Miracle-dz/UniFAR-FTUs huggingface dataset:
Inventory dynamics and the bullwhip effect : studies in supply chain performance

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DNA barcoding the vascular plant flora of southern British Columbia

ii PREFACE . iii TABLE OF CONTENTS . iv LIST OF TABLES . vii LIST OF FIGURES . viii ACKNOWLEDGEMENTS . ix DEDICATION . x CHAPTER 1: INTRODUCTION . 1! 1.1. DNA Barcoding . 1! 1.1.1. Background . 1! 1.1.2. Barcoding Plants . 5! 1.1.3. Applications of DNA Barcoding . 7! 1.2. Composition of the BC Flora . 8! 1.3. Summary . 10 CHAPTER 2: MATERIALS AND METHODS . 11! 2.1. Taxon Sampling . 11! 2.1.1. Field Collections . 12! 2.1.2. Herbarium Tissue Samples . 13! 2.1.3. Additional Downloaded Sequences . 14! 2.2. DNA Sequencing . 15! 2.2.1. DNA Extraction, Amplification, and Sequencing . 15! 2.2.2. Sequence Alignment and Validation . 17! 2.3. Analysis.19! 2.3.1. Sequence Recoverability . 19! 2.3.2. Species Resolution . 19! 2.3. 3. Tests of Monophyly . 20! 2.3. 4. BLAST Analyses . 22 CHAPTER 3: RESULTS . 26! 3.1. Sequence Recoverability . 26! 3.2. Species Resolution . 28 CHAPTER 4: DISCUSSION . 33! 4.1. Sequence Recoverability . 33! 4.2. Genus and Species Resolution . 37!
Cloning and Expression of an Indigenous Mesophile lipase and Evaluation of Bacillus Codon Translation in Pichia Pastoris under Control of Two Different Promoters

Lipases are versatile biocatalysts with a wide range of application in food, dairy, leather, paper, pharmaceutical and detergent industries. In this study, mesophilic lipase gene from an indigenous Bacillus pumilus F3 that already its gene had been sequenced and identified, was cloned and expressed in methylotrophic yeast Pichia pastoris and codon translation of lipase gene was evaluated in P. pastoris under control of‌ two different promoters (alcohol oxidase (AOX1) and glyceraldehid phosphate dehydrogenase(GAPDH) promoters). In addition, the expression conditions of recombinant lipase F3 was optimized in P. pastoris expression system using BMMY medium at pH=3 ,26oC in 0.75% methanol. The lipase gene of 648bp with natural signal peptid sequence from B. pumilus F3 and the codon optimized lipase gene cloned and expressed in methylotrophic yeast P. pastoris. The lipase gene was excised from the recombinant plasmid with BamHI, EcoRI enzymes and ligated to the pPIC9 and pGAP9 linearized with the same enzymes. The recombinant plasmids were confirmed by the PCR and restriction enzyme digestion. The Bgl II linearized Ppic9 and pGAP9 recombinant plasmids were introduced into the yeast P. pastoris GS115 genom by electroporation and confirmed by PCR. Lipase expressing yeast was cultivated in a 250-ml shaking flask containing medium expression. Expression of lipase gene was confirmed using p-nitrophenyl palmitate test and SDS-PAGE. Codon optimized lipase produced as well as native gene and lipase expression was low in both. Also, these results suggest that protein structure is more important than codon preference in expression of proteins such as lipases.
A comparison of four different methods to estimate population size of Alpine marmot (Marmota marmota)

Obtaining reliable information on animal abundance in mountainous landscapes is challenging. Highly heterogeneous habitats tend to reduce detection probabilities, and the three-dimensional, rugged nature of the terrain poses severe limits to the fulfilment of a number of assumptions underlying several statistical methods. In this study, we aimed to compare the performance of 4 different methods to estimate population size of Alpine marmot ( Marmota marmota ), a highly social semifossorial rodent widely distributed on the European Alps. Between May and August 2015, in a study area within the Stelvio National Park (Italy) we conducted 8 sessions of capture-mark-recapture, 6 sessions of mark-resight from vantage points, 8 sessions of line distance sampling along 4 transects, and 2 sessions using double-observer methods from vantage points. The minimum number of animals alive, obtained during the mark-resight surveys, was n=54 individuals. Capture-mark-recapture models estimated a population size of n=56 individuals [95% CI (45,87)]; similar, but more precise estimates were obtained with the mark-resight approach {Bowden’s estimator: n=62 [95% CI (54,71)]; Poisson log-normal estimator: n=62 [95% CI (55,69)]}. Line distance sampling and double-observer methods were severely biased low {Line distance sampling: n=24 individuals [95% CI (19,31)]; Independent double-observer: n=24 [95% CI (22, 35)]; Dependent double-observer: n=15 [95% CI (15,20)]}. Our results suggest that the probabilistic approach based on marked individuals yielded fairly robust estimates of population size. The underestimates obtained using distance sampling and double-observer methods were likely due to the violation of some underlying assumptions. While the topography of the mountainous landscape makes it difficult to randomize the sampling scheme, the semifossorial behaviour of the target species is likely to lower the detection probabilities and violate the assumption of perfect detection on the transect.
Avoidance of oil contaminated sediments by estuarine fishes

The explosion of the Deepwater Horizon drilling platform and subsequent discharge of hydrocarbons into the Gulf of Mexico is the largest oil spill that has affected US waters. To date, studies of ecological effects on coastal fishes have produced complex results. While laboratory studies indicate that oil has widespread, pervasive impacts on fish physiology, field assessments often document few impacts to fish abundance and biomass following a spill. The dichotomy of such results suggests that negative individual-level effects do not translate to population/community-level consequences. One explanation for this discrepancy is that mobile organisms may avoid oil, which was very patchily distributed. Here, I present the results of experiments using 3 estuarine fishes (gulf killifish Fundulus grandis, sailfin molly Poecilia latipinna, and sheepshead minnow Cyprinodon variegatus) to determine whether behavioral avoidance occurs at a range of concentrations (0, 10, 20, and 40 ml oil l−1 of sediment) and weathering (fresh or weathered oil) scenarios. All 3 species avoided medium (35, 18, 10% of trial time, respectively) and high concentrations of fresh oil (30, 20, and 15%, respectively), while time spent over contaminated sediments at low concentrations of fresh oil was higher (30, 40, and 40%, respectively). Weathered crude elicited no significant avoidance behavior, with fish occupying between 40 and 60% of the trial period over these sediments, regardless of concentration. This research highlights the heretofore unrecognized role of behavior in fish resilience, as well as the need for future studies to incorporate ecologically relevant weathering rates. Such results are critical to the successful management of motile resources, such as estuarine fishes, in response to anthropogenic disasters such as oil spills.
Post-Clearcutting Chronosequence in the B.C. Coastal Western Hemlock Zone

Abstract There is increasing interest in the use of simulation models to evaluate the sustainability of various forest management decisions. A key need in the development and use of such models is field validation of their predictions. Data from studies of a 26-year post-clearcutting chronosequence in the coastal western hemlock (CWH) zone of British Columbia, undertaken originally as an evaluation of the FORCYTE-11 and FORECAST models, were synthesized into a simple input-output model of forest floor N-storage. This model estimated forest floor N storage within 10% of field measured values in a 400-year-old Pacific silver fir (Abies amabilis [Dougl.] Forbes)-western hemlock (Tsuga heterophylla [Raf.] Sarg.) stand, and in three of four adjacent clearcuts ranging in age from 3- to 26-years. However, it overestimated forest floor N storage on the 6-year-old clearcut site by 78% (1027 kg N ha∼1). There appear to be three main possible causes of this overestimate: (i) the 6-year-old site was not a valid member of the chronosequence, (ii) overestimation of forest floor N inputs, or (iii) underestimation of forest floor N outputs. The latter was considered to be the most likely, and the source of error was hypothesised to be the failure to include dentrification losses in the model. Two laboratory studies were conducted to measure the production of N2O in soils from the old forest and clearcut sites that had been amended with various substrates and placed in an atmosphere enriched with acetylene. Actual and potential in situ de nitrification rates were estimated from these measurements. Actual denitrification rates increased after clearcutting but remained far too low to explain the discrepancy between the modeled and the measured forest floor N storage on the 6-year-old site. Potential denitrification rates were, however, within the range of values needed to balance the N-budget model with measured field values. Based on these measured potential rates, on a review of the factors controlling denitrification rates, and on past studies reporting high in situ rates occurring in favorable settings, it is proposed that enough presumptive evidence exists to support the theory that hotspots or hot intervals of denitrification occur during the assart flush following clearcutting, and that this may substantially reduce forest floor N storage.
EXPRESSION OF THE BAR AND UIDA GENES BY GLADIOLUS FOLLOWING THREE SEASONS OF DORMANCY

Gladiolus is propagated by corms that undergo dormancy each year, and at least three seasons of growth are required before the plants from tissue culture produce flowers. Successful genetic engineering of the flowering bulb crops will require long-term expression of transgenes. Transgenic Gladiolus plants containing the bar-uidA fusion gene under control by either the CaMV 35S, rolD, mannopine synthase (mas2), or ubiquitin (UBQ3) promoters were characterized for levels of GUS expression following three seasons of dormancy. The highest levels of GUS expression were found in callus, shoots, and roots of plants containing the CaMV 35S promoter as compared to shoots and roots from plants containing the rolD, UBQ3, and mas2 promoters. Gene silencing of the bar and uidA genes did not occur in the 28 independently transformed plants analyzed following dormancy when both genes were expressed under the CaMV 35S, rolD, mas2 and UBQ3 promoters.
Distinct neural systems for the production of communicative vocal behaviors

Vocalizations are the production of sounds by the coordinated activity of up to eighty respiratory and laryngeal muscles. Whilst voiced acts, modified by the upper vocal tract (tongue, jaw, lip and palate) are central to the production of human speech, they are also central to the production of emotional vocalizations such as sounds of disgust, anger, laughter and crying. Evidence suggests that the speech and emotional vocalizations may comprise distinct classes of vocal movements: patients with speech production deficits are often able to produce emotional vocalizations. In addition to this, the ontogeny of the two articulations is largely distinct, with some culturally universal emotional vocalizations emerging soon after birth and human speech being a culture specific, highly learnt motor act, which must develop to some degree before a critical period in development. Here we investigate the motor pathways underlying these two classes of vocal movements for the first time by directly comparing BOLD responses during production of speech and non-speech vocal movements. Using functional magnetic resonance imaging, we report distinct patterns of activity in both subcortical and cortical regions (putamen and bilateral inferior frontal and parietal cortices) during the production of emotional vocalizations compared to speech production. In contrast we show that responses in primary sensorimotor regions do not differ during the production of speech and emotional vocalizations, suggesting partially overlapping, and partially non-overlapping neural structures for the motor control of these two classes of movement. In addition to this we report that responses in auditory cortices are distinct during the production of speech and non-speech vocalizations, suggesting that feedback control of speech and emotional vocalizations are distinct. These data provide novel evidence for the presence of dual pathways for the neural control of complex articulatory movements in humans. These findings are discussed in relation to the clinical and primate literature of vocal motor control. Significance Statement This work marks the first evidence in healthy humans for dual routes to vocal behaviors. Clinical evidence suggests that patients unable to produce speech may still be able to produce other vocal behaviors that employ the same set of effectors. Here we demonstrate that the production of different classes of vocal behavior is associated with overlapping and distinct networks of activity. Moreover, we show that auditory processing that occurs during the production of these movements may be distinct, suggesting that feedback may be used differently for these distinct classes of vocal movement.
The Effects of Dietary ß-Hydroxy-ß-Methylbutyrate + ß-Alanine and Physical Activity on Muscle Morphology and Function in Aged Rats

ACKSEL, CARA L. , M.S., December 2014, Food and Nutrition Sciences The Effects of Dietary β-Hydroxy-β-Methylbutyrate + β-Alanine and Physical Activity on Muscle Morphology and Function in Aged Rats Director of Thesis: Robert G. Brannan Loss of muscle mass and strength is a major health concern for the aging population. Both physical activity and dietary amino acid supplementation are suggested to play a role in increasing muscle mass, though little is known regarding the effect of these interventions on strength and muscle quality. In the present study, forty 22-month Sprague-Dawley rats were placed on a supplemental diet, running regimen, both, or neither (control). Running habits were tracked and analyzed. The medial gastrocnemius was tested to determine muscle mass, force, quality, fatigability, and fiber type. A significant difference was seen in MHC I fiber concentration, MuRF-1 activity, and absolute change in running pace between some groups. The results suggest that that physical activity might have played a larger role then HMB in MHC composition, MuRF1 activity, muscle quality, and running pace.
Structural insights into flavones as protein kinase CK2 inhibitors derived from a combined computational study

Flavones, which belong to the large group of flavonoids, have attracted considerable attention in relation to their therapeutic potential. Recently, this series of compounds has been shown to inhibit CK2 with outstanding efficiency and safety. However, to date, the exact binding modes between CK2 and flavones, as well as the basis of their effects on the biological activities remain unclear. In this study, we report the detailed account of the interactions between CK2 and flavones at the atomic level through computational approaches. Starting from four different molecular docking protocols, we obtained the relatively reliable initial complex structures by comparing docking scores. With subsequent molecular dynamic simulations and binding free energy calculations and decompositions, we found that the predicted binding free energies correlated well with pIC50 (R = 0.86), shedding light on the necessity of MD studies. Moreover, the results clearly confirmed that hydrophobic residues such as Val39, Val47, Ile60, Phe107, Asn112, Met157 and Ile168 were responsible for flavones binding and identified the key structural elements necessary for their bioactivities. Based on the structural and energetic features of receptor–ligand interaction mechanism, we designed a series of novel compounds and their higher inhibitory activities were confirmed by a comprehensive modeling study. We expect that these findings could serve as a paradigm for facilitating the process of developing novel and more promising inhibitors targeting CK2.
Is there a role for NF-κB in the suprachiasmatic circadian clock?

Circadian rhythms are recurring patterns in behavioural, physiological, and other parameters that display periods of approximately every twenty four hours. The molecular basis of the circadian timekeeping involves clock genes which act as transcription factors in a serious of feedback loops. Disruption of clock genes in transgenic models leads to dysregulation of the temporal architecture of behaviour and physiology. The master circadian pacemaker is the suprachiasmatic nuclei (SCN) in the anterior hypothalamus. There are circadian oscillators in numerous brain areas and peripheral organs and tissues. NF-κB is composed of dimers of members of the Rel family, including p65 (RelA), p50, p52, c-Rel and Rel B. NF-κB transcription factors are required for regulating cell survival and differentiation and also are important for inflammatory and immune responses. Dysregulation of this transcription factor has been shown to lead to inflammatory and autoimmune diseases. NF-κB is expressed in neurons and glia throughout the brain. We hypothesised that the NF-κB pathway may play a role in the generation and perhaps the phase setting of the circadian rhythms in the master mammalian circadian pacemaker. Understanding the role NF-κB system may play in the free running circadian clock, may be of great importance in understanding the effects of ageing, neuroinflammation and neurodegeneration on circadian rhythms. We set out to examine whether there might be a role for the NF-κB system in the master suprachiasmatic clock. We have examined expression of constituents of the pathway across the circadian cycle in the SCN, we examined the effects of pharmacological inhibition of the pathway on circadian processes in vivo and in vitro and have examined whether there is evidence for circadian regulation of NF-kB-mediated transcription in the SCN. Furthermore, we examined whether the NF-κB pathway played a role in ageing. Overall, we found no evidence that the NF-kB pathway is involved in the basal functioning of the SCN clock or in photic resetting. We do find some evidence that the NF-kB pathway may have a role in transducing immune events in the SCN. This data suggest that while the NF-kB pathway may be involved in circadian function in peripheral clocks, it does not appear to play a major role in the SCN.
Pseudomonas aeruginosa biofilms in drinking water and the evolution of antibiotic resistance

In nature, bacteria grow attached to surfaces in communities called biofilms. Biofilm bacteria are phenotypically distinct from free-floating planktonic bacteria, and one of the phenotypic characteristics of biofilms is that they are highly resistant to antimicrobials. Because of this, biofilms growing inside water distribution systems are not killed by the residual water disinfectant. Bacteria that live inside drinking water distribution system biofilms are under stress due to the constant exposure to the residual disinfectant and the nutritional stress of living in an oligotrophic environment. These stresses can activate the bacterial stress response mechanisms, resulting in increased mutation rates. The mutations that occur are random, but the possibility exists for a mutation to arise that confers increased resistance to antibiotics. The objective of this study was to determine if biofilm bacteria acquire antibiotic resistance when exposed to the residual water disinfectant chloramine. I grew biofilms of Pseudomonas aeruginosa in drinking water bioreactors and treated them with chloramine. The bacteria were sampled over time for isolates that were resistant to ciprofloxacin; isolates were obtained from both the chloramine treated and control biofilms. The ciprofloxacinresistant isolates had some phenotypic differences from the wildtype P. aeruginosa, as well as being resistant to rifampicin and chloramphenicol, but not resistant to tobramycin and gentamicin.
Isolasi dan Identifikasi Bakteri Asam Laktat Asal Rumput Raja ( Pennisetum purpureophoides ) sebagai Kandidat Probiotik pada Ternak

Santoso B, Maunatin A, Hariadi BT, Abubakar H. 2013. Isolation and identification of lactid acid bacteria originated from king grass ( Pennisetum purpureophoides ) as candidate of probiotic for livestock. JITV 18(2): 131-137 A study was conducted to isolate and identify strain of lactic acid bacteria (LAB) isolated from king grass, and to determine their potential as candidate of probiotic for livestock. The LAB was isolated by culturing king grass extract in De Man, Rogosa and Sharpe (MRS) medium. The pure culture LAB was used to identify strain of bacteria using Analytical Profile Index (API) 50 CH kit. The result showed that the strain bacteria was identified as Lactobacillus plantarum. L. plantarum was able to survive in extreme condition at pH 2 and 0.3% bile salt. L. plantarum also survived against pathogenic bacteria i.e. Staphylococcus aureus , Escherechia coli and Salmonella thypi . It is concluded that L. plantarum isolated from king grass could potentially to be used as probiotic for livestock.
Coping with strong variations in winter severity: plastic habitat selection of deer at high density

Lay SummaryThe capacity of animals to alter their foraging strategy is essential to cope with changing environmental conditions and survive at high population densities. White-tailed deer used different foraging tactics between mild and harsh winters. As winter severity increased, deer decreased their exposure to cold temperature, and traded-off the costs associated with locomotion in deep snow cover with the benefits of forage acquisition. Ultimately, they selected different foraging areas between harsh and mild winters.
Preparation of Tungsten-Bronze Thin Films

Tungsten-bronze films such as Pb0.6Ba0. 4Nb2O6 (PBN), Pb2KNb5O15 (PKN), K3Li2Nb5O15 (KLN), K2.7Na0. 3Li2Nb5O15 (KNLN) and K2BiNb5O15 (KBN) have been sputtered on sapphire and fused quartz substrates using ceramic targets. The sputtering conditions for growing tungsten-bronze structure films were investigated. (001)-oriented tungsten-bronze PBN films have been successfully grown by epitaxy onto (011̄2) sapphire substrates at a substrate temperature of around 650°C. The PKN films with tungsten-bronze structure have not been obtained by this sputtering using a target with the composition of stoichiometry. The c-axis-oriented films of KLN and KNLN have been grown on (011̄2) sapphire substrates. A KLN film sputtered on fused quartz at substrate temperatures higher than 480°C has also shown the [001]-axis orientation aligned perpendicular to the surface.
New Species of Halticoptera spinola (Hymenoptera: Chalcidoidea: Pteromalidae) from Himachal Pradesh, India with a Revised Key to Indian Subcontinent Species

A new species of Halticoptera Spinola, viz., Halticoptera shimlica Narendran and Girish Kumar sp. nov. is described and illustrated from Himachal Pradesh, India. Affinities of the species with its closest relatives are discussed. A revised key to the species of Halticoptera of the Indian subcontinent is also provided.