Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Phosphatase 6 Subunit with Conserved Sit4-associated Protein Domain Targets IκBϵ*

Protein Ser/Thr phosphatases compose a PPP family that includes type-2 PP2A, PP4, and PP6, each with essential functions. The human PP6 gene rescues sit4ts mutants of Saccharomyces cerevisiae, and Sit4 phosphatase function depends on multiple Sit4-associated protein (SAP) subunits. We report here finding a SAPS sequence domain encoded in only a single gene each in Schizosaccharomyces pombe, Caenorhabditis elegans, and Drosophila but in three distinct open reading frames in Xenopus, Mus musculus, and Homo sapiens. The SAPS proteins are more divergent in sequence than PP6. Northern hybridization showed differential distribution of the human SAPS-related mRNA in multiple human tissues, named as PP6R1, PP6R2, and PP6R3. Antibodies were generated, distribution of endogenous PP6, PP6R1, PP6R2, and PP6R3 proteins was examined by immunoblotting, and the abundance of mRNA and protein in various tissues did not match. FLAG-tagged PP6R1 and PP6R2 expressed in HEK293 cells co-precipitated endogenous PP6, but not PP2A or PP4, showing specificity for recognition of phosphatases. The SAPS domain of PP6R1 alone was sufficient for association with PP6, and this predicts that conserved sequence motifs in the SAPS domain accounts for the specificity. FLAG-PP6R1 and FLAG-PP6R2 co-precipitated HA-IκBϵ. Knockdown of PP6 or PP6R1 but not PP6R3 with siRNA significantly enhanced degradation of endogenous IκBϵ in response to tumor necrosis factor-α. The results show SAPS domain subunits recruit substrates such as IκBϵ as one way to determine specific functions for PP6.
The Purification and Characterization of Bacillus subtilis Tripeptidase (PepT)

A tripeptidase (PepT) was purified to homogeneity from Bacillus subtilis through four sequential chromatographies including DEAE-Sepharose ion exchange, hydroxylapatite, mono-Q FPLC ion exchange, and Superose-12 FPLC gel filtration. The apparent molecular mass of the enzyme was 49,200 Da and 51,400 Da as determined by sodium dodecylsulfatepolyacrylamide gel electrophoresis (SDS-PAGE) and gel filtration chromatography, respectively, and the enzyme exists in a monomeric form. The physicochemical properties of the enzyme were as follows: optimum pH at 7.5, optimum temperature at , and pI at 4.9. The and values of the enzyme were 4.3 mM and 2.5 mmol/min/mg, respectively, with MetAla-Ser as substrate. The B. subtilis PepT requires ion(s) for activation, while it is inactivated by EOTA and 1,10-phenanthroline, suggesting that it is a metalloprotein. The enzyme was not inhibited by any of serine protease, aspartic protease, or leucine aminopeptidase inhibitors. The enzyme showed comparable activities towards four different substrates including Met-Ala-Ser, Leu-Gly-Gly, Leu-Ser-Phe, and Leu-Leu-Tyr. The amino terminal sequence of PepT determined by Edman degradation was found to be MKEEIIERFTTYVXV and turned out to be identical to that of PepT deduced from a cloned B. subtilis pepT.
Ethephon Reduction of Redroot Pigweed (Amaranthus retroflexus) Seed Populations

Freshly collected redroot pigweed seeds were buried 5 cm deep in the field in November of 3 yr in succession. Treatments applied to the soil surface included KNO3 (400 kg ha-1) in midwinter, ethephon (11 kg ha-1) in late spring, and a soil cover (polyethylene sheet for 2 wk) in late spring. Seeds were recovered within 1 yr after treatment, examined for in situ germination, and tested for viability. The 3-yr averages for viable seeds remaining by October in the year after treatment with KNO3 or soil cover, either alone or in combination, did not differ from nontreated checks and averaged 47% of the original population. Viable seeds remaining in soil treated with ethephon either alone or combined with KNO3 were reduced to 21% of the beginning population. The most effective treatments were ethephon either combined with a soil cover or with a soil cover plus KNO3 which reduced the viable seeds to an average of 8% of the original. Ethephon plus a soil cover has the potential to reduce greatly redroot pigweed seed populations in the field.
Geometry underlies the mechanical stiffening and softening of thin sheets

A basic paradigm underlying the Hookean mechanics of amorphous, isotropic solids is that small deformations are proportional to the magnitude of external forces. However, slender bodies may undergo large deformations even under minute forces, leading to nonlinear responses rooted in purely geometric effects. Here we identify stiffening and softening as two prominent motifs of such a material-independent, geometrically-nonlinear response of thin sheets, and we show how both effects emanate from the nontrivial yet generic features of the stress and displacement fields. Our insights are borne out of studying the indentation of a polymer film on a liquid bath, using experiments, simulations, and theory. Starting at small displacement, the first nonlinearity occurs when radial retraction of the film begins to reduce azimuthal stresses --- this underlies a wrinkling instability and causes the effective spring constant of the system to stiffen as radial forces are transmitted more effectively through the sheet. The response then softens when the sheet reaches large slopes, indicating a second nonlinearity that is accompanied by localization of the vertical profile. We thus find that stiffening is due to growing anisotropy of the stress field whereas softening is due to changes in the overall shape. These general mechanisms should apply to any sufficiently thin sheet, and we discuss similarities with the mechanics of fiber networks, suggesting that our results are relevant to a wide range of two- and three-dimensional materials.
Interventies jeugdige daders cybercrime

Met de sterke groei van de mogelijkheden en het gebruik van internet in de afgelopen decennia is ook de criminaliteit in de digitale wereld (cybercrime) aanzienlijk toegenomen. Jongeren zijn sterk vertegenwoordigd op het internet en uit onderzoek blijkt dat zij ook relatief vaak dader zijn van cybercrime. Er is echter nog weinig systematisch inzicht in mogelijke interventies die dit daderschap kunnen terugdringen. Dit onderzoek heeft als doel dit inzicht ter vergroten ten einde beter te kunnen voorkomen dat jongeren beginnen of doorgaan met het plegen van cybercrime. Daartoe wordt onderzocht wat bekend is over de opzet, (beoogde) werking en effecten van interventies gericht op het voorkomen en/of tegengaan van cybercrime onder jongeren.
Evaluation of thrips resistance in pepper to control Tomato spotted wilt virus infection

The objective of this study was to analyse the effect of thrips ( F. occidentalis ) resistance in pepper ( Capsicum ) on the spread of Tomato spotted wilt virus (TSWV). Results demonstrate that the rate of primary TSWV-infection is effectively limited in a thrips-resistant (TR) pepper crop compared to a thrips-susceptible (TS) crop, and that this is based on a decreased preference of thrips for TR plants. Secondary TSWV-infections were effectively restricted in the TR pepper crop and this is based on a greatly reduced thrips population built-up. The effect of thrips resistance on the spread of TSWV was also analysed in a virus-resistant genotype. TSWV-resistant plants respond with a hypersensitive reaction after infection with TSWV, resulting in necrotic local lesions on leaves and fruits. Under the same infection pressure, fewer local lesions were found in the thrips-resistant accession PI 152225 than in the thrips-susceptible PI 159236 accession, indicating a synergistic effect of thrips- and virus resistance. Studies presented in the last part of the thesis show mutual benefits for F. occidentalis and TSWV from the attraction to virus-infected plants. Attraction resulted in more offspring on these plants and thereby enhancing the chance for virus transmission. Besides, thrips developed significantly faster on TSWV-infected plants than on non-infected plants. It was demonstrated that volatiles released from TSWV-infected plants may be involved in the attraction of thrips to TSWV-infected plants.
Site-specific labeling of cellular proteins with unnatural substrates of biotin ligases

E. coli biotin ligase (BirA) catalyzes the site-specific ligation of biotin to the lysine within its 15-amino acid peptide substrate (AP). We harnessed the high peptide substrate specificity of BirA to develop a general methodology for site-specific protein labeling with biophysical probes. We synthesized an isosteric ketone analog of biotin and discovered that BirA also ligates it to the AP with similar kinetics while retaining the high peptide specificity of the native reaction. Because ketones are absent from native cell surfaces, recombinant AP-fused cell surface proteins can be tagged with the ketone analog, and then specifically conjugated to hydrazideor hydroxylamine-functionalized molecules. We demonstrated this two-step protein labeling methodology on purified protein, in the context of mammalian cell lysate, and on epidermal growth factor receptor expressed on the surface of live HeLa cells. Both fluorescein and a benzophenone photoaffinity probe were incorporated, with total labeling times as short as 20 minutes. To develop new protein labeling methodology, we synthesized azide analogs of biotin, but found that BirA did not accept them as substrates. Our efforts to rationally design mutations in the active site to accommodate these analogs met with little success. We thus investigated in vitro compartmentalization as a platform for re-engineering the substrate specificity of BirA through in vitro evolution. Selections did not enrich for BirA mutants that could catalyze ligation of the azide analog to the AP, but instead highlighted the technical difficulties of our in vitro compartmentalization strategy. We used phage display to engineer a new and orthogonal biotin ligase-acceptor peptide pair for site-specific protein labeling. Yeast biotin ligase (yBL) does not biotinylate the AP, but we discovered a new 15-amino acid substrate for yBL, which we call the yeast acceptor peptide (yAP). The yAP is not biotinylated by BirA, and thus we were able to specifically label AP and yAP fusion proteins co-expressed in the same cell with differently colored quantum dots. We fused the yAP to a variety of recombinant proteins and demonstrated biotinylation by yBL at the N-terminus, C-terminus, and within a flexible internal region. yBL is also very sequence-specific, as endogenous proteins on the surface of yeast and HeLa cells are not biotinylated. This new methodology expands the scope of biotin ligase labeling to two-color imaging and yeastbased applications. Thesis Supervisor: Alice Y. Ting Title: Pfizer-Laubach Associate Professor of Chemistry
Size and trends of the House Sparrow Passer domesticus population in Great Britain

House Sparrow Passer domesticus populations have declined throughout Europe over the last two to three decades; this is of particular concern in urban areas. We analysed data from extensive census schemes organized by the British Trust for Ornithology to determine the current population size of the House Sparrow in Britain, and to assess long-term patterns of change, both in the wider countryside and in urban environments. The national breeding population of House Sparrows was estimated at approximately 13 million individuals (95% confidence interval, 11.9-14.8 million), or about six million pairs. Most of these occur in southeast England and densities are greatest in suburban and rural garden habitats. Overall, populations in rural areas have declined by 47% since the mid 1970s, whereas those in urban and suburban areas have declined by about 60%. Changes in farming practices are likely to account for at least some of the decline in the wider countryside, probably related to changes in food resources, with a loss of grain in fields and more secure storage of harvested grain, though these changes are unquantified. In urban areas, there was an earlier period of decline in the first half of the 20th century due to the loss of horse-drawn transport and generally cleaner streets. The overall national decline since the 1970s masks much heterogeneity in trend among regional populations, and evidence suggests that population processes in the House Sparrow may be relatively fine-grained.
The Giant Pandas of Wolong

The giant panda is threatened with extinction. Only about a thousand survive in the wild in China, about half of them protected in reserves. In an effort to save this remarkable species, the government of China and the World Wildlife Fund began cooperative research in 1980. "The Giant Pandas of Wolong" is not only the first report of this joint venture but also the first detailed account of the panda's natural history. It describes the environment, distribution, life cycle, and daily and seasonal activities of pandas in the wild. Although giant pandas have few natural enemies, the periodic die-off of bamboo, their main food, threatens their survival. In order to understand the panda's vital link to bamboo, the research team has explored many aspects of the animal's life, collecting information on both wild and captive pandas. Though a herbivore, the panda retains the simple digestive tract of a carnivore. Unable to digest cellulose in plants, it receives relatively little nutrition from the bamboo it eats. As a result, it must eat many kilograms of bamboo each day, foraging for fourteen hours or more throughout a day and night. Known to the Chinese for several thousand years as "daxiongmao," "large bear-cat," the giant panda has defied easy classification. The authors review anatomical, biochemical, behavioral, and paleontological evidence, concluding that the animal is neither bear nor raccoon but belongs in a separate family, perhaps with the small red panda. The giant panda has captured the imagination of the public more than any other animal. By presenting their groundbreaking and crucial research to the public, the authors of "The Giant Pandas of Wolong "hope to spur further research and action that will help this precious animal survive.
Automatization of an inverse surface temperature modelling procedure for Greenland ice cores, developed and evaluated using nitrogen and argon isotope data measured on the Gisp2 ice core

In order to study Northern Hemisphere climate interactions and variability during the Holocene, access to high resolution surface temperature records of the Greenland ice sheet is an integral condition. Surface temperature reconstruction relies on firn densification combined with gas and heat diffusion [Severinghaus et al. (1998)]. In this study we use the model developed by Schwander et al. (1997). A theoretical δ15N record is generated for different temperature scenarios and compared with measurements by minimizing the mean squared error (MSE). The goal of the presented study is an automatization of this inverse modelling procedure. To solve the inverse problem, the Holocene temperature reconstruction is implemented in three steps. First a rough first guess temperature input (prior) is constructed which serves as the starting point for the optimization. Second, a smooth solution which transects the δ15N measurement data is generated following a Monte Carlo approach. It is assumed that the smooth solution contains all long term temperature trends and (together with the accumulation rate input) drives changes in firn column height, which generate the gravitational background signal in δ15N. Finally, the smooth solution is superimposed with high frequency information directly extracted from the δ15N measurement data. Following the approach, a high resolution Holocene temperature history for the Gisp2 site was extracted (posteriori), which leads to modelled δ15N data that fits the measurements in the low permeg level (MSE) and shows excellent agreement in timing and strength of the measurement variability. To evaluate the reconstruction procedure different synthetic data experiments were conducted underlining the quality of the method. Additionally, a second firn model [Goujon et al. (2003)] was used, which leads to very similar results, that shows the robustness of the presented approach.
The Role of the Regenerating Protein Family on Skeletal Muscle Regeneration

Skeletal muscle regeneration is dependent upon the influences of intrinsic and extrinsic factors that stimulate satellite cells. Regenerating proteins are upregulated at the onset of trauma or inflammation in the pancreas, gastrointestinal tract, liver, neural cells and other tissues. Studies have shown that Reg proteins have a mitogenic, anti-apoptotic and anti-inflammatory function in damaged tissues and is necessary for normal progression of regeneration. As skeletal muscle is also able to regenerate itself at a rapid rate, it seems highly likely that Reg proteins function to promote myogenesis in skeletal muscle regeneration. Therefore, the goal of our research was to characterize the expression of the Reg proteins and receptor in regenerating skeletal muscle and satellite cells, investigate the effect of exogenous Reg protein on myogenesis, and to examine direct Reg protein effect on satellite cell activity. To determine whether Reg proteins participate in skeletal muscle regeneration, mice were injected with marcaine in their tibialis anterior muscles to induce skeletal muscle damage. The gene expression analysis of undamaged and marcaine-damaged tibialis anterior muscles and mice satellite cells showed that Reg I, II, IIIα, IIIγ, IV and EXTL3 genes are present during skeletal muscle regeneration and satellite cells significantly express Reg I, IIIα, IIIγ and EXTL3. As Reg I and IIIα are most prevalent in vivo and in vitro respectively, we advocate these isoforms as the predominant candidates in skeletal muscle regeneration. To determine the effect of exogenous Reg protein on myogenesis, we performed gene expression and muscle morphometry analysis of Reg IIIα or PBS injected tibialis anterior muscles. Interestingly, our results indicate that the addition of Reg IIIα to damaged muscles
Identification and Functional Characterization of CNS Pericytes and the Role they Play in Neurovascular Coupling in Physiological and Pathological Conditions

Brain blood flow increases, evoked by neuronal activity, power neural computation and are the basis of BOLD functional imaging. However, it is controversial whether blood flow is controlled solely by arteriole smooth muscle, or also by capillary pericytes. The experimental work within this thesis examines capillary pericytes, and the role they play in neurovascular coupling in physiological and pathological conditions. I show that pericytes can be identified using several protein markers and that, using the same technique, pericytes can be distinguished from other perivascular cell types. I demonstrate that pericytes respond to the neurotransmitters noradrenaline and glutamate. Noradrenaline depolarizes pericytes and constricts capillaries, and this constriction reflects pericyte contraction while glutamate, mimicking neuronal activity, hyperpolarizes pericytes and dilates capillaries, and this dilation reflects pericyte relaxation. Glutamate-evoked dilation is mediated by prostaglandin E₂ or a related compound acting at EP4 receptors, but requires nitric oxide release to suppress synthesis of the vasoconstrictor 20-HETE. In pathology, I show that pericytes die when exposed to ischaemia. This may lead to pericytes irreversibly constricting capillaries and to damage of the blood-brain barrier. Pericyte death increases on reperfusion after ischaemia, and is reduced by block of glutamate receptors or Ca2+ removal, but not by scavenging reactive oxygen species. These data establish pericytes as active regulators of capillary tone and thus as potential regulators of brain blood flow. My data also suggest prevention of pericyte death as a strategy to reduce the long-lasting blood flow decrease which contributes to neuronal death after stroke. This thesis also contains a discussion of how energy supply to the brain alters with age, and how this may affect the BOLD signal.
Metabolic analysis of neural tube defects

Neural tube defects (NTDs), such as exencephaly and spina bifida, occur when the neural tube fails to close properly during embryonic development. Folic acid supplementation has been shown to effectively reduce the occurrence of NTDs and low folate is a known risk factor for human NTDs. However despite extensive research, the mechanism explaining how the folate status affects the incidence of NTDs remains unknown. One effect of sub-optimal folate could be suppression of the methylation cycle, which is interlinked with the folate cycle. To explore this hypothesis, a method has been developed to quantitatively measure the substrate, S-Adenosylmethionine (SAM), and the product, S-Adenosylhomocysteine (SAH), of methylation reactions in neurulation-stage mouse embryos by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). To investigate the link between methylation perturbation and neural tube defects, the abundance of SAM and SAH has been quantified in a series of experimental models and human NTD cell lines. Using a folate-deficient diet, this study also investigates folate deficiency using mouse models (splotch and curly tail) for NTDs. Results illustrate that folate deficiency, in both mouse models, caused an increase in the incidence of neural tube defects and, embryos were growth retarded. To examine the effect the folate deficient diet was having on endogenous folate metabolism, embryonic folate levels were analysed, in addition to maternal folate. Furthermore, using the established Ic-ms/ms method, the effect of folate deficiency on the abundance of SAM and SAH was determined. Increasing evidence suggests that myo-inositol may prove effective in preventing NTDs, in conjunction with folic acid. Thus, a double-blind, randomised clinical trial has been designed to investigate this and, in order to monitor patient compliance an LC-MS/MS method has been developed to quantify myo-inositol in urine.
Statistische genomweite Analyse von MeDIP-Seq Daten zur Identifizierung differentiell methylierter Regionen.

During the last years, novel DNA sequencing technologies have been developed. Next Generation Sequencing offers the opportunity to sequence entire genomes fast and cost-efficient. The biggest challenge for next generation sequencing approaches is the development of experiment specific data-analysis software. Within this study a new tool for the analysis of sequencing data derived from high-throughput Methyl-DNA Immunoprecipitation (MeDIP-Seq) experiments has been developed. In particular various statistical tests were applied in order to identify differentially methylated regions within the genome. The newly developed methods were used to analyse MeDIP-Seq data from 14 colorectal cancer patients and differentially methylated genomic regions were identified. These regions showed DNA methylation differences between 5 tumor and normal tissue. Based on the identified differentially methylated regions, a clustering approach was performed. The results show that the several examined samples can be classified into separated groups according to their histological origin. Subsequently, the identified regions were analyzed for biologically relevant coherency and were annotated by known biological functions. Finally, for selected regions, known biomarkers were visualized in the UCSC Genome Browser. Schlüsselwörter: MeDIP-Seq, DNA Methylierung, Darmkrebs
Interrelationships of Fishes

Preface. Teaching as Applied Behavior Analysis: A Professional Difference. The Learn Unit: A Natural Fracture of Teaching. The Repertoires of Teachers Who Are Behavior Analysts. The Strategic Analysis of Instruction and Learning. Teacher Repertoires for Students from Prelistener to Early Reader Status. Teaching Practices for Students with Advanced Repertoires of Verbal Behavior (Reader to Editor of Own Written Work). Behavioral Selection and the Content of Curriculum. Writing and Designing Curricula. Teaching and Mentoring Teachers. The School Psychologist and Other Supportive Personnel: A Contemporary Behavioral Perspective. Glossary. Index.