Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a novel cell division protein in Bacillus subtilis

FtsZ is a tubulin-like protein that polymerizes into a ring like structure at midcell, which is the first step in septum formation. The dynamics of FtsZ polymerization is regulated by a set of proteins, one of which is ZapA. ZapA is a non-essential positive regulator of FtsZ polymerization. In this study we have performed a screen for mutations in Bacillus subtilis that result in a cell division defect when combined with ∆zapA. Three such mutations were found in the yvcL gene. Since this gene is homologous to whiA from Streptomyces coelicolor, and the lack of both proteins imposes in some instances similar phenotypes, we proposed to rename the gene whiA. Mutation of whiA alone had only a mild effect on cells, which became 20-60% longer. However, the double mutant ∆whiA ∆zapA is filamentous and sick. Evidence is provided that the filamentation is caused by delocalization of FtsZ, and that WhiA is implemented in the early stage of cell division. Interestingly, WhiA localizes to the nucleoid and is important in cells that overinitiate replication. We also found that this protein is essential for survival after UV-induced DNA damage. Its binding sites on DNA were identified using a ChIP-on-chip method and the dif site, which is important for chromosome dimer resolution, was found to be a possible target of WhiA. A transcriptome analysis using whole genome microarray showed that WhiA does not function as transcriptional regulator. We conclude that WhiA is involved in both cell division and chromosome dynamics.
4 Probing RNA Structure, Function, and History by Comparative Analysis

Life on this planet is a profusion of incredibly complex systems. From the biologist’s perspective it is indeed fortunate that all these systems have sprung from a common ancestor. They have by their nature retained traces of their ancestries, and so are similar — homologous — to a greater or lesser extent. The science of biology has been built from its beginning upon cataloging similarities and differences among different living systems (and various states of the same system), the method that has become known as comparative analysis. It is only through this simple and sometimes tedious approach that biologists could begin to understand the complexity with which they are confronted, could begin to distinguish the important elements from the unimportant, and so reduce living systems to a set of understandable essentials. It is also through such comparisons, through measuring similarity and difference in degree and kind, that biologists have come to learn the genealogical relationships among all organisms. Despite its compelling utility, comparative analysis has never been a commonly used tool in molecular biology. This is not because comparative analysis is without value at the molecular level: The secondary structures of the ribosomal RNAs, major accomplishments of modern molecular biology, are tribute to the comparative approach (Woese et al. 1980; Noller et al. 1981). The molecular biologist’s aversion to comparative analysis would seem to lie in the molecular paradigm itself. Molecular biology arose from chemistry and physics. The entities with which these sciences deal, atoms and their relatively simple chemical combinations, do.
TESTS AND ANALYSES OF RC SHEAR WALLS WITH VERTICALLY ALIGNED OPENINGS

This study investigates fundamental behavior of reinforced concrete (RC) shear walls with vertically aligned openings through laboratory tests and numerical analyses. A series of structural tests was conducted using scaled models representing typical multistory RC shear walls in Japan. Three 1/6 scale shear wall specimens were designed and manufactured with different opening configurations: W0 with no opening, W1 with single-aligned openings, and W2 with double-aligned openings. The specimens were subjected to static cyclic lateral loads. The W1 and W2 specimens with openings failed with concrete crushing at the wall bottom and shear failure of the beams above openings, while the W0 failed in shear. The maximum strengths were 318 kN, 145 kN, and 93 kN for the W0, W1, and W2 specimens, respectively; hence, the experimental strength reduction factors due to the openings were 0.46 and 0.29 for the W1 and W2. These results were simulated by FEM analyses mainly to investigate detailed behavior of the components of the W1 and W2 specimens. The analytical results, in particular the maximum strengths and failure patterns, agreed well with the experimental results. It was numerically verified that high compression was applied to the wall bottom with the tensile boundary column and the beams above openings, as observed during the tests, which should be considered in practical design for this type of wall.
Étude génomique des fonctions du facteur de transcription Otx2 dans la rétine de souris adulte

Pour comprendre comment les genes du developpement exercent de multiples fonctions temporelles, nous prenons comme modele le facteur de transcription Otx2. Celui-ci est implique dans la gastrulation, le developpement de l’œil, du systeme olfactif, de la glande pineale, du thalamus et de la region cranio-faciale. Dans la retine adulte, deux tissus distincts expriment Otx2 : l’epithelium pigmente (RPE) et la retine neurale, contenant les photorecepteurs. L’ablation globale du gene Otx2 entraine la degenerescence exclusive des photorecepteurs alors qu’elle modifie l’expression de genes surtout dans le RPE. Ces faits suggerent un mecanisme non autonome, confirme par des experiences de gain et perte de fonction restreintes au RPE. Pour approcher les fonctions de la proteine Otx2 dans la retine neurale et le RPE, une etude a grande echelle de ses cibles genomiques a ete menee. Les profils distincts d’occupation du genome du RPE et de la retine neurale suggerent des fonctions differentes d’Otx2. Dans la retine neurale, ce profil est tres proche de celui du facteur paralogue Crx, indiquant une redondance fonctionnelle entre Otx2 et Crx. Nous avons emis l’hypothese qu’une combinatoire de partenaires proteiques differents permet de moduler l’action d’Otx2 en selectionnant des cibles genomiques distinctes. Pour identifier cette combinatoire in vivo et la correler aux fonctions exercees par Otx2, nous avons cree une lignee de souris exprimant une proteine de fusion Otx2-TAP-tag a un niveau physiologique. Cet outil permettra la purification des complexes proteiques Otx2 in vivo et leur identification par analyse proteomique.
Bacterial Plant Pathology: Cell and Molecular Aspects

1. Bacteria as plant pathogens 2. Bacterial structure and function 3. Taxonomy of plant pathogenic bacteria classification, nomenclature and identification 4. Plant pathogenic bacteria in the environment 5. The infection process 6. Compatible interactions: the hypersensitive response 7. Bacterial virulence and plant disease 8. Genetical analysis of plant pathogenic bacteria 9. Disease control Index.
DELLA proteins as hubs in signaling networks in plants

As sessile organism plants are extremely plastic. This feature is due their ability to integrate external and internal signals to modulate development. Therefore, understand the molecular mechanism underlying this feature is of great importance. Signals such as light, hormones and the circadian clock contribute to this plasticity. During this Thesis we use the plant model Arabidopsis thaliana to address how the circadian clock and the DELLA proteins, negative regulators of the gibberellin (GA) signaling integrate environmental signals and relay this information to transcriptional networks. We have demonstrated that the circadian clock modulate transcriptional levels of the GAs receptors GIDs, which promote the degradation of DELLA proteins, this result in a daily oscillation of DELLA proteins, which reach a minimum at the end of the night. This oscillation is key to modulate hypocotyl rhythmic growth and to control transcription of many genes. In this Thesis we present mechanisms of cross-talk among GAs and two plant hormones; ethylene and cytokinin. These mechanisms of cross-talk relies on the interaction between DELLA proteins and two transcriptional factors involved in signaling of these two hormones. The interaction with RAP2.3, prevents the transcription factor activity, this inactivation contributes to the regulation of apical hook opening by ethylene and GAs. On the contrary, the interaction with ARR1, a transcription factor that promotes cytokinin signaling, is positive for the activity of ARR1, thus contributing to the regulation of some developmental processes which are antagonistically regulated by GAs and cytokinin, for example root growth and photomorphogenesis. This interaction defines a new mechanism of DELLAs action. Additionally, by chromatin immunoprecipitation followed by massive sequencing, allowed us to show that DELLA proteins are near the promoter of many genes, this indicated that this mechanism is broad extensive. Based in these results an in the identification of more than 50 transcription factors as interactors of the DELLA GAI, we propose that DELLAs act as ? hubs? in signaling networks. In particular we propose that this is the mechanism by which these proteins are key for the integration of internal signals and developmental processes.
Rapid Harvest of Algae for Biofuel Production with the Aggregating Bacterium Bacillus sp. strain RP1137.

Title of Dissertation: RAPID HARVEST OF ALGAE FOR BIOFUEL PRODUCTION WITH THE AGGREGATING BACTERIUM BACILLUS SP. STRAIN RP1137 Ryan J. Powell, Doctor of Philosophy, 2014 Directed By: Dr. Russell T. Hill, Professor, University of Maryland Center for Environmental Science Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However significant challenges remain before algal based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economic and low energy manner. In this dissertation I describe the isolation of the bacterium, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production. This bacterium aggregates algae in a pH dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation. The optimal ratio of bacteria to algae is described as well as the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions and likely occurs via charge neutralization through binding of calcium ions to the cell surface of both algae and bacteria. I show charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. A comparison of the aggregation efficiency of RP1137, Bacillus megaterium QM B1551 and Bacillus subtilis SMY showed that RP1137 and B1551 are equally efficient at aggregating algae while SMY does not aggregate algae. The genome of RP1137 was sequenced to understand the molecular underpinning of the mechanism of aggregation. The difference in aggregation phenotypes between the three bacilli was used to inform a genomic comparison which revealed two putative proteins that are predicted to be bound to the cell wall and are found only in RP1137 and B1551 but not SMY. This work characterizes the conditions under which Bacillus sp. RP1137 aggregates algae and the mechanism by which that aggregation occurs. RAPID HARVEST OF ALGAE FOR BIOFUEL PRODUCTION WITH THE AGGREGATING BACTERIUM BACILLUS SP. STRAIN RP1137
Provenance, lifespan, and phylogeny : testing a conceptual framework for plant community management

approved: Elizabeth T. Borer Eric W. Seabloom Successful conservation management requires an understanding of how species respond to intervention. Native and exotic species may respond differently to management interventions due to differences arising directly from their native or exotic origin (i.e., provenance) or from differences in life-history or phylogenetic lineage that are associated with provenance. Thus, selection of a successful management regime requires knowledge of the life history and provenance-bias in the local flora and an understanding of the interplay between species characteristics across existing environmental gradients in the landscape. In my thesis, I examine the Pacific Northwestern upland prairies where the exotic grass flora contains more annual species and species within the Aveneae and Poeae tribes than does the native grass flora, presenting an opportunity to examine how provenance, phylogeny, and life span can interact to determine species distributions along natural gradients of soil chemistry. I analyze data collected in 2005 and 2006 in ten upland prairie sites from southern British Columbia, Canada to the central Willamette Valley in Oregon, USA for grass species abundance and soil chemistry. I then test the co-structure between grass species characteristics (provenance, phylogeny, and lifespan), patterns of abundance, and underlying soil chemistry. I find that while soil chemistry exerts strong control over community composition, community differences among sites were unrelated to provenance, life span, or phylogenetic grouping. I performed a greenhouse fertilization study to examine more carefully the biomass and root-to-shoot ratio response of common grass species to nitrogen and phosphorous supply. In this more controlled setting, nitrogen and planting density had the strongest effects on individual plant biomass. As with the field data, species responses to nutrient additions did not vary as a function of provenance, lifespan, or phylogeny. Thus manipulations of nutrient supplies may have predictable effects on single target species but are unlikely to alter the overall balance between native and exotic species. These results from my thesis work can guide future grassland restoration and management planning. © Copyright by Cara D. Benfield November 23, 2009 All Rights Reserved Provenance, Lifespan, and Phylogeny: Testing a Conceptual Framework For Plant Community Management
Seasonal changes in the gonadal state of the oysters Crassostrea iridescens and Crassostrea corteziensis (Filibranchia: Ostreidae) in the Northwest coast of México.

The reproductive cycle in oysters has been the subject of several studies in temperate zones. However, little information is available for tropical and subtropical species. This study describes the seasonal changes in the gonadic index (GI) of two species of oysters, Crassostrea iridescens and Crassostrea corteziensis, which differ markedly in their hàbitad and time of reproduction. Both oysters were sampled at 45 days intervals in the Northwest coast of Mexico between November 1989 and October 1990. Gonadal and somatic tissue per individual were dried for three days at 90°C, weighed and recorded. The gonadic index (GI) applied in this work was calculated from: GI = Wg/ws. Were WG is the average gonadal tissue dry weight, and Ws is the average somatic tissue dry weight. Seasonal variations in the gonadal state were evident for the two species. C.iridescens exhibited only a single maximum in the year, while C. corteziensis two peaks. This situation is presumably related to the contrastable environmental conditions that prevail in the sites where each species inhabit.
Mentorship through the Lens of Servant Leadership: The Importance of Accountability and Empowerment 1

1The Oklahoma State University Institutional Review Board approved the study protocol and all participants provided written informed consent prior to participation in the study. 2OSU Department of Agricultural Education, Communications and Leadership; 448 Agricultural Hall, Stillwater, OK 74078; (575)590-0030; shannon.norris@okstate.edu. 3OSU Department of Agricultural Education, Communications and Leadership; 448 Agricultural Hall, Stillwater, OK 74078; (405)744-8036; shelly.sitton@okstate.edu. 4OSU Department of Agricultural Education, Communications and Leadership; 448 Agricultural Hall, Stillwater, OK 74078; (405)744-8036; bakerma@okstate.edu. Abstract Connecting with the Millennial Generation can be challenging, as this generation is often described as unmotivated, incoherent and lazy. Servant leadership focuses on placing the needs of the follower before the needs of the leader, and empowers followers to take ownership for their efforts. Implementing quality mentorship through the lens of servant leadership could be a missing link to connecting purpose to content in college classrooms. The study describes firstsemester students’ perceptions of servant leadership in personal mentors at the beginning and end of the Fall 2014 Freshmen Orientation course in the College of Agricultural Sciences and Natural Resources at Oklahoma State University. Students rated accountability and empowerment as the highest servant leadership traits desired in their personal mentors in both the preand post-evaluations. The study yielded the following recommendations: Higher education institutions should develop student leadership groups around desired servant leadership qualities, such as accountability and empowerment; implement projects and assignments in classroom settings allowing students to take ownership of personal work; and investigate the influence of servant leadership in various college student settings. As the needs of college students evolve, the need to embrace student ownership and service in higher education programs becomes imperative.
Synthesis of 4-thia[5-13C]lysine

This report describes the synthesis of 4-thia[5-13C]lysine, an isotopomer of 4-thialysine that is an analog of lysine. It was synthesized from 2-amino[1-13C]ethanol hydrochloride (1) in two steps. In the first step, 1 was converted to 2-bromo[2-13C]ethylamine hydrobromide (2). The reaction of cysteine with 2 in basic condition followed by acidification afforded 4-thia[5-13C]lysine hydrochloride (3).
27 Myxococcus xanthus: Cultivation, Motility, and Development

This chapter presents a description of methods for cultivation of Myxococcus xanthus laboratory strains, as well as specific protocols for analysis of motility and development. Here the authors attempt to cover representative techniques, and to mention variations only occasionally. In nature, communities of M. xanthus reside in the soil on decaying plant material or herbivore dung and obtain nutrients by secreting digestive enzymes (such as proteases and lysozyme) to digest macromolecules from prey microorganisms or decaying organic matter. Initiation of the developmental program resulting in fruiting body formation requires (i) nutrient limitation, (ii) a solid surface, and (iii) sufficient population density. Fruiting body morphology and timing are greatly dependent on the medium surface. Therefore, solid media for development should be prepared the day before and plates should be cured (prewarmed) by incubating the plates with lids cracked open at least 20 min at 32oC just before use. M. xanthus powers its movement over solid surfaces by using two genetically distinct motility systems. Social (S) motility—the coordinated movement of cells in large groups—predominates on soft and moist surfaces and is directly mediated by the extension and retraction of polar type IV pili. Adventurous (A) motility—the movement of single isolated cells—predominates on harder and drier surfaces and has been proposed to be based on either a jet engine-like extrusion of carbohydrate slime, a twisting or inching-like motion on the part of the M. xanthus cell, or intracellular motors pushing against dynamic focal adhesion points within the cell.
Computational Studies on the Molecular Structure of the Hydrophobic Region PrP 109-136

Prion diseases caused by the conversion from a soluble normal cellular prion protein into insoluble abnormally folded infectious prions, are invariably fatal and highly infectious degenerative diseases that affect a wide variety of mammalian species. The palindrome and the Glycine-rich conserved segment in the hydrophobic region 109-136 control the conversion from normal prion protein to form into diseased prions. This paper gives detailed reviews on the 109-136 region and presents the studies of its 3D structures and structural dynamics.
Mycobacterium Tuberculosis Signaling via c-AMP

Adelynate cyclases (ACs), which catalyze synthesis of cAMP from ATP and yield pyrophosphate as a by-product, can be classified into four different classes according to their common features: Class I cyclases, related to enterobacterial adenylate cyclases; Class II, toxic adenylate cyclases isolated from bacterial pathogens; Class III, a large and probably ancient class that comprises cyclases from both eukaryotes and prokaryotes and is strongly related to guanylate cyclases; and Class IV, with mainly one example that differs entirely from all other classes (McCue et al., 2000).
First description of the male of Gonatopus javanus (R.C.L. Perkins) determined by mitochondrial COI sequence (Hymenoptera: Dryinidae)

Gonatopus javanus (R.C.L. Perkins) was newly recorded from Japan and India. The males collected together with females of G. javanus from Japan were identified as previously unknown opposite sex of the species because they share identical sequences of mitochondrial COI. The sequence was different from that of G. clavipes (Thunberg) by 11%. The male of G. javanus was described as new to science. Doratulina producta (Matsumura) is implied as host in Japan. The utility of molecular marker to identify the dryinid taxa showing sexual dimorphism is discussed.
Remotely sensed vegetation phenology for describing and predicting the biomes of South Africa

Questions: What are the patterns of remotely sensed vegetation phenology, including their inter-annual variability, across South Africa? What are the phenological attributes that contribute most to distinguishing the different biomes? How well can the distribution of the recently redefined biomes be predicted based on remotely sensed, phenology and productivity metrics? Location: South Africa. Method: Ten-day, 1 km, NDVI AVHRR were analysed for the period 1985 to 2000. Phenological metrics such as start, end and length of the growing season and estimates of productivity, based on small and large integral (SI, LI) of NDVI curve, were extracted and long-term means calculated. A random forest regression tree was run using the metrics as the input variables and the biomes as the dependent variable. A map of the predicted biomes was reproduced and the differentiating importance of each metric assessed. Results: The phenology metrics (e.g. start of growing season) showed a clear relationship with the seasonality of rainfall, i.e. winter and summer growing seasons. The distribution of the productivity metrics, LI and SI were significantly correlated with mean annual precipitation. The regression tree initially split the biomes based on vegetation production and then by the seasonality of growth. A regression tree was used to produce a predicted biome map with a high level of accuracy (73%). Main conclusion: Regression tree analysis based on remotely sensed metrics performed as good as, or better than, previous climate-based predictors of biome distribution. The results confirm that the remotely sensed metrics capture sufficient functional diversity to classify and map biome level vegetation patterns and function.
Computational classification of small RNAs and their targets

Small RNAs, and in particular microRNAs, are currently receiving a great deal of attention due to their important roles in gene regulation and organism development. Recently, new high-throughput technologies have made it possible to sequence hundreds of thousands of small RNAs from a single experimental sample. In this thesis we develop new computational tools to process such high-throughput small RNA datasets in order to identify microRNAs and other biologically interesting small RNA candidates and to predict their target genes. We apply these tools to a variety of plant and animal datasets and present some novel discoveries including miRNAs involved in fruit development in tomato (Solanum lycopersicon).