Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemotaxis of Escherichia coli to controlled gradients of attractants: Experiments and Mathematical modeling

Chemotaxis is a phenomenon in which a microorganism or multi-cellular organisms are able to direct their movements in the presence of certain chemicals in their environment. This could be either towards favorable chemicals called chemoattractants or away from unfavorable chemicals called chemorepellents. The understanding of this phenomena is important in many biological processes including immune response, embryo-genesis, wound healing, bio-film formation and bio-remediation of subsurface contaminants. The objective of this thesis is to study the response of microorganisms in the presence of controlled gradients of chemoattractants using a micro-capillary. This would involve developing mathematical models that describe the chemotaxis pathway in a chemotactic cell and to relate the kinetics to the motion of cell in the presence of chemoattractants. The predictions of the model will be compared with experiments where the motion of cell in the presence of chemoattractants will be tracked. The previous studies have reported average drift velocities for a given gradient and do not measure drift velocities as a function of time and space. To address this issue, a novel experimental technique was developed to quantify the motion of E. coli cells to varying concentrations and gradients of chemoattractant so as to capture the spatial and temporal variation of the drift velocity. The statistics of single cell motions such as cell velocity, tumbling frequency, rotational diffusion, drift velocity and translational diffusivity are obtained independently. An existing two state receptor model of Barkai and Leibler (1997) was used for the intracellular pathway and into this the extra-cellular influence such as ligand concentration and Brownian motion was incorporated to predict the response for the experimental conditions. The model predicted the ex-
MAYFIELD LOGISTIC REGRESSION: A PRACTICAL APPROACH FOR ANALYSIS OF NEST SURVIVAL

Abstract Mayfield logistic regression is a method for analyzing nest-survival data that extends the traditional Mayfield estimator by incorporating explanatory variables (e.g. habitat structure, seasonal effects, or experimental treatments) in a logistic-regression analysis framework. Although Aebischer (1999) previously showed that logistic regression can be used to fit Mayfield models, few ornithologists have put that finding into practice. My purpose here is to reintroduce this underused method of nest-survival analysis, to compare its performance to that of a dedicated survival-analysis program (MARK), and to provide a practical guide for its use. Like the traditional Mayfield method, Mayfield logistic regression accounts for the num ber of “exposure days” for each nest and allows for uncertain fates (censoring), thus avoiding the bias introduced by typical applications of logistic regression. Mayfield logistic regression should be widely applicable when nests are found at various stages in the nesting cycle and multiple explanatory variables influencing nest survival are of interest.
Plant pathogen diagnostics : immunological and nucleic acid-based approaches

Accurate disease diagnosis and precise identification of any pathogens involved is an essential prerequisite for understanding plant diseases and controlling them effectively. Traditional methods of identifying plant pathogens can be slow and inconclusive, and this has prompted the search for alternative diagnostic techniques. Here, we review recent developments in antibody-based and nucleic acid-based diagnostic methods, and their applications in plant pathology. We also highlight some new developments in diagnostics that are likely to make an impact in the future.
Using a transponder system to monitor incubation routines of Snowy Plovers

Abstract We investigated the incubation behavior of a ground-nesting shorebird, the Snowy Plover (Charadrius a. alexandrinus) by developing a transponder system that recorded the identity of parents on their nest over 24 h. The system consisted of a small chip glued on the tail of the parent, an antenna that was buried under the nest, and a recording device that was buried nearby. The transponder system was both accurate and reliable, since only 0.2% of records were false. The records of the transponder system were augmented by visual observations, and these data were analyzed by randomization tests. We found strong daily incubation routines: females incubated during the day, whereas males incubated mostly at night. Overall, the females spent significantly more time incubating the nest (11.3 h (median)/day) than the males (9.4 h/day). We discuss several hypotheses for the observed daily incubation routines of the sexes, and propose experimental studies to test these hypotheses.
Energy cost of ectoparasitism: the flea Xenopsylla ramesis on the desert gerbil Gerbillus dasyurus

Metabolizable energy intake and changes in body mass was measured in the desert gerbil Gerbillus dasyurus when parasitized by the flea Xenopsylla ramesis. We hypothesized that energy requirements for maintenance, or average daily metabolic rate, of parasitized gerbils would be higher than those of nonparasitized gerbils. We also hypothesized that the efficiency of utilization of energy for maintenance would be the same for parasitized and non-parasitized gerbils, as this measurement is dependent mainly on dietary quality. Fifty fleas feeding on a gerbil consumed 3.68 a 1.19 mg blood, in total. This amounted to 34.3 a 1.8% of body mass of a starving flea and only about 0.17% of the blood volume of the host. The absolute amount of blood consumed by X. ramesis is the lowest reported for fleas in other studies. This suggested that the pressure of parasitism of X. ramesis on G. dasyurus in terms of blood consumed was relatively low. Both our hypotheses were confirmed. Average daily metabolic rate of the parasitized gerbils (7.75 kJ g 70.54 d 71 ) was 16% higher than that of non-parasitized gerbils (6.69 kJ g 70.54 d 71 ). In addition, at zero metabolizable energy intake, the parasitized gerbils lost body mass at a faster rate than the nonparasitized gerbils (4.34 vs 3.95% body mass d 71 ). The efficiency of utilization of energy in the parasitized and non-parasitized gerbils was similar.
Effects of modified atmosphere and vacuum packaging on inhibition of Listeria monocytogenes and quality in hot-smoked rainbow trout fillets.

Hot-smoked rainbow trout were inoculated with Listeria (L.) monocytogenes, then packaged under vacuum or under 100% CO 2 (MAP 1) or 50% CO 2 and 50% N 2 (MAP 2). Afterwards, the samples were stored at +2°C. Non-inoculated samples packaged under the same conditions served as controls. Listeria growth and quality parameters were observed in all samples stored at +2°C over a period of seven weeks. L. monocytogenes counts in samples stored under vacuum, MAP 1 and MAP 2 packaging decreased significantly over time. The results obtained from this study showed that the inoculation of L. monocytogenes in hot-smoked rainbow trout is best inhibited at 100% CO 2 (MAP 1). The sensory acceptability scores for odour, taste and texture of hot-smoked vacuum and modified atmosphere packaged trout decreased with storage time. The results of this study indicated that the shelf-life of non-inoculated vacuum packaged and MAP 1 as well as MAP 2 packaged smoked trout stored at +2°C as determined by sensorial data is four and five weeks, respectively. Total volatile basic nitrogen and thiobarbituric acid values gave acceptable results for up to six weeks for the hot-smoked rainbow trout stored in vacuum and MAP1 or MAP 2 storage.
Microbial nitrogen cycling in Arctic snowpacks

Arctic snowpacks are often considered as chemical reactors for a variety of chemicals deposited through wet and dry events, but are overlooked as potential sites for microbial metabolism of reactive nitrogen species. The fate of deposited species is critical since warming leads to the transfer of contaminants to snowmelt-fed ecosystems. Here, we examined the role of microorganisms and the potential pathways involved in nitrogen cycling in the snow. Next generation sequencing data were used to follow functional gene abundances and a 16S rRNA (ribosomal ribonucleic acid) gene microarray was used to follow shifts in microbial community structure during a two-month spring-time field study at a high Arctic site, Svalbard, Norway (79° N). We showed that despite the low temperatures and limited water supply, microbial communities inhabiting the snow cover demonstrated dynamic shifts in their functional potential to follow several different pathways of the nitrogen cycle. In addition, microbial specific phylogenetic probes tracked different nitrogen species over time. For example, probes for Roseomonas tracked nitrate concentrations closely and probes for Caulobacter tracked ammonium concentrations after a delay of one week. Nitrogen cycling was also shown to be a dominant process at the base of the snowpack.
Dans le génome des Paramyxovirinae, les promoteurs et leurs activités sont façonnés par la « règle de six »

Les Paramyxovirus forment une famille de virus dont le genome est compose d’une seule molecule d’ARN simple brin de polarite negative etroitement associee a de multiples copies de proteines N, dans une nucleocapside de symetrie helicoidale. Dans la sous-famille des Paramyxovirinae, la replication du genome est soumise a la « regle de six » qui stipule que seuls les genomes dont le nombre total de nucleotides est un multiple de six sont repliques. Cette revue a pour but de faire le point sur la definition des elements de sequence nucleotidique impliques dans le fonctionnement de l’ARN polymerase virale ARN-dependante, ceci dans le contexte du mecanisme d’application de la « regle de six », et dans celui de la regulation de ses activites de replication et de transcription.
Using multiple methods to assess detection probabilities of riparian-zone anurans: implications for monitoring

Abstract Context. Both manual call surveys (MCS) and visual encounter surveys (VES) are popular methods used to monitor anuran populations. Recent statistical developments, specifically the development of occupancy models that permit the use of data from various survey methods to assess method-specific detection probabilities, provide a rigorous framework for evaluating the effectiveness of field methods. Aim. To compare species-specific detection probabilities generated by MCS and VES and to evaluate the effectiveness of these methods throughout the activity season of several riparian-zone anuran species. Methods. During 2010 and 2011, we sampled 21 sites along the Broad and Pacolet Rivers, in South Carolina, USA, using MCS and VES. Anuran species were surveyed across three seasons (fall, spring and summer) each year. Key results. For six species, MCS resulted in a higher mean probability of detection, whereas VES resulted in a higher mean probability of detection for four species. In addition, survey date was an important influence on detection probability of most anurans when using MCS, but largely unimportant when employing VES. Conclusions. Our findings indicated that VES are as effective as MCS for detecting some species of anurans, and for others, VES represent a more effective method. Furthermore, when using VES outside the breeding window, some anurans can be reliably detected, and in some cases, detected more easily than by using MCS. Implications. We suggest that VES is a complimentary technique to MCS and a potentially important tool for population monitoring of anurans. VES can provide more flexibility for anuran researchers, as robust estimates of detection and occupancy can be obtained outside a narrow breeding window.
Black bear density in Glacier National Park, Montana

We report the first abundance and density estimates for American black bears (Ursus americanus) in Glacier National Park (NP), Montana, USA. We used data from 2 independent and concurrent noninvasive genetic sampling methods—hair traps and bear rubs—collected during 2004 to generate individual black bear encounter histories for use in closed population mark–recapture models. We improved the precision of our abundance estimate by using noninvasive genetic detection events to develop individual-level covariates of sampling effort within the full and one-half mean maximum distance moved (MMDM) from each bear's estimated activity center to explain capture probability heterogeneity and inform our estimate of the effective sampling area. Models including the one-half MMDM covariate received overwhelming Akaike's Information Criterion support suggesting that buffering our study area by this distance would be more appropriate than no buffer or the full MMDM buffer for estimating the effectively sampled area and thereby density. Our model-averaged super-population abundance estimate was 603 (95% CI = 522–684) black bears for Glacier NP. Our black bear density estimate (11.4 bears/100 km2, 95% CI = 9.9–13.0) was consistent with published estimates for populations that are sympatric with grizzly bears (U. arctos) and without access to spawning salmonids. Published 2013. This article is a U.S. Government work and is in the public domain in the USA
Characterization of the microflora associated to Scaphoideus titanus, the insect vector of the "flavescence dorée"

Several wine production areas in Europe are afflicted by "flavescence doree" (FD), a grape yellows caused by 'Candidatus Phy- toplasma vitis', transmitted by the phloem-feeder leafhopper Scaphoideus titanus Ball (Hemiptera Cicadellidae). Symbiotic con- trol of disease transmission, exploiting natural symbionts of the vector, could represent an innovative strategy against FD diffu- sion. A study was conducted to characterize the microflora associated to S. titanus specimens, collected from FD-contaminated vineyards in the Italian region of Piedmont. By length heterogeneity PCR we identified a major peak associated with almost all the individuals examined. Characterization by denaturing gradient gel electrophoresis confirmed the presence of a major band cor- responding to sex-ratio-distorting endosymbionts of the 'Candidatus Cardinium hertigii' group; electron microscopy of tissues of S. titanus showed bacterial cells with the typical morphology of 'Ca. Cardinium hertigii' together with cell morphologies resem- bling those of 'Ca. Phytoplasma vitis'. Our findings suggest that this endosymbiont, named ST1-C, described for the first time in Cicadellidae, is transovarially transmitted and could have a complex life cycle in the insect body; in addition it colocalizes with 'Ca. Phytoplasma vitis' several host tissues. These results make ST1-C an interesting candidate for the symbiotic control of FD diffusion.
Screening and Characterization of Lignin Degrading Bacteria from Decayed Sawdust

In this study an attempt was made to isolate and ch aracterize the lignolytic bacteria. The decayed sawdust sample was collected and screened for lignolytic bacteria using Crawford medium conta ining of tannic acid as lignin equivalent. Seven bacterial isolates such as Bacillus spp1, Streptococcus spp , Pseudomonas spp2, Acinetobacter spp, Serratia spp , Escherichia spp , and Proteus spp2 were selected based on their solubiliz ation index against tannic acid. All these isolates were further characterized for their activity to degrade lignin analogue i.e., tannic acid in various growth conditions such as various concentration of tannic acid viz.,0.25, 0.50, 0.75, 1.0 and 1.25 different temperature viz.,28°C, 37°C and 45°C and various pacidic neutral and alkaline conditions. The bacterial isolates such as Bacillus spp1, Pseudomonas spp2, Acinetobacter spp, and Serratia spp were sho wed the better lignolytic activity at a concentration of 1.0 percent tannic a cid in the acidic (pH 6.0) and neutral (pH 7.0) conditions at 37 o C.
Effects of Invasive Amur Honeysuckle (Lonicera maackii) and White-Tailed Deer (Odocoileus virginianus) on Litter-Dwelling Arthropod Communities

Abstract Litter-dwelling arthropods play crucial roles in litter decomposition and nutrient cycling, and changes in their diversity or abundance can affect these processes. Previous studies have outlined individual effects of invasive plants and overabundant ungulates on litter-dwelling arthropod communities but have paid little attention to whether invasive plants and ungulates interact to affect these arthropod communities. We examined how invasive Amur honeysuckle (Lonicera maackii) and grazing by white-tailed deer (Odocoileus virginianus) affected diversity, abundance, and taxonomic composition of litter-dwelling arthropod communities in a deciduous forest in southwestern Ohio. We also examined whether deer or honeysuckle affected substrate composition and depth of litter. We found no significant effect of honeysuckle, deer, or their interaction on arthropod diversity, but exclusion of deer increased total arthropod abundance and abundance of Araneae, and thereby affected taxonomic composition of the litter community. These effects were likely related to greater plant cover and less soil compaction in areas from which deer were excluded. Honeysuckle negatively affected Araneae abundance and positively affected Acari abundance, possibly revealing an indirect effect of Araneae on Acari. A honeysuckle × deer interaction on abundance of Acari was important only during the first year of our study. There were no differences in arthropod abundance between honeysuckle-absent and honeysuckle-removed plots, indicating rapid restoration of the litter community after honeysuckle removal. Neither honeysuckle nor deer affected composition or depth of litter. Our findings suggest that current management techniques that control the effects of honeysuckle and deer on native plant communities by separate measures may be sufficient to reduce impacts on litter-dwelling arthropods.
Impoundments and the Decline of Freshwater Mussels: a Case Study of an Extinction Gradient

Abstract: One major factor leading to the imperilment of freshwater mussels ( Bivalvia, Unionidae) has been the large‐scale impoundment of rivers. We examined the distribution and abundance of mussels at 37 sites along a 240‐km length of the Little River in southeastern Oklahoma, U.S.A. , which is affected by both mainstem and tributary reservoirs. We observed a mussel extinction gradient downstream from impoundments in this river: with increasing distance from the mainstem reservoir there was a gradual, linear increase in mussel species richness and abundance. Mussel species distributions were significantly nested, with only sites furthest from the impoundment containing relatively rare species. Below the confluence with the inflow from the second reservoir these same trends were apparent but much weaker, and overall mussel abundance was greatly reduced. Our results suggest that considerable stream lengths are necessary to overcome the effects of impoundment on mussel populations, and such information should be considered in conservation and management plans.
Development of a regeneration system via nodal segment culture in Veronica anagallis-aquatica L. – an amphibious medicinal plant

Abstract The present study describes an effective, reproducible and rapid regeneration protocol for in vitro shoot development of the medicinally important, semi-aquatic plant Veronica anagallis-aquatica L. through mature nodal segments on Murashige and Skoog (MS) medium. The most effective medium for shoot regeneration was MS medium fortified with 0.5 µM 6-benzyladenine (BA), on which the maximum number (43.7±1.85) of shoots per explant having a shoot length of 5.0±0.25 cm were produced. The addition of auxins along with optimal concentration (0.5 µM) of BA did not further improve the regeneration capacity of the explants; instead, it resulted in an adverse effect. Nodal segments cultured in MS liquid medium without agar provided a better and early response for efficient shoot regeneration, and simultaneous rooting as compared to solidified medium. The optimal liquid medium comprised of MS+BA (0.5 µM) on which a maximum 20.7±1.76 shoots per explant were produced and grew healthier. Both half strength MS and MS basal medium supplemented with α-naphthaleneacetic acid (NAA) responded equally for root induction. Rooted shoots were successfully transferred to field conditions with 80% survival. Histological studies revealed the de novo origin of shoots which would make this protocol suitable for transformation techniques.
EVALUATION AND CHARACTERIZATION OF RESISTANCE TO TOMATO MOTTLE VIRUS (ToMoV) CONFERRED BY A MODIFIED COAT PROTEIN OF ToMoV

1999 Dedication To my parents who taught me that dreams are to be pursued and challenges to be met. To my daughter whose smile gives me a reason to wake up everyday. iv ACKNOWLEDGMENTS I wish to thank Dr. Jane E. Polston for giving me adequate advice and for having a strong commitment to my education. I would like to thank Dr. Ernest Hiebert for his helpful suggestions and for allowing me to do part of my research in his laboratory. I would like to thank Dr. valuable time that they invested serving on my graduate committee. I am grateful for the technical advice and special kindness that I received from Kris Beckham, also I would like to thank Christopher Patte for his technical advice and delicious cakes. I wish to thank for helping me to keep my sanity, and finally I would like to thank COLCIENCIAS for awarding me a scholarship-loan during part of my doctoral program. Tobacco plants (Nicotiana tabacum ' Xanthi ') were transformed with a binary vector containing the coat protein gene of tomato mottle begomovirus (ToMoV) (Geminiviridae) modified by the deletion of 30nucleotides in the 5' end. The R 1 generation was screened for resistance against ToMoV, by inoculation with viruliferous whiteflies. Symptom development was recorded every week for 16 weeks using a five level visual scale, and ToMoV infection was confirmed by PCR and ELISA. The response to ToMoV infection was variable, wild type, enhanced wild type, immunity and recovery phenotypes were observed. Some transformed plants developed an unusual viii bright vein yellowing. All plants transformed with a binary vector lacking the truncated ToMoV coat protein gene were susceptible to ToMoV infection. Southern blot analysis of immune R 1 plants showed the presence of multiple copies of the transgene in 80% of the plants tested. The transgene transcript was detected by northern blot analysis, but the transgene product was not detected by western blot analysis using antisera reactive with ToMoV coat protein. Selected resistant R 1 transgenic plants were also screened for resistance against tobacco mosaic tobamovirus, cucumber mosaic cucumovirus, and tomato yellow leaf curl begomovirus. Disease development was evaluated by visual assessment of symptoms and the presence of the viruses was determined by ELISA or dot blot hybridization. The transgenic plants evaluated did not show resistance to any of the three viruses indicating a narrow breadth of resistance. The R 2 generation of …