Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico Driven Metabolic Engineering Towards Enhancing Biofuel and Biochemical Production

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non-edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle of mass balance driving the analysis. In this dissertation, two industrially relevant organisms were examined for their potential to produce biofuels. First, Saccharomyces cerevisiae was used to create biodiesel in the form of fatty acid ethyl esters (FAEEs) through expression of a heterologous acyl-transferase enzyme. Several genetic manipulations of lipid metabolic and / or degradation pathways were rationally chosen to enhance FAEE production, and then culture conditions were modified to enhance FAEE production further. The results were used to identify the rate-limiting step in FAEE production, and provide insight to further optimization of FAEE production. Next, Clostridium thermocellum, a cellulolytic thermophile with great potential for consolidated bioprocessing but a weakly understood metabolism, was investigated for enhanced ethanol production. To accomplish the analysis, two models were
Impact of Hessian fly, Mayetiola destructor, on Developmental Aspects of Hard Red Winter Wheat in Kansas

Abstract. The Hessian fly, Mayetiola destructor (Say), has historically been a major pest of wheat, Triticum aestivum L. , in Kansas. Resistant cultivars are used to protect seedling wheat plants from damage by Hessian fly larvae in the fall. However, it is not known if the cultivars are resistant after winter vernalization. Experiments in a greenhouse indicated that ‘Armour', a cultivar considered intermediately resistant, remained resistant under low levels of infestation by Hessian fly, but kernel weight was significantly reduced by a mean of 0.13 g per spike when Hessian flies were abundant. In the field, Armour was not resistant post-vernalization, with infested plants having culm heights reduced by an average of 14.2 cm and kernel weight reduced by 0.10 g per spike compared to noninfested plants. In addition, infested plants had significantly fewer spikelets per spike, and fewer kernels per spike. ‘Duster', a cultivar considered very resistant, was resistant to Hessian fly larvae in the greenhouse and the field, and even produced significantly heavier kernels when Hessian flies were abundant in the greenhouse. Infestation of susceptible cultivar ‘Fuller' in the greenhouse and field resulted in culm heights reduced by up to a mean of 11.2 cm per spike as well as significantly fewer kernels per spikelet. Kernel weight was significantly reduced by a mean of over 0.1 g per spike in both the greenhouse and the field. The results suggested that all cultivars resistant to Hessian fly should be evaluated after vernalization to determine if each continued to be resistant into the spring. Little information is available on if and how feeding by Hessian fly larvae on more mature hard red winter wheat (Feekes 7 to 10) after vernalization impacts plants, aside from lodging. Growers are aware when Hessian fly larvae kill seedlings or cause plants lodging, but small and significant, although less dramatic, yield loss might occur undetected.
Amino acid profile of broiler chickens meat fed diets supplemented with bee pollen and propolis

The objective of this study was to evaluate the effects of diets supplemented with bee pollen and propolis on the amino acid (AA) profile of chicken meat. A total of 360 one day-old Ross 308 broiler chicks were randomly assigned to three treatments: a basal diet without supplementation as control (C); a basal diet supplemented with bee pollen extract (400 mg kg−1 of feed mixture: E1); and a basal diet supplemented with propolis extract (400 mg kg−1 of feed mixture: E2). Chickens were slaughtered at 42 d of age. After slaughter, the AA profile of breast and thigh samples was determined. The data were analyzed using analysis of variance. The AA profile was not affected by dietary bee pollen supplementation (E1) in breast and thigh muscles (disregarding sex), except for higher concentration of Tyr (p ≤ 0.05) in breast and lower concentration of Pro (p > 0.05) in breast and thigh muscles compared with those in C. However, the AA profile was improved in response to propolis supplementation (E2). In breast muscle (disregarding sex), the highest concentrations of Glu (11.81 g 100 g−1), Gly (3.5 g 100 g−1), and Tyr (4.12 g 100 g−1) were found in the propolis-supplemented group (E2), Glu and Tyr were higher (p ≤ 0.05) in E2 compared with those in C, while Gly was higher (p ≤ 0.05) in E2 compared to E1. Additionally, many other AAs (Asp, Ser, Ala, Tyr, Arg, Thr, Ile, Leu, Phe, and Lys) were observed as the highest (p > 0.05) in breast muscle of broilers fed a diet with propolis extract (E2). In thigh muscle (disregarding sex), higher concentrations (p ≤ 0.05) of Tyr (2.46 g 100 g−1) and His (2.35 g 100 g−1) were found in the propolis-supplemented group (E2) compared with those in C. Many other AAs (Glu, Gly, His, Arg, Thr, Val, Ile, Leu, and Lys) in thigh muscle from propolis-supplemented group (E2) were also higher (p > 0.05) than those in the other groups. After bee pollen (E1) and propolis (E2) supplementation, no differences in amino acid concentrations between males and females, or in breast or thigh muscle were found. In general, breast was demonstrated to contain higher proportions of AAs than thigh muscle. In conclusion, dietary propolis supplementation in amount of 400 mg kg−1 of feed mixture elicited the best AA profile of chicken meat among the dietary treatments and may thus be a promising method to improve meat quality.
Performance of Beef Heifers Grazing Stockpiled Endophyte-infected, Endophyte-free or Non-toxic Endophyte-infected Tall Fescue

OLIPHANT, ERINN JOYCE. Performance of beef heifers grazing stockpiled endophyte-infected, endophyte-free or non-toxic endophyte-infected tall fescue. (Under the direction of Dr. Matthew H. Poore). A two-year grazing study was conducted from December to February of 20022003 and 2003-2004. The objective of this study was to evaluate animal performance and agronomic persistence of non-toxic endophyte-infected (EN) fescue in comparison to endophyte-infected (E+) and endophyte-free (E-) tall fescue in a stockpiling system. Forty-eight (year one) and 60 (year two) Angus-cross heifers were grazed on one of three treatments for 70 days in year one and 86 days in year two. Plots were established in the fall of 1999 and averaged 1.01 ha. All plots were clipped in August and fertilized in September with 94.9 kg/ha (year one) and 84.2 kg/ha (year two) nitrogen from 30% liquid urea/ammonium nitrate. From August forward the forage was allowed to accumulate until the initiation of the study in December. Each day heifers were given a fresh allotment of forage through use of a stripgrazing management system. Digestibility of the forage did not differ by treatment (P = 0.51) but was higher in year one than in year two (IVTDMD 80% year one, 65% year two; P < 0.01). Crude protein tended to be greater in year one (10.9%) than in year two (9.74%; P = 0.08). Average daily gain (ADG) did not differ by treatment (P > 0.21) and was higher on pasture during year two than year one (0.48 kg/d vs. 0.40 kg/d, respectively; P = 0.03; SE ± 0.053). Final body condition scores (BCS) were higher in year one (5.25 E+, 5.26 E-, 5.14 EN) than in year two (5.06 E+, 4.98 E-, 4.96 EN; P = 0.01; SE ± 0.049). Serum urea nitrogen (SUN) did not differ by treatment (P = 0.77) but there was a significant
Biochemical composition of stored pigeon pea (Cajanus cajan L) in relation to bruchid damage

Etude du comportement des grains conserves pendant un an dans des recipients divers (bois, acier, terre), a des temperatures et degres d'hygrometrie variables. L'infestation par Callosobrochus chinensis est plus importante dans les recipients en terre. On note une hydrolyse de l'amidon en sucres reducteurs, une augmentation des teneurs en fibres et en proteines brutes mais une diminution de la valeur nutritive apres un an de stockage
Nutritional profile and yield of oyster mushroom cultivated on selected agricultural wastes

Research on mushroom production and products is gaining more grounds globally and in particular Nigeria. This study was carried out to determine nutritional relationship between the substrate used for cultivation and the fruiting body on each of the substrates. Agro-wastes, namely: palm ( Elaeis guineensis ) fruit shaft, plantain ( Musa paradisiaca ) leaves, sawdust and kenaf ( Hibiscus cannabinus ) stem, were assessed for suitability as substrates for cultivation of oyster mushroom ( Pleurotus floridanus Singer). The spawn of the mushroom was used to inoculate each of the substrates, using a complete randomised design, with five replicates for each substrate. Results showed that all the substrates supported mycelia growth and development of fruiting bodies of the fungus. There were significant differences (P<0.05) among substrates in terms of number of days to complete mycelia run, with the least recorded in palm fruit shaft (25.20), and the highest in kenaf (32.40). Total yield also differed significantly (P<0.05), with the highest in palm fruit shaft (51.4 g 100 g -1 ) and lowest in plantain leaves (6.0 g 100 g -1 ). There was also significant difference (P<0.05) in the nutritional content of fruiting bodies, the highest fat content being on plantain leaves (1.72 g 100 g -1 ) and the lowest on palm fruit shaft (0.55 g 100 g-1). The trend was similar for mushroom substrates, plantain leaves having (2.55 g 100 g-1) and palm fruit shaft, (0.41g 100 g -1 ). Starch content for fruiting bodies was highest on sawdust (5.31 g 100 g -1 ) and lowest on kenaf (2.66 g 100 g -1 ), while for mushroom substrates, kenaf was (0.33g 100 g -1 ) and palm fruit shaft was (4.45g 100 g -1 ). There was a positive correlation (r = 0.24) between the nutrient of fruiting bodies and that of the substrate on which it was cultivated. Key Words: Kenaf, nutrient composition, mushroom fruiting body, mushroom substrate, Pleurotus floridanus
Patterns of variation in Lathyrus sativus and some related species

The main objective of the present work is to broaden our knowledge on grass pea germplasm. 280 entries mainly represented by L. sativus, L. cicera, L. ochrus have been included in this study. Eighteen quantitative and qualitative descriptors were observed. Quantitative data together with qualitative information were subject to multivariate statistical procedures. The analysis of the principal components on quantitative traits was carried out to study the total variation of the entries under test. To summarise between-species variation and to get information in accordance with the classification of each entry, a canonical discriminant analysis was applied. Descriptive statistics for 8 quantitative traits relative to the investigated species are reported. Frequency distributions for 8 qualitative traits have also been considered. The species L. ochrus showed earliness, tallest plants, smallest seeds, lowest 100-seed weight and more secds/pod; late flowering, late maturity, shortest plants and intermediate values for the other traits were observed for L. cicera. Biggest seeds and highest 100-seed weight have characterised the L. sativus entries. The presence of high diversity within the L. sativus (primary gene pool) and L. cicera (secondary gene pool) confirms the use of both species as a valuable source of genetic material for grass pea improvement.
Development and nutritional evaluation of antioxidant rich products of bottle gourd (Lagenaria siceraria) incorporating inulin and their impact on hypercholesterolemic subjects

Ten value added products namely missi roti, ghia kheer, ghia balls, idli, raita, chutney, dal, biscuits and extruded products were developed using bottle gourd and inulin for hypercholesterolemic males. The products were standardized using different levels of bottle gourd and inulin. The products were found to be acceptable at different levels i.e. missi roti at 35% level, kheer at 75% level, idli at 45% level, raita at 50% level, chutney at 30% level, ghia balls at 65% level and dal at 80% level of fresh bottle gourd whereas biscuits and extruded snacks were acceptable at 7.5% level and 5% level of bottle gourd powder respectively. Incorporation of inulin was acceptable in all the developed products at 5 per cent level. The bottle gourd was subjected to five different thermal treatments i.e. boiling, steaming, pressure cooking, microwaving and sautéing. Raw, thermally treated bottle gourd and developed products were analyzed for nutritional composition. Steaming was found the best method for the retention of antioxidant content. Nutritional analysis of all the accepted products was found to be high in vitamin C, total phenolics content, total flavonoid content, antioxidant activity and low in fat. Ninety at risk hypercholesterolemic volunteer male subjects were selected and equally divided into three groups i.e. control group I, experimental group II and III for feeding trial. The subjects of the group II and III were supplemented with bottle gourd powder and inulin for a period of three months. A significant reduction (p≤0.05) in the energy, carbohydrates and fat intake and an increase in protein and fiber intake was observed in the experimental groups. After supplementation, BMI, MUAC and TSFT was reduced significantly in the subjects of group II and III as compared to group I. Serum total cholesterol, triglycerides, LDL-C in the group II and III were significantly (p≤0.01) reduced after the supplementation. An impressive increase in HDL-C by 2.14 and 4.50 percent was observed in group II and III respectively. A significant increase in serum retinol, ascorbic acid and glutathione peroxidase was observed in the experimental groups after supplementation. It was observed that improved results in anthropometry and biochemical profile were obtained in group III followed by group II. It is thus concluded that supplementation of bottle gourd and inulin along with nutrition counselling significantly improved the lipid profile and antioxidant status of hypercholesterolemic subjects.
Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts

Understanding variation in rates of speciation and extinction – both among lineages and through time – is critical to the testing of many hypotheses about macroevolutionary processes. Bayesian Analysis of Macroevolutionary Mixtures (BAMM) is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an analysis. The consequences of this ‘model prior’ for inference are poorly known but could potentially influence both the probability of accepting models that are more (high error rate) or less (low power) complex than the generating model. The hierarchical Poisson process prior in BAMM reduces to a simple geometric distribution on number of rate shifts, and we use this property to increase the efficiency of model selection with Bayes factors. Using BAMM v2.5, we analysed phylogenies simulated with and without diversification heterogeneity across a broad range of prior parameterizations. We also assessed the impact of the model prior on MCMC convergence times and on diversification rate estimates. For all simulation scenarios, model evidence (Bayes factor support) for the number of shifts is not sensitive to the choice of model prior over the wide range examined here. The best‐supported model found using BAMM rarely includes spurious shifts (<2% of all runs) when diversification models are selected using Bayes factors. BAMM was reliably able to infer the true number of diversification rate shifts across prior expectations that varied by three orders of magnitude. However, we find a strong effect of model prior on MCMC convergence properties: a flatter prior distribution (larger expected number of shifts) can dramatically increase the efficiency of the MCMC simulation. Our results support the use of a liberal model prior in BAMM, as it reduces computation time without distorting the evidence for rate heterogeneity.
Reproductive biology of Impatiens coelotropis Fisher, a critically endangered balsam from the Southern Western Ghats

A study of floral phenology, pollination biology and breeding system of Impatiens coelotropis Fischer, an endemic and endangered balsam of Western Ghats was carried out in wild conditions. The flowers are beautifully coloured and open in the night between 2130 and 2330 h. Anther dehisced one day before flower opening, which confirmed the protandrous condition. Flowers offer pollen and nectar to the visitors, which include predominantly honeybees, hawk moths, butterflies, etc. It reproduces by means of cross-pollination. Manual pollinations revealed that the species permits only xenogamous pollination. The percentage of fruit set in manually pollinated flowers is higher than that resulting from open pollination. Its high altitude habitat, narrow environmental niche, fragmentation of population, poor fruit set, low percentage of seed germination and floral damage caused by the insects could be the reasons for its limited distribution in the wild.
Habitat assessment for ecosystem services in South Africa

ABSTRACT Biodiversity is the foundation of life-support systems on earth and underpins the delivery of ecosystem services (ES) important for human well-being. The loss of biodiversity worldwide, however, remains one of the most daunting challenges. Among the major causes of biodiversity loss is habitat loss due to transformation of land to agricultural, mining and urban areas. We applied the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) biodiversity modelling tool to assess the condition of habitats to support the delivery of ES in a biosphere reserve (BR) in South Africa. Results indicated that 72% of the surveyed habitats were of high quality to provide the necessary services. However, some of the habitats were found to be affected by threats as follows: low (0–20%) to moderate (20–32%) habitat loss was recorded in habitats adjacent to mining and plantation areas, and high (32–56%) to severe (56–95%) habitat loss was recorded in habitats in close proximity to urban and cultivated areas. At least 56% of the vegetation types found in the study area were threatened by transformation to agriculture, mining and urban areas. We strongly recommend that existing biodiversity policies and legislation should be enforced to avoid habitat loss and degradation.
Studies on the induced breeding and post-larval rearing of shing (Heteropneustes fossilis Bloch)

An experiment was conducted on induced breeding and fry rearing of shing, Heteropneustes fossilis (Bloch) in the Department of Aquaculture, Bangladesh Agricultural University for a period of four months from April to July 1994. Hatching rate was calculated at 21.50h and was found to be 45 to 55 % and the survival rate of larvae was 30 to 40 % at 26 to 29°C. Survival rate and growth rate of post larvae were found to be 50 to 60% and 96.6 to 117.2% respectively. Feed-3 (F3) showed the highest survival rate and growth rate of post larvae.
Comparison of the chromosome banding patterns in three species of social voles (Microtus irani karamani, M. schidlovskii, M. anatolicus) from Turkey

Atilla ARSLAN*, Kubilay TOYRAN, Serdar GÖZÜTOK, Tarkan YORULMAZ, Jan ZIMA Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey Department of Biology, Faculty of Science and Arts, Bitlis Eren University, Bitlis, Turkey Department of Wildlife and Ecology, Faculty of Agriculture and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı, Turkey Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Genetic architecture of seed yield and its components in winter oilseed rape (Brassica napus L.) grown under limiting nitrogen condition

The increase of rapeseed (Brassica napus L.) oil production to answer the demand for human consumption and industrial applications requires the optimisation of seed yield in a context of reduction of inputs, including the nitrogen fertilization. Genetic approaches are a way to respond to this challenge. Indeed, determining the genomic regions (QTLs) and mechanisms controlling seed yield components under nitrogen limitation is a prerequisite for plant breeding programs. In this context, the scientific questions raised in this thesis are: i) what is the genetic architecture of seed yield components in rapeseed grown under limiting nitrogen condition? ii) how do the QTLs interact with the environment, and especially with the nitrogen stress? , and iii) how the combination of agronomic, genetic and genomic information can lead to the improvement of traits of interest in rapeseed? A strategy of QTL detection by linkage and linkage disequilibrium analyses was set up on two biparental populations and a winter oilseed rape diversity set. Those populations were trialled in seven location and six growing seasons (2009-2014) under low and sufficient nitrogen conditions. For each trial, seven seed yield-related traits were acquired. Few genotype × nitrogen condition interactions were detected and an important number of QTLs were common to the two nitrogen regimes. On the contrary, strong genotype × environment interactions were evidenced for most of the traits under study and the majority of the QTLs were location-specific. Ten critical genomic regions for yield associated traits stable through the environments and populations were identified and their structural organization in the rapeseed genome was investigated. The genetic control of oil content was then studied by combining the information from ten independent reports, the genomic information provided by the recent release of the B. napus genome and the haplotype variations among a winter oilseed rape population within one particular region identified on the A1 chromosome.