Miracle-dz/UniFAR-FTUs huggingface dataset:
TARGET-DIRECTED BIOSYNTHETIC EVOLUTION: REDIRECTING PLANT EVOLUTION TO GENOMICALLY OPTIMIZE A PLANT’S PHARMACOLOGICAL PROFILE

OF DISSERTATION TARGET-DIRECTED BIOSYNTHETIC EVOLUTION: REDIRECTING PLANT EVOLUTION TO GENOMICALLY OPTIMIZE A PLANT’S PHARMACOLOGICAL PROFILE The dissertation describes a novel method for plant drug discovery based on mutation and selection of plant cells. Despite the industry focus on chemical synthesis, plants remain a source of potent and complex bioactive metabolites. Many of these have evolved as defensive compounds targeted on key proteins in the CNS of herbivorous insects, for example the insect dopamine transporter (DAT). Because of homology with the human DAT protein some of these metabolites have high abuse potential, but others may be valuable in treating drug dependence. This dissertation redirects the evolution of a native Lobelia species toward metabolites with greater activity at this therapeutic target, i.e. the human DAT. This was achieved by expressing the human DAT protein in transgenic plant cells and selecting gain-of-function mutants for survival on medium containing a neurotoxin that is accumulated by the human DAT. This created a sub-population of mutants with increased DAT inhibitory activity. Some of the active metabolites in these mutants are novel (i.e. not detectable in wildtype cells). Others are cytoprotective, and also protect DAergic neurons against the neurotoxin. This provides proof-of-concept for a novel plant drug discovery platform, which is applicable to many different therapeutic target proteins and plant species.
Molecular evolution of carotenoid biosynthesis from bacteria to plants

β-Carotene and derivatives are important pigments in plant photosynthesis. They are found not only in green plants but also accumulate in archea, prokaryotes and fungi. For β-carotene biosynthesis, enzymes are necessary to catalyse the formation of phytoene, several desaturation steps and cyclization reactions. This review is focused on the molecular phylogeny of the enzymes, the genes involved and their diversity. It outlines how genes and enzymes from prokaryotes and archea were modified to give rise to the corresponding plant constituents. In the cases of phytoene synthase, a direct line of evolution can be drawn. For other carotenogenic enzymes, new genes and enzymes have been acquired at certain stages of evolution. In addition, phytoene desaturases and lycopene cyclases are examples of convergent evolution of different types of enzymes, which are structurally completely unrelated but functionally identical. Finally, several gene duplications led to homologous enzymes with different catalytic functions including those involved in the synthesis of α-carotene.
Optimal use of SSRs for establishing genetic Relationships and variety identification in a collection of Sugarcane hybrids

Simple sequence repeat (SSR) analysis was carried out to assess genetic diversity and to establish genetic relatedness among sugarcane hybrids in a collection of 62 genotypes. Molecular data were also used to determine the discriminating power and utility of different SSR primers for sugarcane genotype identification and to find the optimal primer combination to ensure unambiguous identification. In 62 sugarcane hybrids, a total of 107 loci were detected with 13 SSR primers. The percentage of polymorphic loci was quite high (94%), with the NKS23, mSSCIR19 and NKS34 primers revealing the highest levels of polymorphism. The dissimilarity coefficients ranged from 0.064 to 0.68 with a mean of 0.46. The majority-rule consensus tree showed eight main clusters supported by more than 50% occurrences with several subgroups with the maximum bootstrap score (100%). A total of 315 banding patterns were detected. Discrimination power analysis revealed that the efficiency of a given primer does not depend only on the number of bands or the banding pattern but also on the frequency of differences between patterns generated by the primers. The primers NKS23 and mSSCIR19 generated patterns at the same frequency (isofrequencies) and have a maximal discriminating power. PIC values close to 1 (0.719 to 0.985) demonstrated that, in spite of the low number of primers, these SSR were sufficiently polymorphic, discriminating, and informative and will be useful in sugarcane variety registration and in genetic identity tests.
Planothidium lagerheimii comb. nov. (Bacillariophyta, Achnanthales) a forgotten diatom from South America

A new combination in the genus Planothidium is proposed. The identity of Planothidium lagerheimii (Cleve) C.E. Wetzel & Ector comb. nov. (≡ Cocconeis lagerheimii Cleve), from South America is revisited. This rather common species often reported from freshwater and aerial environments was identified in previous studies either as Cocconeis rudis Frenguelli or Planothidium salvadorianum (Hust.) Lange-Bert. (≡ Achnanthes salvadoriana Hust.). After having measured the original images and based on photographs gathered in the literature we concluded that the three species, Cocconeis lagerheimii , Cocconeis rudis and Achnanthes salvadoriana , belong to the same taxon. Following the International Code of Nomencalture the correct name is the earliest legitimate one with the same rank. Thus the species having priority should be Cleve’s species described in 1894. Freshwater material from southern Brazil was investigated to illustrate ultrastructural details.
ECOLOGICAL CHARACTER DISPLACEMENT

A theoretical study is made of the conditions under which competition mediated by a quantitative character in each of two species will result in the convergence or divergence of the mean values of the character. Both within— and between—species competition are considered and a general model of the genetical basis of the character is used. Both the genetical and ecological parts of the model are based on the biological assumptions that are made in discussions of ecological character displacement, which include the assumptions that there are no constraints on the evolution of the character in either species and that individuals in each species with the same value of the character use the limiting resources in the same way. One of the main results is that the usual biological assumptions do not necessarily lead to permanent and significant displacement (i.e., d/w > 1). While some previous models have led to different conclusions, it is shown that those results are due to other, implicit, assumptions in those models. In the present model, two types of conditions lead to significant character displacement under biologically reasonable assumptions. One type of condition, which would apply to species that are roughly equally abundant at equilibrium, is that there be some differences in the set of limiting resources of the two species. In that case, the equilibrium displacement would be much larger than the differences between the resource spectra. Small and possibly unmeasurable differences between species could lead to significant displacements. The other type of resource distribution that leads to significant displacements is a skewed distribution. This requires no differences between the resource spectra for the two species but it leads to an equilibrium in which one of the species is much more abundant than the other. One consequence of these results is that the relative abundances of two species thought to have undergone character displacement are important to understand the possible mechanism leading to that displacement.
Revision of Iphimediidae and similar families (Amphipoda : Gammaridea)

— The amphipod families Acanthonotozomatidae, Amathillopsidae, Astryidae, Epimeriidae (=Paramphithoidae), Iphimediidae, Ochlesidae and Stilipedidae are rediagnosed and three new families, Acanthonotozomellidae, Dikwidae, and Odiidae are described. New keys distinguish these families; other similar families, Lafystiidae and Laphystiopsidae are diagnosed and included in the keys. In the process of rediagnosing the Ochlesidae Stebbing, 1910 (see Coleman & Barnard 1991a), as a family distinct from Iphimediidae, we determined that other alterations to the taxonomy of the Iphimediidae and Epimeriidae were necessary. Our contribution here offers a different division than used in the past based on characters not previously used or inconsistently used to define these groups. For example, we found relatively good consistency of characters on incisors, rakers, gnathopods and coxae in proposing this new division of the
Interclutch Variation in Sex Ratios Produced at Pivotal Temperature in the Red-eared Slider, a Turtle With Temperature-dependent Sex Determination

Abstract Many reptiles exhibit temperature-dependent sex determination (TSD) in which the incubation temperature of the egg determines the sex of the embryo. The purpose of the current study was to examine intraspecific variation in temperature sensitivity during TSD. Two aspects of temperature sensitivity were evaluated in the Red-Eared Slider, Trachemys scripta: (1) clutch-specific variation in sex ratios produced at pivotal temperature and (2) variation in clutch sex ratios produced over the nesting season (e.g., early nesting season, midnesting season, late nesting season). Relatively large numbers of clutch sex ratios were examined from two or three time periods (e.g., early nesting season, midnesting season, late nesting season), during each of three nesting seasons. The results indicate that pivotal temperatures vary significantly among clutches, with clutch sex ratios ranging from all male to all female when incubated near the putative pivotal temperature. The results on seasonal variation in clutch sex ratios were more ambiguous. Data from two of the nesting seasons do not reveal significant variation between time periods. During the third nesting season, sex ratios from the first two time periods were not significantly different from one another, but the sex ratios from the very end of the nesting season were significantly different from those of the two earlier time periods. In summary, the results reveal a clutch-specific variation in pivotal temperatures, but the results from the seasonal study of sex ratios did not consistently reveal a shift in sex ratios over each nesting season.
Phylogenetic position of Lycodon gongshan Vogel and Luo, 2011, a snake endemic to China (Reptilia: Colubridae)

Lycodon gongshanVogel and Luo, 2011 is a newly described snake species that is endemic to southwestern China. Based on two mtDNA gene fragments and two nuclear genes, a molecular phylogeny for the genus Lycodonwas reconstructed and the systematic position of L. gongshanwas evaluated. The results revealed that L. gongshanformed a strongly supported monophyletic clade with L. fasciatus, and ( L. cavernicolus + L. butleri), although the relationships among them were unresolved. The close genetic relationship between L. gongshanand L. fasciatusis consistent with hypotheses based on morphological data. Additionally two specimens from Guangdong, previously identified as L. fasciatus, showed a sister relationship with L. liuchengchaoiwith low genetic difference, indicating that the two specimens were misidentified, and illustrating that L. liuchengchaoimay have much broader distribution than previous thought.
EVALUATION OF COTTONSEED MEAL AS PARTIAL ANI) COMPLETE REPLACEMENT OF FISII MEAL IN PRACTICAL DIETS OF NILE TILAPIA, OREOCHROMIS NILOTICUS (BOULENGER) FINGERLINGS

he main objectives of this study was to determine the effect of partial and total replacement of fish meal by cotton seed meal in practical diets of Nile tilapia fingerlings on growth performance, feed utilization, body composition and some biological measurements of Nile tilapia, Oreochromis niloticus (L.). Fish of an average weight 18.1 ± 0.2 g were stocked in 15 glass aquariums (80 l each) at a rate of 15 fish per aquarium. Fish meal (40 % of the diet) was used as the sole source of animal protein in the control diet. Percent replacement of fish meal by cottonseed meal on the basis of crude protein were as follows: 0 % (control diet A), 25 % (diet B), 50 % (diet C), 75 % (diet D) and 100 % (diet E). Diets were fed to fish at a rate of 4 %, then gradually reduced to 3 % of the total fish biomass daily, for a period of 14 weeks. The results of this study revealed that, the fish fed diet B had significantly (P ≤ 0.01) best average body weight, average body length, specific growth rate (SGR), weight gain %, feed conversion ratio (FCR), and protein efficiency ratio (PER) from those of fish fed control diet A and all other diets. The same parameters of fish fed diet C were not significantly different (P > 0.05) from those of fish fed the control diet A. Condition factor (K), hepatosomatic index (HSI) and survival rate % of the fish fed
A dynamic similarity hypothesis for the gaits of quadrupedal mammals

The dynamic similarity hypothesis postulates that different mammals move in a dynamically similar fashion whenever they travel at speeds that give them equal values of a dimensionless parameter, the Froude number. Thus, given information about one species, it could be possible to predict for others relationships between size, speed and features of gait such as stride length, duty factor, the phase relationships of the feet and the patterns of force exerted on the ground. Data for a diverse sample of mammals have been used to test the hypothesis. It is found to be tenable in many cases when comparisons are confined to quadrupedal mammals of the type described by Jenkins (1971) as “cursorial”. Most mammals of mass greater than 5 kg are of this type. Although the hypothesis applies less successfully to comparisons between cursorial and non-cursorial mammals it is shown to be a reasonable approximation even for such comparisons and for comparisons between quadrupedal mammals and bipedal mammals and birds.
Isolation, identification, and sequence analysis of rDNA-ITS of Pythium species sampled from rhizosphere soil of corn.

Pythium spp.were isolated from the rhizosphere soils of corn sampled from Honggu and Qilihe districts of Lanzhou using a baiting method.Twenty three isolates were obtained after subculture and purification.Based on the morphology,culture characteristics,growth rate,adaptation to temperatures and sequence analysis of rDNA-ITS,the 23 isolates were all identified as P.scleroteichum,P.ultimum or Pythium sp.This is the first report of P.scleroteichum in China and of P.ultimum from corn in Gansu.P.ultimum was the dominant population of the three species(60.9% of the isolations),while Pythium sp. (26.1%) was second,and,P.scleroteichum(13.0%) was third.
VARIABILITY OF MUSKRAT SKULLS: MEASUREMENT ERROR, ENVIRONMENTAL MODIFICATION AND SIZE ALLOMETRY

The biometrical consequences of measurement error, environmental effects caused by habitat quality, and effects of allometry transformation were studied in 22 morphometric traits of the skull of the muskrat, Ondatra zibethicus. Analyses were conducted at a regional level using four Finnish muskrat populations living 85-750 km apart, and at a local level using five subpopulations living 2-9 km apart in one Finnish lake. Only spring samples of animals born in the previous summer were used (n = 508), but sexes were pooled because they were not found to differ in variability. Reduced variability was found in traits connected with feeding. In larger variables the coefficient of variation (CV) was moderately negatively correlated with the mean, but in the smallest measurements the variability increased sharply. The dependence of the CV on the mean of the trait, thus, is hyperbolic. Corrected variabilities for each trait were calculated as the residuals from this function. Measurement error was estimated by repeated measurings of the same skulls, using two methods differing in accuracy. The proportion of measurement error in the CV varied from 3 to 23%, if measuring accuracy was 0.1 mm, and from 13 to 45%, if accuracy was only 0.5 mm (mean of the variables ranged from 4 to 63 mm). The proportion of measurement error in the CV increased with a decreasing mean value of the trait, but this cannot alone explain the great variability in the small traits. Environmental effects on variability were studied by grouping animals on the basis of their condition, classified by a growth index that measured body-weight gain per unit of molar wear. Improvement in animal condition decreased general morphological variability. We concluded that habitat quality, especially poor diet, was the main stress factor increasing variation, and specimens with the poorest condition were particularly exposed to this effect. In order to examine and compare allometric relationships. on both a local and regional scale, each variable was divided by condylobasal length of the skull (CL; calculated by subtraction in log scale). If the corrected variability of a trait was lower or equal to that of CL, the transformation often induced a negative correlation with general size. In comparisons between local subpopulations, the effect of this bias was not serious: the allometric transformation reduced size differences that depend on habitat quality. If the correlation structure of the data was more heterogeneous, as in regional data, the transformation produced partly confusing results in univariate and principal component analyses, but discriminant function analysis was not seriously affected. (Morphometrics; measurement error; environmental modi- fication; allometry transformation; variance components; principal components; muskrat.)
Leaf traits and litter flammability: evidence for non‐additive mixture effects in a temperate forest

1. Although it is recognized that plant species vary in their flammability, we currently lack a mechanistic understanding of how plant traits influence fire and how litter mixtures behave in a fire. As modified fire regimes and climate change shift the species composition of communities, a mechanistic perspective is especially important to understand and predict fire in potentially novel plant communities. This work addresses three questions: (i) How do eight species common in Sierra Nevada mixed‐conifer forest differ in their litter flammability? (ii) What leaf traits are associated with various flammability components? and (iii) Do individual species measurements predict multi‐species combinations, or are there non‐additive effects?
A Comparison of Selected Quality and Compositional Characteristics of Brown and White Shell Eggs II. Interior Quality

Abstract This paper compares interior quality measurements from three brown and three white shell commercial layer strains. Eggs were obtained during twelve 28-day production periods. Forty-eight eggs were randomly selected from each of the six strains during the last week of each period. Individual interior quality measurements were then taken. Significant differences were found in Haugh units, albumen indexes, and albumen pH measurements for the two color groups. The overall means for Haugh units were 85.11 and 81.92, for albumen indexes . 1027 and . 0938, and albumen pH 7.98 and 8.04 for the brown and white shell eggs, respectively. Yolk indexes for the shell color groups were . 504 for brown shell eggs and . 509 for white shell eggs and did not differ significantly.
Antibacterial and synergistic effects of Nardostachytis rhizoma extracts on methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious clinical problem worldwide. Few new drugs are available against MRSA, because it has the ability to acquire resistance to most antibiotics which consequently increases the cost of medication. In the present study, the antibacterial activity of Nardostachytis rhizoma was investigated. The most effective method is to develop antibiotics from the natural products without having any toxic or side effects. Therefore, there is a need to develop alternative antimicrobial drugs for the treatment of infectious diseases. The use of two drugs in combination is a good alternative to slow the process of developing drug resistance and to restore the effectiveness of drugs that are no longer prescribed. Combination therapy is the most commonly recommended empirical treatment for bacterial infections in intensive care units, where monotherapy may not be effective against all potential pathogens, and for preventing the emergence of resistant. Five clinical isolates (MRSA) were obtained from five different patients at Wonkwang University Hospital (Iksan, South Korea). The other two strains were S. aureus ATCC 33591 (methicillin-resistant strain) and S. aureus ATCC 25923 (methicillin-susceptible strain). Antibacterial activity (minimal inhibitory concentrations, MICs) was determined by broth dilution method, disc diffusion method, MTT test and checkerboard dilution test. Antimicrobial activity of n-hexane fraction of N. rhizoma was significant. Against the seven strains, the disc diffusion test was in the range of 14 to 18 mm and had a MICs ranging from 31.25 to 125 ig/ml. FICI values for n-hexane fraction (HFL) of N. rhizome + ampicillin (AM) and HFL + oxacillin (OX) were 0.1875 and 0.078125-0.09375, showing the increase of synergistic effect. When combined together, these antibiotic effects were dramatically increased. These effective combinations could be new promising agents in the management of MRSA and MSSA. Key words : Nardostachytis rhizoma, synergism, antibacterial, methicillin-resistant Staphylococcus aureus (MRSA).
Tracing the genetic origin of brown trout ( Salmo trutta ) re-colonizing the Ecker reservoir in the Harz National Park, Germany

for comparison ‐ from two areas downstream of the dam being physically isolated for about 70 years. Genetic variability within populations (average number of alleles per locus), genetic differentiation between populations ( FST values and genetic distances), occurrence of certain alleles and results of assignment tests indicated that the Ecker reservoir was re-colonized from two sources: the Grose Peseke, a small direct inflow into the reservoir, and the Fuhler Lohnsbach, a parallel flowing brook connected to the reservoir by a pipe. Genetic data also supported recolonization of the main tributary from the reservoir but not in the opposite direction. Moreover, bottleneck effects were evident in brown trout populations upstream of the dam compared to the two populations downstream of the dam.
Expression and evaluation of a 24-kDa recombinant protein of the N-terminal E2 glycoprotein of chikungunya virus

Chikungunya is an acute febrile illness caused by chikungunya virus (CHIKV). In this study, a short 24-kDa N-terminal of E2 glycoprotein of chikungunya virus was cloned and expressed in E.coli expression system. The E2 recombinant proteinwas expressed as a fusion protein to 6-Histidine for ease of purification. The expression of the 24-kDa recombinant protein was detected by SDS-PAGE and the protein reactivity was evaluated by western blot analysis. The immunogenicity of the 24 kDa proteinwas further tested against human positive and negative sera for chikungunya and dengue. The results showed that the recombinant antigen was able to detect CHIKV positive sera and no cross reactivity was observed with dengue virus positive serum.