-mm, y un control sin lluvia. El movimiento del agua afecto el movimiento de R. reniformis de manera minima a traves del perfil del suelo. Se observaron nematodos hasta una profundidad de 30 cm despues de una lluvia de 25 mm. Se detecto el nematodo hasta una profundidad de 45 cm despues de una lluvia de 76 mm, y hasta la profundidad maxima de muestreo (75 cm) despues de una lluvia de 127 mm. La raices de la planta de algodon alcanzaron una profundidad maxima de 75 cm a los 60 dias despues de la siembra (DDS). Los estados vermiformes se encontraron a 75 cm de profundidad a los 45 DDS. Las hembras colonizaron raices hasta una profundidad de 62 cm a los 90 DDS. Se observo menor crecimeinto de las raices de la planta de algodon cuando el numero de hembras en las raices fue mas alto.
Prediction of body weight from testicular and morphological characteristics in indigenous Mengali sheep of Pakistan using factor analysis scores in multiple linear regression analysis.

The objective of the investigation was to predict body weight (BW) from testicular and morphological characteristics of the indigenous Mengali Sheep in Balochistan, Pakistan. The characteristics recorded were: body weight (BW), testicular length (TL), scrotal length (SL), scrotal circumference (SC), body length (BL), withers height (WH) and heart girth (HG) of 107 indigenous Mengali sheep in age range of 12 to 48 months. Only multiple linear regression analysis fitting to the available data showed tendency to multicollinearity problem with VIF >10 and didn’t present optimal solutions. With the purpose of removing the multicollinearity problem and especially making more correct interpretation biologically, the data were exposed to a combination of Factor and Multiple Linear Regression analyses. The appropriateness of factor analysis for the current data was determined by using criteria such as Kaiser-Meyer Olkin (KMO) measure of sampling adequacy and Bartlett’s test of spherity. These criteria showed that the data were appropriate for the factor analysis, one of the multivariate statistical analysis techniques. Thereafter, the factor analysis was applied to explanatory variables in order to derive new-uncorrelated latent explanatory variables from the variables. In the factor analysis, three new latent variables whose eigenvalues were greater than one were considered as explanatory variable for multiple linear regression analysis. Results obviously illustrated that 79.1% of variation in body weight was effectively explained by these new latent explanatory variables. Consequently, if confirmed at genetic level, the testicular and body traits might provide a significant contribution in the genetic improvement of the body weight of the indigenous Mengali for sheep breeding. © 2012 Friends Science Publishers