Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and control of gene networks in living cells

System identification is a branch of control engineering aimed at developing computational approaches to derive, from measurement data, a quantitative dynamical model of a physical system able to predict its future behaviour. There is a long tradition in the successful application of system identification approaches to Medicine and Physiology, however, in Molecular Biology, only few attempts have been made to infer a quantitative model of gene regulation due to experimental limitations of current techniques. Indeed, whereas in Engineering it is now common to measure thousands of time-points at a desired sampling rate for a physical system to be modelled, this has been very difficult in Biology, where time-series data consist of very few samples. In order to overcome the current limitations, I devised an experimental platform based on a microfluidic device, a time-lapse microscopy apparatus and, a set of automated syringes all controlled by a computer, that allows to provide a time varying concentration of any molecule of interest (input) to a population of cells, and to measure the single-cell response in the form of the fluorescence level of a reporter protein, at a sufficiently high sampling rate, thus making it possible to evaluate the dynamics of the process of interest. I tested the experimental platform to implement and compare different linear and nonlinear system identification approaches to a transcriptional network in the yeast S. cerevisiae. The results I obtained confirm that the experimental system identification platform I developed can successfully be used to infer quantitative models of a eukaryotic promoter in a rapid and efficient manner. Moreover I have used the same experimental set up for the study and the it in-vivo implementation of novel feedback control strategies meant to precisely regulate the level of expression of a protein from the GAL1 endogenous promoter and from a complex synthetic transcriptional network in yeast cells. The proposed effective control approach, allows to generate custom time profiles of a desired protein, and it can be exploited to study trafficking or signalling pathways and the endogenous control mechanisms of a cell.
Microbial Composition and Structure of Aerobic Granular Sewage Biofilms

Microbial Composition and Structure of Aerobic Granular Sewage Biofilms S. D. Weber, G. Wanner, W. Ludwig, K. -H. Schleifer, and J. Fried Lehrstuhl für Mikrobiologie, Technische Universität München, Am Hochanger 4, 85350 Freising, Germany; Institut für Ökologie, Universität Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria; and Institute of Botany, Ludwig-Maximilians-Universität, Menzinger Str. 67, 80638 München, Germany
The Issues of Antioxidant Therapy

Interest in antioxidants and antioxidant therapy has been growing during the last decade. Antioxidants are generally considered to have the capability to protect people from harmful effects of reactive oxygen and nitrogen species (RONSs), including free radicals (FR), when these are present in excessive amounts. RONS and free radicals perform a variety of useful biological functions in the body. Their excess is controlled by a natural antioxidant protection system in humans. This protection is provided at three levels: by simple molecules (such as cysteine, glutathione (GSH), uric acid, ubiquinol, etc.), medium-molecular weight, and high molecular weight compounds (enzymes, etc.). Under certain adverse conditions, this system does not manage to provide adequate protection and the RONSs and free radicals begin to damage vital DNA, proteins, and lipids. In such a case, antioxidant therapy, which includes antioxidant supplements and foods containing natural antioxidants, has been suggested to be of possible benefit. However, there are many unresolved issues related to the effective use of an antioxidant therapy: 1. A person should know the content of antioxidants in everyday food products and its relation to the storage time and processing methods used. 2. How many antioxidants should a person consume? It is known that at high concentrations some antioxidants become pro-oxidants. 3. Are the antioxidants consumed by a person bioavailable and, if so, to what extent; for some food products, bioavailability has already been determined but most foods have not been examined. 4. Many antioxidants are digested by intestinal microflora before they reach the systemic blood circulation. 5. Even those antioxidants that do reach the blood are often rapidly metabolized; the role of their metabolites is unclear; there is some evidence that certain metabolites are also antioxidants. 6. How long do antioxidants and their metabolites stay in the body; how are they distributed in different organs; and when are they excreted? In order to answer these questions, the pharmacokinetics of antioxidants should be studied. 7. The presence of oxidative stress, i.e., excess amounts of RONSs and free radicals, can be detected by various oxidative stress markers but, in order to see the whole picture, the actual concentrations of RONSs
Molecular Differentiation of SevenMalassezia Species

ABSTRACT A system based on PCR and restriction endonuclease analysis was developed to distinguish the seven currently recognizedMalassezia species. Seventy-eight strains, including authentic culture collection strains and routine clinical isolates, were investigated for variation in the ribosomal DNA repeat units. Two genomic regions, namely, the large subunit of the ribosomal gene and the internal transcribed spacer (ITS) region, were amplified by PCR, and products were digested with restriction endonucleases. The patterns generated were useful in identification of five out of sevenMalassezia species. M. sympodialis was readily distinguishable in that its ITS region yielded a 700-bp amplified fragment, whereas the other six species yielded an 800-bp fragment.M. globosa and M. restricta were very similar in the regions studied and could be distinguished only by performing a hot start-touchdown PCR on primers for the β-tubulin gene. Primers based on the conserved areas of the Candida cylindracealipase gene, which were used in an attempt to amplifyMalassezia lipases, yielded an amplification product after annealing at 55°C only with M. pachydermatis. This specific amplification may facilitate the rapid identification of this organism.
Folic acid: investigation of its relevance for DNA methylation and the enzymes that reduce it.

DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation plays a key role in a wide variety of biological processes. Changes in DNA methylation patterns have also been implicated in the pathogenesis of many human diseases. Following up on a randomised control trial (RCT) studying the effects of prolonged folic acid supplementation during pregnancy, we sought to identify regions of the genome that altered their methylation status in response to intervention, considering the methyl-donor for DNA methyltransferase reactions is a product of folate metabolism. Using a genome-wide, array-based method of analysis on a subset of the cohort (n=6) from the RCT, we identified 5 novel folate-sensitive differentially methylated regions (FS-DMRs): Inosital hexakisphosphate kinase 1 (IP6K1), Chromosome 9 Open Reading Frame 44 (Chr9ORF44), RAS p21 protein activator 4 (RASA4), Sphingosine-1-phosphate lyase 1 (SPGL1) and Chromosome 19 Open Reading Frame 75 (Chr19ORF75). A confirmation analysis was carried out using a loci-specific method of analysis across the rest of the cohort (n = 238) on three of these FS-DMRs (IP6K1, RASA4, and Chr9ORF44), but they did not reach statistical significance. In a cell culture model, changes in methylation across selected regions were confirmed to have a significant impact on gene expression (IP6K1, RASA4 and GPS2). A final analysis of dihydrofolate reductase (DHFR), responsible for reducing folic acid to its active form, investigated whether specific post-translational modifications was a feature of this enzyme. Following up on a SUMOylation analysis of DHFR previously published in the literature, our own analysis did not yield the same results, exposing a potential source of false positive results from a commercially available kit wildly used in this field.
Chimeric Cyanovirin-MPER Recombinantly Engineered Proteins Cause Cell-Free Virolysis of HIV-1

Drexel University College of Medicine, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania, USA; Drexel University, School of Biomedical Engineering Science and Health Systems, Philadelphia, Pennsylvania, USA; Duke University, Department of Molecular Genetics and Microbiology, Durham, North Carolina, USA; Drexel University, Department of Chemical and Biological Engineering, Philadelphia, Pennsylvania, USA
Herpes Simplex Virus 1 Immediate-Early and Early Gene Expression during Reactivation from Latency under Conditions That Prevent Infectious Virus Production

Volume 79, no. 23, p. 14516–14525, 2005. Page 14523, column 1, first full paragraph, lines 11 to 15: The sentence beginning “Taken together” should read “Taken together, these data strongly suggest that production of infectious virus, followed by viral spread, for which evidence has recently been provided at 36 h p.e. (33), accounts for the bulk of increase in RNA expression detected after 24 h p.e. in untreated, explanted TG. ” Page 14525: The following should be added to the Discussion. “After these studies were completed, Sawtell and Thompson (33) presented immunohistochemical evidence of spread at 36 h p.e. These data and their detection of infectious virus by 22 h p.e. led those authors to suggest that earlier studies addressing transcriptional events in explanted ganglia from 24 to 48 h p.e. should be interpreted with caution. ”
Bacteria and yeasts from lakes on Deception Island

The bacterial and yeast flora of five lakes—Kroner Lake, a meltwater pool, Relict Lake and two unnamed lakes—on Deception Island in Antarctica were examined. During the sampling and isolation, special care was taken to ensure that the micro-organisms never experienced a temperature above 10 °C. Gram-negative, rod-shaped bacteria predominated in all of the lakes; Kroner Lake also contained large numbers of Gram-positive cocci. Yeasts were isolated from three of the lakes. An examination of the temperature characteristics of the predominant micro-organisms from the lakes showed that over three-quarters had optimum temperatures for growth below about 20 °C, while a third had maximum temperatures of about 20 °C. None of the thirty-one bacteria tested fermented lactose, raffinose or sucrose. Two strains fermented glucose, and one each glycerol and salicin. Several of the bacteria from Kroner Lake utilized compounds that may have been produced by the decomposition of algae in the lake.
Identity between Ramulus libanicus (Uvarov) and Ramulus turcus (Karabaḡ) (Insecta, Phasmatodea): body, egg and chromosome analysis

A detailed study of bisexual populations of stick insects collected near Samandaḡ (southern Turkey) showed that the brown females were Ramulus turcus (Karabaḡ), while males and greenish females morphologically corresponded to R. libanicus (Uvarov) from Mount Carmel. The identity of these two taxa was further supported by egg morphology and structure, which agree with earlier descriptions of R. libanicus. Karyological analysis furthermore showed a chromosome set of 2n = 30 with an XX‐XY sex‐chromosome mechanism which is unusual for stick insects and has never been described before among Ramulini. This supports the identity of R. turcus and R. libanicus and we conclude that these Turkish and Mount Carmel stick insects belong to the same bisexual species and that its name should be R. libanicus (Uvarov).
Search for novel proteolytic enzymes aimed at textile and agro-industrial applications: An overview of current and novel approaches

The types and sources of proteolytic enzymes, enzyme assays, strategies for fermentation yield improvement, and novel proteases and their applications in industrial sectors are widely covered in this review. We give a special focus on alkaline proteases for the textile and detergent industries, as well as for the degradation of keratin-rich wastes.
Diversity of the ribosomal internal transcribed spacers within and among isolates of Glomus mosseae and related mycorrhizal fungi

SUMMARY The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA was amplified, cloned and sequenced from spores of five isolates of the arbuscular mycorrhizal fungus Glomus mosseae and one isolate each of G. fasciculatum, G. dimorphicum and G. coronatum. The sequences comprised ITS1 (113-121 base pairs), 5.8S rRNA gene (154 base pairs) and ITS2 (222-230 base pairs). The ITS sequences were at least 84 % identical, but only distantly related to other published sequences. Their identification as Glomus sequences was confirmed by sequencing part of the adjoining SSU rRNA gene from one isolate; it was 980% identical to the published G. mosseae sequence. Two to four clones were sequenced from each isolate, and in many instances these were substantially different (up to 6 % divergence) even when they were obtained from a single spore. Sequences from a single isolate were generally, but not always, more similar to each other than to those from different isolates. In addition to base substitutions, many ITS sequences differed slightly in length because of the insertion or deletion of up to three nucleotides within short runs of a single base, generally A or T. These changes were found at 22 separate sites within the ITS, and were more common between than within isolates. Phylogenetic relationships deduced from length variation and from base substitution were similar. The variation among isolates from different continents (Europe, Asia, South America) was no greater than among those from a smaller geographic range. The ITS1 and 2 sequences from G. coronatum were clearly distinct from the other isolates (11-16% divergence), but those of G. fasciculatum and G. dimorphicum fell within the range of variation exhibited by G. mosseae.
PARENTAL BEHAVIOR IN ANGUID LIZARDS

Abstract Among 21 species for which information is available (out of ca. 100 extant species), three diploglossines, five gerrhonotines, and six anguines attend their eggs during incubation, implying that parental behavior might be synapomorphic for the more inclusive clade Anguidae. A captive Gerrhonotus infernalis attended her clutch for 62 days, occasionally left it to feed and defecate, and did not pursue prey in the presence of her neonates. Viviparous Barisia imbricata, Elgaria coerulea, and Mesaspis moreleti consume extraembryonic debris and sometimes assist with birth; viviparous M. monticolus and Diploglossus fasciatus (mode of reproduction unknown) likely attend their neonates; and parental behavior is perhaps absent in viviparous Anguis fragilis and Ophiodes. Meager circumstantial evidence suggests that chemical cues influence those activities in anguids, and that thermoregulation, defense of eggs and/or young, and hygienic removal of spoiled eggs or birth debris are among the ecological advantages of their parental behavior. Viviparity has evolved at least four times within Anguidae, consistent with theoretical expectations that live birth is favored in egg-guarding taxa. These diverse lizards thus show much promise for studies of specialized parental investment in ectothermic vertebrates.
Loss of O157 O Antigenicity of Verotoxin-ProducingEscherichia coli O157:H7 Surviving under Starvation Conditions

Verotoxin (VT)-producing Escherichia coli O157:H7 was culturable on agar media after being left in water for 21 months. However, there were a number of colonies which had lost O157 O antigenicity. These colonies produced VTs, which are pathogenic to humans. These observations suggest that the immunologic methods based on O157 O antigenicity are unable to detect and isolate VT-producing E. coli in foods and other environments if the organism has been under starvation conditions for a long period. Transmission of Escherichia coli O157:H7 via water, such as drinking water and lake water, is important in E. coli O157:H7 infection (1, 4, 7, 9, 11, 14). It is suggested that water is con- taminated with E. coli O157:H7 by humans and animals har-boring the organism. There are several studies showing survival of E. coli O157:H7 in water for a long time under starvation conditions (12, 15, 16). For E. coli serotypes other than E. coli O157, expression of genes has been shown to be changed relative to the survival of the organism in water (3, 10). How-ever, for E. coli O157, it is uncertain whether such changes occur with survival. In the present study, we investigated the viability and change in the biochemical and
Detección de glucomacropéptido (gmp) como indicador de adulteración con suero de queseria en leche deshidratada

EL OBJETIVO DEL PRESENTE TRABAJO FUE DETECTAR AL GLUCOMACROPEPTIDO (GMP) COMO INDICADOR DE ADULTERACION CON SUERO DE QUESERIA EN TRES MARCAS DE LECHE DESHIDRATADA, DOS DE LECHE ENTERA Y UNA DE LECHE DESCREMADA, MEDIANTE LA TECNICA DE ELECTROFORESIS EN GEL DE POLIACRILAMIDA-SDS. EL ESTUDIO SE REALIZO EN EL LABORATORIO DEL DEPARTAMENTO DE MEDICINA PREVENTIVA Y SALUD PUBLICA DE LA FACULTAD DE MEDICINA VETERINARIA Y ZOOTECNIA, DE LA UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, SE ESTUDIARON MUESTRAS DE LECHE (N = 108) OBTENIDAS EN DIFERENTES EXPENDIOS DE LA CIUDAD DE MEXICO, CON EL PROPOSITO DE DETECTAR AL GMP, ENCONTRANDOSE 14.81% DE LAS MUESTRAS POSITIVAS. CON BASE EN LOS RESULTADOS OBTENIDOS EN LAS MUESTRAS DE LECHE DESHIDRATADA, SE CONCLUYE QUE TALES MARCAS COMERCIALES NO CUMPLEN LOS LINEAMIENTOS ESTABLECIDOS TANTO POR EL REGLAMENTO DE CONTROL SANITARIO DE PRODUCTOS Y SERVICIOS DE LA LEY GENERAL DE SALUD COMO POR LA NORMA OFICIAL MEXICANA NOM-091-SSA1-1999.
Citizen Science: A Developing Tool for Expanding Science Knowledge and Scientific Literacy

Citizen science enlists the public in collecting large quantities of data across an array of habitats and locations over long spans of time. Citizen science projects have been remarkably successful in advancing scientific knowledge, and contributions from citizen scientists now provide a vast quantity of data about species occurrence and distribution around the world. Most citizen science projects also strive to help participants learn about the organisms they are observing and to experience the process by which scientific investigations are conducted. Developing and implementing public data-collection projects that yield both scientific and educational outcomes requires significant effort. This article describes the model for building and operating citizen science projects that has evolved at the Cornell Lab of Ornithology over the past two decades. We hope that our model will inform the fields of biodiversity monitoring, biological research, and science education while providing a window into the culture of citizen science.
Time spent in the drift by downstream-dispersing invertebrates in a Lake District stream

1. The objective was to determine the time spent in the drift by different taxa of stream invertebrates. Most data were obtained from an earlier experimental study to determine the distances travelled by drifting invertebrates of 16 taxa in Wilfin Beck. Experiments were performed at two sites: ‘site 4’ in a stony, fast-flowing, section of stream, ‘site 3’ in a deeper stream section where macrophytes were abundant. 2. The significant relationship between the mean distance x (m) travelled in the drift and modal water velocity V (m s−1) was described by a power function in the earlier study but, as the power was close to one, a linear relationship has now been found to provide a satisfactory model. The rate of increase in x (m) with increasing V varied considerably between taxa. The mean time [mean t (s)] spent in the drift was estimated by dividing each x (m) by the appropriate V. Mean t (s) for each taxon was usually very constant over a wide range of V at each site (0.10–0.60 m s−1 at site 4, 0.15–0.53 m s−1 at site 3). A simple model estimated the time spent in the drift by different percentages (e.g. 75, 50, 10 and 1%) of the drifting invertebrates. 3. The experimental taxa at site 4 were divided into three groups according to the mean time spent in the drift. Mean t (s) for the five taxa in group 1 (32.8 s) was not significantly different from that obtained in control experiments with a mixed group of dead invertebrates. A similar time (33.0 s) was obtained for the five taxa in group 2, except at water velocities less than 0.2 m s−1 when the mean t (s) decreased to 15–21 s. Mean t (s) was constant for each of the six taxa in group 3, and significantly less than that for groups 1 and 2. Mean values ranged from 28.8 s for Ephemerella ignita to only 9.4 s for Baetis rhodani and Gammarus pulex. All mean values were lower at site 3, presumably because of the dense stands of macrophytes, with mean values of 12.9 s for the five taxa in group 1 (equalling the value for dead invertebrates). Mean values for the six remaining taxa varied from 6.4 s for Simulium spp. to only 4.9 s for Baetis rhodani and 4.8 s for Gammarus pulex. It was concluded from a discussion of this study that the time spent in the drift may provide a useful measure for comparing the downstream dispersal of invertebrates in different streams, and may be a useful addition to models for the drift feeding of salmonids.
Changes in cytochrome P4501A activity during development in common tern chicks fed polychlorinated biphenyls, as measured by the caffeine breath test

Cytochrome P4501A (CYP1A) activity is often used as a biomarker of exposure of wildlife to polyhalogenated diaromatic hydrocarbons and is usually measured ex vivo in liver tissue. A caffeine breath test (CBT) with radiolabeled substrate (14C‐caffeine) was used to measure in vivo CYP1A activity twice during development in 14 common tern (Sterna hirundo) chicks treated with polyhalogenated diaromatic hydrocarbons. Tern hatchlings were fed fish spiked with 3,3′,4,4′,5‐pentachlorobiphenyl (PCB 126) and 2,2′,4,4′,5,5′‐hexachlorobiphenyl (PCB 153) such that the diet contained an average of 23, 99, or 561 pg of 2,3,7,8‐tetra‐chlorodibenzo‐p‐dioxin equivalents per gram offish for 21 d. Sixteen additional common tern chicks were similarly dosed with polyhalogenated diaromatic hydrocarbons but were not subjected to the CBT procedure. In weeks 1 and 2, caffeine N‐demethylation and ethoxyresorufin‐O‐deethylation activity on day 21 were elevated in birds that received the greatest PCB dose. There was less constitutive and greater induction of ethoxyresorufin‐O‐deethylation activity than caffeine N‐demethylation. The 14C‐CBT was less invasive than the ethoxyresorufin‐O‐deethylase assay. Only one morphological parameter differed significantly between CBT subjects and no‐CBT subjects fed the same level of PCBs. Bursa weight was significantly less in control CBT subjects than in control no‐CBT subjects, but bursa weights did not differ among CBT and no‐CBT birds from the two PCB treatment groups. No alterations of survival or growth occurred in CBT subjects compared with no‐CBT subjects.
EPIDEMIOLOGY OF MONGOLISM: THE MANITOBA STUDY *

Following the sudden burst of renewed interest in the pathogenesis of mongolism, many reports on the cytogenetics of numerous series of mongoloid patients have been p ~ b l i s h e d . ~ ~ ~ ~ ~ ~ ’ ~ Very few, however, can be said to be unbiased samples. The purpose of the present investigation was to examine a random series of mongoloids in order to obtain an estimate of the frequency of the various types of chromosomal aberrations and to look for genetic markers among individuals of known karyotype.