Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterizations of aquatic nitrogen-cycling bacterial communities

Investigations into the structure of aquatic bacterial communities involved in nitrogen cycling are necessary for the understanding and management of the systems in which they occur, as well as for their potential impact on global nitrogen dynamics. In aquatic systems, nitrogen moves from organism to organism via the dissolved nitrogen pool or by direct ingestion of biomass. At some point available nitrogen can be lost from a system. The loss of fixed nitrogen in aquatic systems occurs through physical removal or biogeochemical removal. It is the analysis of the bacterial communities responsible for the biogeochemical loss of fixed nitrogen that is the focus of this dissertation. In this study, DNA-based molecular methods are employed to investigate the occurrence and distribution of nitrogen cycling bacterial genes that code for enzymes involved in nitrification and denitrification. Initially, the ammonia-oxidizing bacterial community associated with finfish aquaculture in southern China is examined using TRFLP and principal component analysis and correlations are drawn using various dissolved nitrogen species. These anaylses indicate that the ammonia oxidizing bacterial community is altered in water samples taken above the sediment below the fish cages. Next, the presence and phylogenetic distribution of nitrite reductase ( nirK) gene sequences closely related to those recently found in marine ammonia-oxidizing isolates is examined in DNA extracted from an activated sludge wastewater treatment plant. Primers designed in this study from the ammonia oxidizer nirK sequences specifically amplify sequences that are very closely related to ones from which they were designed. These sequences are not closely related to known heterotrophic denitrifier nitrite reductase sequences and probably represent novel ammonia-oxidizer nirK genes. Finally, current prokaryotic in situ PCR methodology is improved upon and applied to the study of the microscale distribution of bacteria containing heterotrophic denitrification genes in activated sludge flocs. Nitrite reductase and nitrous oxide genes are amplified and detected inside intact bacterial cells. Additionally, an initial attempt at performing a simultaneous taxonomic and functional i situ identification is reported.
Melatonin and thermal stress regulate differential expression of heat shock proteins and melatonin receptors in spleen of mice

Cellular defence by expression of heat shock proteins (Hsps) against stress stimulation is the most universal phenomenon in stress physiology. Melatonin is well known as an anti-stress molecule possessing hypothermic effects. It protects cells and tissues in stressed conditions. Individually, Hsp70 and melatonin shows its functional ability in stressed organisms as well as in immune functions. The aim of the present study was to determine the interaction of melatonin receptors (MT1/MT2) in exogenous melatonin modulated expression of heat shock proteins (Hsp70/Hsc70) in spleen of thermally stressed male mice. Results of the study showed thermal stress significantly increased the Hsp70/Hsc70 and melatonin receptor MT2 expression in spleen of mice. The administration of melatonin significantly increased Hsp70 expression, but decreased Hsc70 expression. Both MT1/MT2 receptor expressions increased after melatonin treatment, whereas thermal stress to melatonin treated mice showed decrease in MT1/MT2 receptor expression than the only melatonin treated mice. MT2 receptor is responding in all experimental conditions corresponding to changes in Hsp70 protein expression. Therefore, the present study might suggest that MT2 receptor is interacting in coordination of melatonin mediated heat shock proteins expression in mice spleen after thermally stressed conditions.
Phytoplankton functional groups in a tropical reservoir in the Brazilian semiarid region

Phytoplankton functional groups structure and species abundance vary according to environmental conditions. The present study investigated the natural and anthropogenic stressors that affect phytoplankton functional group biomass in a Brazilian semiarid region reservoir (Argemiro de Figueiredo reservoir). Sampling occurred between August 2007 and July 2009 on a bi-monthly basis for the first year, and in a monthly basis for the last two years. There were three collection points (PC: river confluence; PNC: near the cages; PD: dam site). The water environment analysis of abiotic variables included: temperature, transparency, coefficient of vertical light attenuation, dissolved oxygen, pH, electrical conductivity, alkalinity, dissolved inorganic nitrogen, and reactive soluble phosphorus. Phytoplankton samples were collected into a Van Dorn bottle, and were then preserved in acetic lugol and were quantified using an inverted microscope to determine phytoplankton density and biomass; the identified species were assembled in functional groups. The data were explored by canonical correspondence analysis. Individual analyses were made to test the temporal and spatial variability of the data and the factors that interfered most with the biotic and abiotic variables. Functional groups S1, SN, and K, consisting of filamentous Planktothrix agardhii (Gomont) Anagnostidis & Komarek, Cylindrospermopsis raciborskii (Woloszynska) Seenaya & Subba Raju, and the coccoid Aphanocapsa incerta (Lemmermann) Cronberg & Komarek, respectively, dominated the dry months when the water was warm, turbid, and alkaline. The overflow reservoir served as a natural disturbance reducing the phytoplankton biomass to less than 50 % and the dominance of cyanobacteria, promoting the domain of functional groups F, M, MP, Lo, and X2. The nutrient inputs from intensive fish farming, associated with a low local depth (Z max = 7.7 m) close to the cages (PNC), resulted in a significant human disturbance that increased the prevalence of functional groups S1, SN, and K, which are composed primarily of cyanobacteria. We concluded that, in reservoirs, overflow events are natural disturbances that have the ability to reduce phytoplankton biomass and alter the structure of local communities, and that intensive fish farming is an anthropogenic disturbance that increases the availability of nutrients and stimulates an increase in biomass of the functional groups that include cyanobacteria. Furthermore, the functional groups of phytoplankton were reliable control of environmental conditions in the reservoirs of tropical semiarid regions.
Genetic structure and diversity of western flower thrips, Frankliniella occidentalis in a French bean agroecosystem of Kenya

Western flower thrips (WFT) (Frankliniella occidentalis) is an introduced pest that harms French bean production in Kenya and other countries. Since new WFT management approaches are being developed, a closer look at the genetic makeup of WFT populations can give new insights into source habitats, crop colonization patterns or host plant preferences, which are prerequisites for integrated pest management (IPM) strategies. For this purpose, we used six microsatellite loci to analyse the genetic structure, diversity and gene flow of WFT sampled on French beans, intercrops and weeds in Kenyan French bean production areas. The results of this preliminary study indicate that the available microsatellites are sufficiently polymorphic for more detailed analyses on local dispersal patterns of WFT in Kenya. Even with the limited data set, the results reveal that F. occidentalis populations show considerable genetic differentiation between host plant species but not between regions, which suggests reduced gene flow and a possible development of biotypes. Possible consequences of the results on IPM are discussed.
In Vitro Regeneration of Shoots From Nodal Explants of Dendrobium Chrysotoxum Lindl

Abstract Transverse sections (2 mm thickness) of stem-nodes from in vitro raised seedlings had morphogenic potential on semisolid and liquid Murashige and Skoog medium supplemented with cytokinins N6-benzyladenine (BA 4.44 μM), furfurylaminopurine (KIN 4.65 μM) and auxin α-naphthalene acetic acid (NAA 5.37 μM) individually and in combinations. The regeneration response was influenced by both the type of growth regulator and physical state of the medium. The explants produced either shoot buds on cytokinincontaining media or protocorm-like bodies (PLBs) on NAA containing media both solid and liquid. More neo-formations were produced on liquid media, especially those containing only NAA. They were formed at nodal and inter-nodal regions. The secondary buds were produced on the surface of primary PLBs. The plantlets were developed on MS medium containing banana homogenate 50 g·dm-3. The current study is the first ever report on successful regeneration of Dendrobium chrysotoxum from stem-node segments.
Absence of small hive beetles from flowering plants

Small hive beetles (SHBs), Aethina tumida (Coleoptera: Nitidulidae), are parasites and scavengers of honey bee colonies in their endemic range in sub-Saharan Africa as well as in their new distribution range. Even though flowering plants may in principle also serve as a food for SHBs, evidence so far suggest that this beetle is unlikely to visit flowers. However, field data remain scarce calling for more efforts to investigate the potential of flowers as reservoirs for this pest of social bees. Here, we conducted extensive field surveys of flowering plants in Australia. Despite the very large sample size, not a single adult SHB was found on any of the flowers. This is in line with an earlier field survey. Since SHBs were also absent from fruits in another surveys, it appears as if alternative food sources outside of bee colonies are of minor importance only for SHBs.
Assessing water-related plant traits to explain slow-wilting in soybean PI 471938

ABSTRACT Soybean [Glycine max (L.) Merr. ] genotype PI 471938 expresses a slow-wilting phenotype in the field, and the progeny of this genotype have shown to have high yield under water deficit conditions. However, the physiological basis for the slow-wilting trait in PI 471938 remains unclear, and failure to understand the causal mechanism may limit future breeding efforts. This study investigated three primary hypotheses for trait expression that could explain slow-wilting trait in PI 471938: (1) a low osmotic potential in the leaves allowing greater water retention, (2) high elastic modulus of leaves resulting in delayed development of wilting, and (3) high hydraulic conductance allowing rapid water redistribution in the plants. Experiments included three other soybean genotypes as references for the results obtained with PI 471938. Surprisingly, the results for PI 471938 did not prove to be unique as compared to the other three tested genotypes for any of the three hypotheses. These negative results indicate that a hypothesis outside the usual candidates describing plant water transport, possibly anatomical features related to specific water transport properties, is required to explain slow-wilting in PI 471938.
INFLUENCE OF FOLIAR SPRAY OF SOME MICRONUTRIENTS AND NITROGEN FERTILIZER ON PRODUCTIVITY OF SUGAR BEET UNDER NEWLY RECLAIMED SOILS.

Two field trials were conducted during 2009/2010 and 2010/2011 seasons in Nubaria Research Station. Alexandria Governorate. The major goal was to study the effect of nine treatments which represented the combination between three foliar spray of some micronutrients solution levels (1/4, 1/2 and 3/4 /300 L water/fed) at 45 and 75 days from sowing and three nitrogen fertilizer levels of (80, 100 and 120 Kg/fed). A split plot design with four replications was used. The main plots were assigned to foliar spray with some micronutrients solution, whereas, nitrogen fertilizer in the sub plots. The obtained results revealed that: foliar spray of micronutrients solution level at 1/2 l/fed attained a highest values for root diameter and fresh weight/plant, as well as, sucrose%, purity%, root and sugar yields/fed. While, N, Na and K% were decreased in both seasons. Foliar spray of micronutrients solution level at 3/4 l/fed increased root length and macroelements (g/100 g DW) in both seasons. Application of nitrogen fertilizer at 120 kg N/fed gave the highest mean values of root length, diameter, fresh weight/plant, root and sugar yields/fed. On the contrary, a gradual reduction in sucrose% and purity% had been detected with the increase in nitrogen level over 80 kg N/fed. Interaction between foliar spray of some micronutrients solution levels 1/2 l/fed and nitrogen fertilizer at 120 kg/fed significantly affected on sucrose%, root and sugar yields/fed in both seasons.
Surveillance study on the most common sea-cucumbers in some Egyptian coasts

Sea cucumbers depletion has become a threat to Egypt because of the extreme harvesting and utility of sea cucumbers for their direct value as food and as source for bioactive products. Therefore, it is necessary to have an updated overview about the current available species in Egyptian fauna, including distribution, anatomy and morphological analysis. Six species of sea-cucumbers were collected from Egyptian coasts (Mediterranean and Red Seas). One of these species, namely Holothuria polii is collected from Mediterranean Sea coasts (Abu-Qir and Miami regions, Alexandria) while, the other five species were found in Hurghada shores. The collected species were identified and separated according to morphometric analysis. The variation of morphological characters between collected samples and their distribution along Egyptian coasts were discussed. The obtained results revealed that Holothuria leucospilota, Holothuria edulis, Bohadschia marmorata and Actinopyga mauritiana can emit fine sticky mass named Cuvierian tubules from their anus while, Holothuria atra and Holothuria polii lack this tubule. In addition, there is a significant difference between Actinopyga mauritiana and other genera in the presence of five distinct teeth around the anus.
Potencial correlated environmental factors leading to the niche segregation of ammonia-oxidizing archaea and ammonia-oxidizing bacteria: A review

Ammonia oxidation is an important step of the nitrogen cycle and was considered to be conducted only by ammonia-oxidizing bacteria (AOB) for a long time. The discovery of ammonia-oxidizing archaea (AOA) caused consideration of the relative contributions of these two functional groups in different niches and factors resulting in their niche segregation. Previous studies showed that some environmental factors may correlate to the abundance and distribution of AOA and AOB, including ammonia/ammonium concentration, pH, organic matters, oxygen concentration, temperature, salinity, sulfide concentration, phosphate concentration, soil moisture, and so on. Despite extensive studies conducted on ecology of AOA and AOB to find key environmental factors dominating niche segregation between AOA and AOB, few studies were conducted to explore the interrelationship among environmental factors. In this review, five main environmental factors which may be related to each other were selectively reviewed independently, including ammonia concentration, pH, temperature, oxygen concentration and organic matters. Furthermore, potential interrelationship among environmental factors was proposed.
Identification of QTLs for Agronomic Traits in the Japanese Chestnut (Castanea crenata Sieb. et Zucc.) Breeding

The chestnut (genus Castanea) has a long juvenile phase, and breeders have to wait three years or more to evaluate nut traits. Therefore, molecular markers associated with genes of interest are required to speed the selection process in chestnut breeding programs. Genetic linkage maps of the Japanese chestnut were constructed using two breeding populations derived from crosses between ‘Kunimi’ and breeding line ‘709-034’ (Kx709), and between ‘Porotan’ and ‘Tsukuba-43’ (Px43). Maps of the four parents and two integrated maps (one representing each cross) were constructed using 443 simple sequence repeat markers (SSRs) and 554 single-nucleotide polymorphism markers. In the Kx709 integrated map, which was the most saturated of the six maps, 12 linkage groups were identified that covered 668.1 cM with an average distance of 0.8 cM between loci. Using anchor SSRs, these six maps were successfully aligned to the Chinese chestnut consensus map. We evaluated eight important traits, including several nut traits, to identify molecular markers associated with these traits. At least one significant quantitative trait locus (QTL) was detected for each of the eight traits (21 in total). Logarithm of odds (LOD) values and phenotypic variance explained by these QTLs ranged from 2.60 to 7.90 and from 11.6% to 29.1%, respectively. In the Kx709 population analysis, several QTLs for nut harvesting date (HARVEST) and pericarp splitting (SPLIT) were detected. Under the assumption that the effects of these QTLs are additive, the percentage of total phenotypic variance explained by the combination of QTLs was high for both HARVEST (47.5%–60.8%) and SPLIT (33.4%–41.7%). Because these mapping populations and their parents are essential materials for Japanese chestnut breeding programs, these QTLs will soon be used for marker-assisted selection to improve breeding efficiency.
Environmental DNA as a detection tool for zebra mussels Dreissena polymorpha (Pallas, 1771) at the forefront of an invasion event in Lake Winnipeg, Manitoba, Canada.

Zebra mussel Dreissena polymorpha (Pallas, 1771), an invasive bivalve in North America, was first recorded in Lake Winnipeg in 2013. Quagga mussel D. bugensis (Andrusov, 1897), a second invasive mussel to North America, has yet to be detected in Manitoba waters. The establishment and continued spread of zebra mussels is of concern. Accordingly, we developed two species-specific and one Dreissena-specific qPCR-based environmental DNA (eDNA) assays designed as a single multiplexed reaction able to identify the presence of zebra mussel and infer the presence of quagga mussel in water samples from at-risk and invaded locations. In 2014, samples were collected from four invaded harbours on Lake Winnipeg during the early (May) and late (October) seasons. Zebra mussel eDNA was detected in 0–33.3% of samples per site early in the season, whereas late season sample detection ranged from 42.9 to 100%. In order to confirm that there was no nonspecific amplification of DNA from local biota, samples were also collected from sites where neither adult nor veliger-stage zebra mussels had been previously observed. These sites included three harbours on Lake Winnipeg and six sites within the Manitoban portion of the Red River. No amplification of eDNA was recorded at these sites except for that at a float-plane dock in the Red River upstream of Lake Winnipeg. Zebra mussels were subsequently detected at this location by sampling for transformed attached individuals. Thus, we demonstrate that eDNA is an early indicator of the presence of zebra mussels and is a useful detection tool at the forefront of their recent invasion in Manitoba. This work provides the foundation for the development of a zebra mussel eDNA monitoring program for waterbodies in Manitoba and western Canada.
Changes in the cerebellar cytoarchitecture of hibernating hedgehog Erinaceus europaeus L. (Mammalia): an immunocytochemical approach

Abstract Hibernation is an amazing animal strategy to survive when the environmental temperature is very low and food resources are scarce. Successful hibernation requires a variety of complex biological adaptations, in which the brain plays a central regulatory role. Currently, little information is available regarding the morphology and functional activity of specific neurons within the cerebellar cytoarchitecture of hibernating animals. In the present study, we investigated the immunohistochemical expression of essential proteins in the cerebellum of a mammalian hibernator (i.e. hedgehog Erinaceus europaeus L.), focusing on (i) Purkinje neurons, the sole output cells of the cerebellar cortex; (ii) selected neurotransmitters involved in hibernation processes; (iii) intracellular calcium homeostasis, considering that calcium is also an important regulator of neurotransmission mechanisms; and (iv) cytoskeletal proteins, involved in maintenance of neuronal shape and axon calibre. Specifically, we studied in situ immunocytochemical changes during the torpor state of hibernation (November–March) versus the activity phase (April–September). We employed different selected markers, i.e. glutamic acid decarboxylase (GAD67) and postsynaptic glutamate ionotropic receptor GluR2-3, different calcium-binding proteins (i.e. calbindin, parvalbumin and calretinin) and cytoskeletal components (i.e. pNF-H and MAP2). In summary, our data in hibernating animals demonstrated: (i) downregulation of GAD67, indicating loss/changes of synaptic contacts on Purkinje somata and dendrites; (ii) GluR2-3 upregulation in Purkinje neurons, with a drastic decrease of calbindin expression; and (iii) decrease of normal mechanisms regulating intracellular calcium homeostasis. We also found a decrease/modification in the distribution of cytoskeletal proteins, particularly evident for pNF-H. Changes in the functional activity of Purkinje cells were accompanied by some morphological dendrite alterations, signs of degeneration in cell somata and flattened basket pinceaux at the Purkinje axon hillock. These findings confirm that hibernation makes heterothermic animals a valuable model to study physiological adaptations to adverse conditions, and also for understanding cellular and molecular mechanisms aimed at preserving mammalian organs from full degeneration and death.
Patterns of seasonal occurrence of sympatric killer whale lineages in waters off Southern Vancouver Island and Washington state, as determined by passive acoustic monitoring

Supervisory Committee Dr. N. Ross Chapman (School of Earth and Ocean Sciences) Supervisor Dr. Richard K. Dewey (School of Earth and Ocean Sciences) Departmental Member Dr. S. Kim Juniper (School of Earth and Ocean Sciences) Departmental Member Dr. John K. B. Ford (Pacific Biological Station) Additional Member Killer whales inhabiting coastal waters of the northeastern Pacific are listed under the Canadian Species at Risk Act, which requires the identification of critical habitats for the recovery of their populations. Little is known about their distribution during the winter and what areas are important for their survival during these months. Passive acoustic monitoring is a valuable complementary method to traditional visual and photographic surveys although it has seldom been used to study killer whales and there are limitations in practice. There is a need to develop tools and protocols to maximize the efficiency of such studies. In this thesis, long-term acoustic data collected with autonomous recorders were analyzed 1) to assess the performance of two types of analysis (Manual and Long Term Spectral Averages) for detecting and identifying killer whale calls and to compare the effects of using two different duty cycles (1/3 and 2/3); and 2) to investigate the seasonal occurrence of different killer whale populations at two sites off the west coasts of Vancouver Island and Washington: Swiftsure Bank and Cape Elizabeth. Both the use of Long Term Spectral Averages and a lower duty cycle resulted in a decrease in call detection and resolution of call identification, leading to underestimations of the amount of time the whales spent at the site. A compromise between a lower resolution data processing method