Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenology, population structure and dynamics of Ringal Bamboo (Arundinaria falcata) in Nainital Hill of Central Himalaya

Des recherches ont ete menees sur la phenologie, la structure et la dynamique de la population d'-Arundinaria falcata Nees (Ringal) d'avril 1984 a avril 1985 a Kumaon dans les Himalayas. Les valeurs les plus elevees en ce qui concerne l'augmentation de la surface foliaire, l'augmentation du poids sec foliaire, le taux de croissance foliaire, celui des hauteurs des pousses et la surace foliaire specifique ont ete enregistrees respectivement en avril, novembre, avril, juillet et mars. La population a montre une structure en forme de pyramide inversee selon les dates de releves d'echantillons 92% de la natalite totale a eu lieu entre avril et aout. Toutefois, le taux maximum de mortalite a ete enregistre entre aout et decembre.
Genetic variation within and among brown hare (Lepus europaeus Pallas, 1778) populations in Serbia as inferred from microsatellites

Brief introduction: The European brown hare ( Lepus europaeus Pallas, 1778) is the only Lepus species that can be found in Serbia, and Balkan Peninsula where it represents an important game species. Previous analyses of brown hares in Serbia based on allozyme and mtDNA sequence variability revealed moderate genetic diversity and indicated possible population structuring in the region. The aim of this study is to detect population genetic diversity and structure in brown hares from Serbia using microsatellites. Material and Methods: A total number of 157 brown hares were collected from six different regions in Serbia and polymorphism of six microsatellite loci was analyzed. Following computer packages were used for the data analyses: ARLEQUINE, STRUCTURE, GENETIX, BOTTLENECK and NEWHYBRIDS. Results: A total number of 81 alleles at 6 loci were found. The highest number of alleles per locus was found at Lsa2 microsatellite loci (20), while the lowest number of alleles was present at loci Sat5 and Lsa3 (9), with an average of 7.86 alleles/locus in total sample. Different statistical approaches revealed that brown hare population from Serbia is structured into two genetic subunits (i.e., subpopulations). First subpopulation, named Northern-Central-Eastern (NCE) Serbia consists of five initially defined groups (Backa, Banat, Srem, Central Serbia and Eastern Serbia) while second subpopulation comprised of individuals from Western Serbia. Higher values of genetic diversity parameters were found in NCE Serbia subpopulation compared to Western Serbia subpopulation. Conclusion: Observed genetic differentiation should be considered in future brown hare management strategies, in order to preserve existing genetic diversity and to avoid further reduction of genetic variability in Western Serbia subpopulation or human mediated admixtures which can disturb present gene pools.
Sterol Composition of Blue Mussels Fed Algae and Effluent Diets from Finfish Culture

ABSTRACT Mussels are an excellent source of phytosterols, which have many health benefits including reduction of the level of cholesterol in the blood. This study examined free sterols in cultivated blue mussels obtained commercially and from laboratory feeding experiments. Mussels were fed algae or the effluent from cultured finfish for 6 mo, and others remained unfed for 10 wk. Mussels feeding on effluent is of interest for integrated multitrophic aquaculture. Fish waste-fed mussels had significantly higher cholesterol concentrations (710 mg/kg) compared with algae-fed mussels (409 mg/kg) and locally cultivated ones (321 mg/kg). Algae-fed mussels had significantly higher campesterol compared with locally cultivated and fish waste-fed mussels. In algae-fed mussels, 24-nordeydrocholesterol decreased significantly, and in fish waste-fed mussels, the concentration of 24-methylenecholesterol decreased significantly. In fish waste-fed mussels, the cholesterol proportion was 50.9% of total sterols and other beneficial sterols were 49.1%, whereas in algae-fed mussels, cholesterol was down to 36.7% and other sterols were 63.3%. In summary, fish waste-fed mussels had significantly higher cholesterol concentrations and proportions compared with locally cultivated and algaefed mussels, and algae-fed mussels had higher proportions of beneficial phytosterols than fish waste-fed mussels.
Higher Order Calcium-Dependent Protein Kinases (CPKs) Mutant Lines Elucidate Roles of CPKs within Abscisic Acid Signal Transduction in Arabidopsis and In Vivo Interactions of Calcium-Dependent Protein Kinases, CPK6 and CPK23, with PP2C Protein Phosphatases within Abscisic Acid Signaling

Stomata, present in the aerial epidermis of land plants, provide gateways for regulating carbon dioxide and water exchange between plants and the atmosphere. The stress- induced phytohormone abscisic acid (ABA) reduces transpirational water loss crucial for the fitness of plants by inducing stomatal closure. Cytosolic Ca²⁺ has been reported to play a major role in ABA-induced stomatal closure through Ca²⁺ sensors, such as Calcium Dependent Protein Kinases (CPKs). Plants lacking transcripts of CPK3 and CPK6 (cpk3cpk6) have shown impaired ABA- and Ca²⁺- induced stomatal closing. Double knockout mutants of CPK4 and CPK11 (cpk4cpk11) exhibit similar ABA-hyposensitive phenotypes in ABA-induced stomatal closing response as well as a reduced ABA response in seed germination and seedling growth. Single mutant cpk23, however, demonstrated increased sensitivity to ABA, indicating a possible negative regulatory role in ABA signaling for CPK23. To improve the understanding of these proteins and their functions, two quadruple mutant plant lines, cpk3cpk4cpk6cpk11 and cpk5cpk6cpk11cpk23, were established. In Chapter 1, the quadruple mutant lines are phenotypically characterized by examining a variety of ABA -dependent biological responses. Other proteins important in ABA-dependent stomatal responses are Protein Phosphatases 2C (PP2Cs). Group A PP2Cs are known negative regulators within the Ca²⁺-independent ABA signaling pathway; however, experimental evidence suggests other regulatory roles exist for PP2Cs within the Ca²⁺-dependent branch of this signaling network which includes CPKs. In Chapter 2, yeast two-hybrid system is used to evaluate whether PP2Cs interact with CPKs. Observed interactions can provide additional insight to these proteins' functions within the Ca²⁺-dependent ABA signaling
The complete mitochondria genome of Aldrichina grahami (Diptera: Calliphoridae)

Abstract Aldrichina grahami is a significant medical and forensic insect belonging to the family calliphoridae. In this study, we present the complete mitochondrial genome of A. grahami for the first time. The mitogenome was 14 903 bp in length, consisting of 22 transfer RNA genes, 2 ribosomal RNA genes and 13 protein-encoding genes. The overall base compositions of A, G, C and T were 39.14, 9.59, 13.65 and 37.62%, respectively. Phylogenetic analysis is conducted using 12 mitochondrial genomes from two families. The monophyletic branches of the phylogenetic tree reveal that the composition of the mitochondrial genome, particularly the gene lengths, is very similar to that of another Calliphoridae fly, C. vicina, but the interspecific variations between them was 5.4%, which could distinguish these two species explicitly. Phylogenetic analyses indicated that phylogenetic analysis of whole mt genome sequences resulted in much stronger support for the identification of A. grahami between other species. This article aimed to enrich the dipteran mitochondrial genomes and provides the complete mitochondrial genome and phylogenetic analyses of A. grahami for species identifications forensic purpose.
Characterisation of cycling tumour hypoxia with magnetic resonance imaging

Hypoxia is defined by a low oxygen concentration state in biological tissue, resulting from an imbalance between oxygen supply and demand. Greater understanding of hypoxia in tumours is essential, as it is associated with disease progression and resistance to therapy, leading therefore to a poorer prognosis. Tumour hypoxia can be classified into two types: chronic and cycling, and this thesis focuses on characterising cycling hypoxia in colorectal carcinoma tumours in mice. For that, magnetic resonance imaging (MRI) was used, as it provides a non-invasive method to dynamically map blood oxygenation changes due to the different magnetic properties of oxygenated and deoxygenated blood. The first approach to characterise cycling tumour hypoxia consisted of a longitudinal study in which the influence of the tumour size on the occurrence, frequency and amplitude of cycling events was investigated. These observations were complemented with tumour vascular properties, inferred from applied vasoactive gas challenges, with blood sampling assessments, and with histological assessments. The influence of systemic variations in blood oxygenation in cycling tumour hypoxia was demonstrated through simultaneous acquisition of MRI and blood oxygen saturation trends. In particular, the computational implementation of independent component analysis (ICA) allowed the identification of the tumour regions that were simultaneously suffering from systemic and tumour-specific effects, and revealed links to tumour pathophysiology. The effect of a therapy on cycling tumour hypoxia was also assessed under the hypothesis of a “vascular normalisation” effect of the drug. In addition, the effects of the therapy on gas challenge response and on histological distributions were studied. This dynamic MRI technique and the ICA protocol were ultimately adapted to a translational study, where cycling hypoxia was investigated as a biomarker for early detection of prostate tumours. Overall, this thesis revealed that the stage of the tumour development can influence some aspects related to cycling hypoxia, and that its occurrence has a contribution of local and systemic effects. Also, it drew attention to the regional effects a therapy can have in tumours and provided a starting point to assess cycling tumour hypoxia in the clinic.
Climate, pollution and grazing drive long‐term change in moorland habitats

Question Dwarf shrub moorland dominated by ericaceous plants is a distinctive, internationally important feature of northwest Europe, with its stronghold in Scotland. There have been major declines in its condition and extent. How has moorland composition changed within Scotland over the past ca. 35 yr and what is the role of climate change, pollution and grazing in driving these changes? Location Five hundred and forty locations across Scotland, UK. Methods We used a long-term resurvey approach to assess change across Scottish moorlands. We relocated plots sampled ca. 35 yr previously in alpine heath, dry heath, wet heath and bog, and recorded vegetation species composition. We assessed change in species group richness and cover and mean Ellenberg values between surveys, using paired t-tests. We used CCA with variation partitioning and regression analysis to analyse the vegetation data with spatial data sets on climate, pollution and grazing, to assess the role of each driver in driving vegetation changes. Results Significant diversity and compositional changes between surveys were found for all habitat types, particularly alpine heath. Significant associations were found with climate (many variables), pollution (N and S) and herbivore number (primarily deer). Species richness generally increased, but several specialist species declined in cover, especially those associated with higher altitude habitats (e.g. Arctostaphylos uva-ursi, Salix herbacea and alpine lichens). Many of the most successful species are ubiquitous, e.g. the widespread grazing- and pollution-tolerant graminoids Anthoxanthum odoratum, Juncus squarrosus, Festuca rubra and Nardus stricta and the generalist mosses Rhytidiadelphus squarrosus and Hylocomium splendens. Conclusions Diversity and composition of moorlands in Scotland have changed significantly over the ca. 35-yr period studied; the drivers of these changes are complex, with climate, pollution and grazing playing variable roles across habitats. The reduction in specialist species, homogenization of alpine heaths and declines in forb and lichen cover all represent negative changes in the biodiversity value of Scottish moorlands.
Improving Cotton Agronomics with Diverse Genomic Technologies

Improving Cotton Agronomics with Diverse Genomic Technologies Aaron Robert Sharp Department of Plant and Wildlife Sciences, BYU Master of Science Agronomic outcomes are the product of a plant’s genotype and its environment. Genomic technologies allow farmers and researchers new avenues to explore the genetic component of agriculture. These technologies can also enhance understanding of environmental effects. With a growing world population, a wide variety of tools will be necessary to increase the agronomic productivity. Here I use massively parallel, deep sequencing of RNA (RNA-Seq) to measure changes in cotton gene expression levels in response to a change in the plant’s surroundings caused by conservation tillage. Conservation tillage is an environmentally friendly, agricultural practice characterized by little or no inversion of the soil prior to planting. In addition to changes in cotton gene expression and biological pathway activity, I assay the transcriptional activity of microbial symbiotes living in and around the cotton roots. I found a large degree of similarity between cotton individuals in different treatments. However, under conventional disk tillage I did find significantly greater activity of cotton phosphatase and sulfate transport genes, as well as greater abundance of the microbes Candidatus Burkholderia brachynathoides and Arthrobacter species L77. This study also includes the use of high-throughput physical mapping of DNA to examine the genomic structure of a wild cotton species, Gossypium raimondii, which is closely related to the economically significant crop species Gossypium hirsutum. This technology characterizes genomic regions by assembling large input DNA molecules labeled at restriction enzyme recognition sites. I created an efficient algorithm and generated 812 whole-genome assemblies from two datasets. The best of these assemblies allowed us to detect 3,806 potential misassemblies in the current release of the G. raimondii genome sequence assembly.
Questionnaire and Intervention Study on Effects of Drinking Cows’ Milk at Breakfast on the Circadian Typology and Mental Health of Japanese Infants Aged 1 - 6 Years

This study examines relationship between drinking cows’ milk at breakfast and several mental and physical characteristics (the diurnal type, sleep habits and mental condition as anger, out of control of emotion, irritation and depression) of Japanese small children aged 1 - 6 years old. A questionnaire study and an intervention one were performed in this study. An integrated questionnaire was administered, in July 2014 to 1112 participants attending one of 10 nursery school and 1 kindergarten located in Kochi (33°N, 133°E), Japan, and 582 parents (mostly mothers) which answered it instead of children (rate of answer: 51.9%). Intervention was done to 111 children attending the kindergarten. Seventy six parents answered the questionnaire which was administered 3 months after the intervention days of 21 (rate of answer: 51.9%). There are two contents of intervention, one is the distribution of cows’ milk for 21 days to be drunk at breakfast and another is the distribution of leaflet entitled “Go to bed early! Get up early! and Take nutritionally rich breakfast and cows’ milk! ” just before the intervention. Just before the intervention, letter was distributed to 111 parents who were asked for their children to follow the contents of the leaflet and drink the cows’ milk distributed every day for the 21 days. Small children who drink cows’ milk at breakfast more than once per week and take nutritionally rich breakfast more than 4 times per week are more morning-typed than the other three groups in which children fit into one or none of the two issues of taking morning cows’ milk and rich breakfast (p p = 0.004). Also there was positive correlation between the implementation value for the 21 days and the diurnal type score 3 months later (r = 0.301, p = 0.018). Drinking cows’ milk at breakfast seems to be effective for small children to become more morning-typed through two sets of syntheses from tryptophan via serotonin into melatonin in the evening.
A technique for capturing northern bobwhite chicks

Lack of a technique to capture northern bobwhite (Colinus virginianus) chicks has hindered research on this life stage. Therefore, we developed a technique for capturing northern bobwhite chicks 3 directions. After the brooding adult was located, we erected a corral composed of screen-covered panels around the brood. Near sunrise, we removed vegetation and ground debris until the adult flushed and all chicks within the corral were captured. We then patagially marked chicks and released them near the radiomarked adult. Between 1997 and 2001, we captured 1,325 chicks from 224 broods. Of these 224 capture attempts, 71% captured all chicks, 17% captured some but not all chicks, and 13% were complete failures. Capture-success rate was independent of chick age, up to 12 days of age. An average of 7.3 (SE = 0.3) chicks were captured per attempt, with fewer chicks captured in older broods than younger broods. Chick loss due to the capture event was negligible. This technique may have utility for researchers studying brood ecology of northern bobwhite or other precocial birds.
Directed Tagging of the Arabidopsis FATTY ACID

The FATTYAClD ELONGATlONl (FAEl) gene of Arabidopsis is required for the synthesis of very long chain fatty acids in the seed. The product of the FAEl gene is presumed to be a condensing enzyme that extends the chain length of fatty acids from C18 to C20 and C22. We report here the cloning of FAE7 by directed transposon tagging with the maire element Activator (Ac). An unstable fael mutant was isolated in a line carrying Ac linked to the FAEl locus on chromosome 4. Cosegregation and reversion analyses established that the new mutant was tagged by Ac. A DNA fragment flanking Ac was cloned by inverse polymerase chain reaction and used to isolate FAEl genomic clones and a cDNA clone from a library made from immature siliques. The predicted amino acid sequence of the FAEl protein shares homology with those of other condensing enzymes (chalcone synthase, stilbene synthases, and p-ketoacyl-acyl carrier protein synthase lll), supporting the notion that FAE7 is the structural gene for a synthase or condensing enzyme. FAEl is expressed in developing seed, but not in leaves, as expected from the effect of the fael mutation on the fatty acid compositions of those tissues.
Sources of variation in production traits and phenotypic and genetic correlations among themselves in Gir cattle

The effects of period, season, sex of born and parity were examined on total lactation yield, lactation period and dry period of 301 Gir cows. The overall least-squares means were 1882.54′37,01 kg, 292.43′4.35 days and 137.94′4.04 days respectively. The effects of period, season, sex of calf and parity were all significant on lactation yield while on lactation period sex of calf had nonsignificant effect and all other factors had significant effect. Dry period was significantly affected only by sex of calf. The heritability estimates for lactation yield and dry period were low (0.06′0.04) while the lactation period was moderately heritable (0.28′0.02). The phenotype correlation of lactation yield with lactation period was positive and significant and with dry period it was negative and significant. The phenotypic correlation of lactation period with dry period was negative and significant. The genetic correlations of dry period with lactation yield and lactation period were significant and negative.
Phylogenetic identification of bacteria within kefir by both culture-dependent and culture-independent methods

A combination of culture-dependent and independent methods was used in an attempt to identify the bacteria present in kefir grains and kefir liquid. Culture-independent methods involved direct extraction of DNA by mechanical means from either grains or liquid, followed by PCR amplification and sequencing of 16S rRNA genes. Culture-dependent methods were performed by inoculating samples from both the kefir grains and the kefir liquid to solid media followed by incubation under either aerobic or anerobic conditions in order to selectively enrich aerobic and anaerobic bacteria. Pure cultures were isolated from enriched bacteria and their DNA was extracted for the amplification and sequencing of 16S rRNA genes. Results indicate that kefir grains had a different bacterial composition compared to the kefir liquid. While Lactobacillus kefiranofaciens, Lactobacillus kefiri,Enterococcus faecium and Acetobacter syzygii were found only in the kefir grains,Lactobacillus helveticus was found only in the kefir liquid. On the other hand, Lactococcus lactis subsp. lactis, Leuconostoc mesenteroides and Acetobacter lovaniensis were found to be present in both the grains and the liquid. To the best of our knowledge, this work is the first to report the presence of A.lovaniensis, A. syzygii and Enterococcus faecium in kefir. Key words: Kefir, 16S rRNA gene analysis, bacterial ecology.
Life history tradeoffs, incubation behavior and conservation of horned larks (Eremophila alpestris)

ii TABLE OF CONTENTS.iv LIST OF TABLES.vii LIST OF FIGURES.viii LIST OF PHOTOS.x ACKNOWLEDGEMENTS.xi DEDICATION.xiii CO-AUTHORSHIP STATEMENT.xiv CHAPTER 1: GENERAL INTRODUCTION AND THESIS OVERVIEW.1 Thesis Objectives.4 Study Species.4 Study Area.6 Thesis Overview.7 References.14 CHAPTER 2: LIFE HISTORY TRADEOFFS IN TWO SUBSPECIES OF HORNED LARK ACROSS A LATITUDINAL AND ELEVATIONAL GRADIENT.18 Introduction.18 Methods.22 Study site and study species.22 Data collection. 22 Demographic rates of horned larks. 24 Data Analysis.27 Results.29 Discussion.33 Acknowledgements.46
Construction and practice of experimental course for integrative life science curriculum

Experimental course for integrative life science curriculum is designed for medical students, which integrates basic knowledge and skills of cellular biology, biochemistry, genetics, molec- ular biology, molecular genetics, and immunology disciplines. Tongji University School of Medicine start- ed to implement integration-based new curriculum system since 2010. This article discussed on teaching philosophy, teaching content, teaching methods, teaching team construction and explored the effect and significance of experimental course for integrative life science curriculum. Key words: Life science; Experimental course; Teaching reform
Habitat restriction in Mammillaria pectinifera

This study deals with the habitat restriction of Mammillaria pectinifera, a threatened cactus species, con- fined to a few low density localities of the Tehuacin valley in tropical Mexico. We analysed the patterns of presence/ab- sence of M. pectinifera in relation to the presence/absence of 48 other plant species, and the variation of environmental factors in 120 sampling plots. A Principal Components Analy- sis revealed a clear segregation between plots with and with- out individuals of M. pectinifera. A classification analysis resulted in four groups: two with low prevalence and two with high prevalence of M. pectinifera. Paired comparisons be- tween plots with and without M. pectinifera allowed the characterization of its patterns of occurrence related to the variation of environmental factors. M. pectinifera was found on deep alkaline soils with relatively high surface stoniness and high water retention capacity, showing low species rich- ness compared with plots where it was absent. The limited distribution of M. pectinifera in the Tehuacin Valley seems to be related to particular requirements of this species, being restricted to certain suitable habitat patches. Nevertheless, it is likely that other aspects, such as poor dispersal and establish- ment abilities, or biotic interactions could be associated with the observed patterns.