Miracle-dz/UniFAR-FTUs huggingface dataset:
Stay-on-Task Exercises as a Tool To Maintain Focus during a CRISPR CURE

Course-based undergraduate research experiences (CURE) offer the chance for students to experience authentic research investigation in a classroom setting. Such hands-on experiences afford unique opportunities work on a semi-independent research project in an efficient, structured environment. ABSTRACT Course-based undergraduate research experiences (CURE) offer the chance for students to experience authentic research investigation in a classroom setting. Such hands-on experiences afford unique opportunities work on a semi-independent research project in an efficient, structured environment. We have developed a CRISPR CURE in which undergraduate and graduate students use in silico, in vitro, and in vivo techniques to edit a fungal genome. During the development of this course, we have found that the asynchronous nature of the CRISPR CURE activities can be disruptive and lead to unproductive class time. To overcome this challenge, we have developed stay-on-task exercises (SOTEs). These short low-stakes assessments provide structured activities that are performed during these asynchronous incubation periods. SOTE activities leverage potentially unproductive class time and complement the CURE learning objectives. We have found SOTEs to be one method of maintaining classroom structure during a CURE. Furthermore, SOTE complexity, length, and subject can be easily modified to match course learning objectives.
Affordable Diffusion Microchamber Array Designs for Isolating Microbes in Classrooms and Laboratories

Diffusion microchamber array (DMA) devices have provided contemporary microbiologists with a successful alternative to the century-old plating method using petri dishes to isolate and cultivate environmental bacteria. The “ichip” DMA device, developed by the research group of Slava Epstein, is exemplary of this technology, using membranes to culture rare or otherwise nonmodel bacterial taxa, whereby the target cells are nourished by environmental medium across the separating membrane. ABSTRACT Diffusion microchamber array (DMA) devices have provided contemporary microbiologists with a successful alternative to the century-old plating method using petri dishes to isolate and cultivate environmental bacteria. The “ichip” DMA device, developed by the research group of Slava Epstein, is exemplary of this technology, using membranes to culture rare or otherwise nonmodel bacterial taxa, whereby the target cells are nourished by environmental medium across the separating membrane. However, DMA devices have not sufficiently infiltrated the university-level microbiology curriculum, and the size and shape of the ichip make the device challenging for use by students. The following work provides guidance in the creation and use of a suite of DMA devices called “iplates,” which are ichip-like tools for use in microbiology education. An iplate mimics the shape and size of a 96-well plate, making it a simpler, more affordable, and customizable design for the isolation and incubation of bacteria and other microorganisms using fresh environmental media. Iplates and their many customizations are intended to enable teachers, students, and researchers to isolate, grow, and analyze the widest possible diversity of microorganisms, complementing standard plating methods. We offer additional tips and tools to help instructors and students get started creating DMA devices to meet their unique needs and research interests.
Cation-dependent Flocculation in a Flavobacterium Species Predominant in Activated Sludge

The predominant bacterium of activated sludge classified as belonging to the genus Flavobacterium showed good flocculent growth in the presence of both calcium and magnesium ions, although capsular material or gelatinous matrix was not detectable in the flocs. The bacterium accumulated a large amount of poly-β-hydroxybutyrate when grown on glucose, but not on peptone, in spite of good flocculent growth on both substrates. When the flocs formed during growth phase were suspended in deionized water and shaken for a few minutes, they disintegrated perfectly, and a uniformly dispersed cell suspension was obtained. Furthermore, when the dispersed cell suspension thus obtained was added with each of various mineral salts and shaken for a few minutes, the cells flocculated again, the resultant supernatant solution being almost clear. Even if the dispersed cells were killed by heat or treated by trypsin, they did not lose the ability to form flocs when added with mineral salts. Since the electric charge of the cell surface was negative, a possible mechanism of floc formation was suggested as follows: negatively charged surfaces of adjacent cells are bridged by ionic bonds intermediated by cations. The bacterium utilized a relatively wide variety of organic compounds and showed high metabolic activity comparable to that of naturally activated sludge. These properties, along with floc-forming ability, were considered to be factors for making the bacterium predominant in activated sludge.
Separation of Prodigiosenes and Identification as Prodigiosin Syntrophic Pigment from Mutant Pairs of Serratia marcescens

Countercurrent distribution is capable of resolving mixtures of closely related prodigiosene pigments. Syntrophic pigment produced by several pairs of Serratia marcescens color mutants was identified as prodigiosin (2-methyl-3-amyl-6-methoxyprodigiosene) by countercurrent distribution, soda lime pyrolysis, and other techniques. The metabolic block of mutant strain H-462, derived from parent strain HY, was located between the blocks of mutant strains OF and WF, both derived from parent strain Nima.
Fatty acids of the genus Bacillus: an example of branched-chain preference

Unsaturated Fatty Acids . 401 Stereospecific Synthesis of Anteiso Fatty Acids . 401 Branched, Short-Chain Fatty Acids . 401 FACTORS AFFECTING FATTY ACID PATTERN AND CONTENT . 402 Pattern of Saturated Fatty Acids . 402 Relative activity of chain initiators . 402 Factors related to chain initiators . 403 Factors related to chain extender . 405
Cytotoxic and Apoptotic Eff ects of Curcumin on D-17 Canine Osteosarcoma Cell Line [1]

Cancer is a major health problem in dogs. Types of cancer seen in dogs include melanoma, Non-Hodgkin lymphoma, osteosarcoma, soft tissue sarcomas and prostate, breast, lung and colorectal carcinomas. Osteosarcoma (OSA) is the most common malignant primary bone tumor in domestic dogs. It constitutes 85% of skeletal tumors. It is derived from primitive bone cells that occur in both the appendicular (~75%) and axial (~25%) skeleton. The present study was intended to determine the cytotoxic and apoptotic eff ects of curcumin administration at certain doses and in certain periods on D-17 canine osteosarcoma cells. Canine osteosarcoma cells were treated with curcumin and the eff ects of it on proliferation were determined by WST-1, apoptosis by caspase 3/7 activity (MuseCaspase 3/7) and the ratio of proapoptotic Bax gene to antiapoptotic Bcl-2 gene expression level by qRT-PCR. Our data demonstrated that curcumin decreased cell proliferation and viability, ultimately inducing caspase 3/7 mediated apoptosis in treated D-17 canine osteosarcoma cells. Furthermore, the application of curcumin on canine osteosarcoma cells downregulated the expression of Bcl-2 and upregulated the expression of proapoptotic gene Bax. Thus, these results may provide a basis for further study of curcumin in the treatment of canine osteosarcoma.
Rapid Extraction Method with Pronase B for Grouping Beta-Hemolytic Streptococci

The enzyme, Pronase B, was used to extract the C carbohydrates of betahemolytic streptococci for serological grouping. Reference strains of streptococci, groups A through N, were accurately grouped by using this extraction method. Of the beta-hemolytic streptococci isolated from patients' cultures, 1,197 were classified as either group A or not group A by this method. There was 100% correlation with the reference Lancefield method. In contrast, false reactions occurred with the presumptive bacitracin disc method in 4.1% of the group A and 12.7% of the non-group A cultures. The Pronase method proved simple, accurate, and readily adaptable to the clinical laboratory routine.
Production of Tumor-Inhibitory L-Asparaginase by Submerged Growth of Serratia marcescens

Production of a tumor-inhibitory asparaginase by submerged fermentation with Serratia marcescens ATCC 60 was studied to ascertain optimal nutritional conditions for large-scale production leading to enzyme purification studies. Five strains of S. marcescens were screened in shake-flask studies and were found to produce 0.8 to 3.7 IU/ml 48 hr after inoculation. The requirements for asparaginase production with S. marcescens ATCC 60, the high producing strain, included the following: 4% autolyzed yeast extract medium (initial pH 5.0), an incubation temperature of 26 C, and limited aeration for a zero level of dissolved oxygen during the fermentation. Addition of various carbohydrates to the fermentation medium did not enhance yields. The peak cell population in the fermentation medium and the maximal asparaginase yields occurred simultaneously. Highest enzyme yields were found when the pH of the fermentation cycle rose to approximately 8.5. Yields of 4 IU of asparaginase/ml of cell suspension have been obtained consistently in 40 to 42 hr from 10-liter volumes (500 ml/4-liter bottle) produced on a reciprocating shaker. Scale-up to a 60-liter fermentor yielded 3.1 IU/ml in 35 hr.
Method for the Preferential Isolation of Actinomycetes from Soils

Species of the genus Streptomyces and of related genera of the Actinomycetales, at one time considered to be microbiological curiosities of no great economic importance, have become the subjects of intensive searches for sources of new, biologically active compounds. The demonstrated ability of these microorganisms to produce useful antibiotics and to carry out other transformations of commercial interest has focused attention on factors bearing on their isolation from their natural habitat, the soil. It would be desirable, therefore, to be able to isolate aerobic soilinhabiting actinomycetes with a minimum of interference from associated bacteria and higher fungi. There have been a number of reports in the literature dealing with selective isolation of the higher fungi at the expense of bacteria or of bacteria at the expense of molds. Several investigators used antibiotics as the selective agents. For example, Beech and Carr (1955) found cycloheximide, gliotoxin, and frequentin to be effective selective yeast and mold inhibitors in apple juices and ciders. Phillips and Hanel (1950) found cycloheximide to be inactive against representatives of 27 species of bacteria and suggested that this antifungal antibiotic might be used to rid bacterial cultures of contaminating molds. On the other hand, Butler and Hine (1958) selectively isolated fungi from soil plated
Nontoxic (CH3NH3)3Bi2I9 perovskite solar cells free of hole conductors with an alternative architectural design and a solution-processable approach

Methylammonium iodide bismuthate ((CH3NH3)3Bi2I9) (MBI) perovskite was introduced as a new lead-free and air-stable absorber for hole conductor-free perovskite solar cells. The two-step soaking-assisted sequential solution (2-S) method was adopted to fabricate MBI films for the first time. We compared the formation processes and final morphologies of the MBI films fabricated using the 1-S and 2-S methods on planar and mesoporous TiO2 layers, respectively. We also investigated the effects of the morphologies of MBI films and device architectural design on device performance. Results showed that the MBI films fabricated using the 2-S method achieved a superior coverage both on the compact TiO2 and mesoporous TiO2 layers. The mesoporous structure devices presented higher power conversion efficiencies than the planar structure devices. In addition, all devices exhibited excellent thermal and long-term stabilities. The presented architectural design and solution-processable approach could inspire further research and practical applications on lead-free organic–inorganic hybrid perovskite solar cells.
Factors affecting the growth of canine herpesvirus in dog kidney cells

A virus morphologically similar to the herpesviruses and designated canine herpesvirus (CHV) has recently been isolated from neonatal and fetal dogs suffering from a fatal septicemic disease (2, 9, 10). Reports have shown that the virus develops, at least in part, in the nucleus of infected dog kidney (DK) cells (9, 10), and that it is immunologically related to herpes simplex virus (1). The objectives of this communication are to report on the growth characteristics of CHV in infected DK cells and to document several factors which affect virus yields. The first factor investigated was the temperature of incubation. Replicate monolayer cultures
Selective Culture Medium to Survey the Incidence of Haemophilus Species

A culture medium for the selective isolation of Haemophilus species is described. Bacitracin and nutritional supplements were incorporated in a rich basal agar medium to which rabbit blood was added to distinguish hemolytic species. Colony counts of seven typed strains of H. influenzae on this medium were within practical limits of counts on other media tested for clinical use. The bacitracin medium was as reliable as hemoglobin-agar for detecting H. influenzae and more sensitive for detecting other Haemophilus species in a clinical survey with the advantage of selectivity. Images
Chemical Composition of Variants of Aerobic Actinomycetes

It has been shown previously that aerobic actinomycetes can be separated into four main groups on the basis of their cell wall composition. Six representatives of aerobic actinomycetes (Nocardia asteroides and Micropolyspora brevicatena, cell wall type IV; N. madurae, Microbispora rosea, cell wall type III; Actinoplanes sp., cell wall type II; Streptomyces griseus, cell wall type I) were subjected to selecting agents which permitted the isolation of stable variants morphologically different from the parent strain. Whole cell analyses of 134 substrains from the six parents revealed no significant change in the isomeric form of diaminopimelic acid or in sugar constituents. Analyses of cell wall preparations from 52 of these did not reveal any change in the diagnostic constituents of their murein or polysaccharides.
A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It

Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. ABSTRACT Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.
Loss of Rubella Antibody from Immune Globulin Treated with Kaolin

Sera and immune globulin (IG) preparations are customarily treated with kaolin before titration of their rubella hemagglutination-inhibiting (HI) antibody in order to rid them of nonspecific inhibitors of hemagglutination. The treatment was shown in this investigation to have no adverse effect on the antibody level of the sera but was found to remove considerable amounts of gamma-globulin from IG preparations. Evidence of this removal was obtained by serological tests, by spectrophotometric determination of protein concentration and by disc electrophoresis. In contrast to kaolin, heparin-manganese chloride (MnCl2) treatment of IG preparations had essentially no effect on the level of antibody globulin by all the criteria used. Heparin-MnCl2-treated IG lots were in these respects similar, if not identical, to their untreated counterparts. Since nonspecific inhibitors associated with the β-lipoprotein fraction of serum are removed by the method employed to fractionate the IG samples, it seems unnecessary to treat the latter in any way for the HI test. No difficulty was encountered in this investigation with several untreated IG lots.
SERUM AND TISSUE INHIBITORS OF VIRUS

That so-called "natural immunity" is dependent upon a series of complex factors is agreed by most, and is certainly attested to by the scope of papers presented in the present symposium. It is tempting, as one reviews published reports and personal research experiences, to consider those natural substances of the host which inhibit biological properties of viruses as being important participants in this constant contest between parasites and their potential prey. Materials isolated from tissues, body secretions, or serum, which can inhibit viruses under experimental conditions, have received particular emphasis in the investigation of nonspecific resistance to viral infections. Theoretically it is possible to increase resistance to viral infection at various steps in the infectious process: (a) the virus particle itself may be inactivated; (b) the host cell may be altered so that attachment of virus cannot be accomplished; (c) the susceptible cells may be affected so that the essential infectious viral materials cannot enter the cell; (d) the host cells' metabolic apparatus may be sufficiently influenced to prevent the synthesis of essential viral materials; (e) egress of newly formed virus from the host cells may be prevented; and (f) host reaction to the infectious process may be sufficiently diminished so that many of the injurious effects of viral invasion are eliminated. It should be possible to affect one or more of these stages in viral infection and thus increase nonspecific resistance, but in actuality the known host materials of tissues and serum which inhibit viral infections act directly only upon the viral particle. The inactivation of various biological properties of viruses by combination of inhibitor with viral particle will therefore be considered. This paper will not attempt to review the literature completely on all inhibitors of viral activity, but rather will discuss those substances in tissues or serum which can serve as models for a consideration of the role these materials may play in "natural resistance" to viral infections. The evidence will be considered which bears upon the function these substances may have in the host.
Control of Growth Rate by Initial Substrate Concentration at Values Below Maximum Rate

The hyperbolic relationship between specific growth rate, μ, and substrate concentration, proposed by Monod and used since as the basis for the theory of steady-state growth in continuous-flow systems, was tested experimentally in batch cultures. Use of a Flavobacterium sp. exhibiting a high saturation constant for growth in glucose minimal medium allowed direct measurement of growth rate and substrate concentration throughout the growth cycle in medium containing a rate-limiting initial concentration of glucose. Specific growth rates were also measured for a wide range of initial glucose concentrations. A plot of specific growth rate versus initial substrate concentration was found to fit the hyperbolic equation. However, the instantaneous relationship between specific growth rate and substrate concentration during growth, which is stated by the equation, was not observed. Well defined exponential growth phases were developed at initial substrate concentrations below that required for support of the maximum exponential growth rate and a constant doubling time was maintained until 50% of the substrate had been used. It is suggested that the external substrate concentration initially present “sets” the specific growth rate by establishing a steady-state internal concentration of substrate, possibly through control of the number of permeation sites.
Fluorescent-Antibody Reagent for the Identification of Cryptococcus neoformans

A sensitive and diagnostically applicable conjugate for the rapid and accurate detection and identification of Cryptococcus neoformans has been developed. C. neoformans rabbit antisera were produced by 14 daily intravenous injections of 36 million cells for a total dosage of approximately 500 million cells. Cross-staining reactions with species of Cryptococcus other than C. neoformans, as well as with Candida species, were eliminated by adsorption of the C. neoformans conjugate with cells of C. diffluens and C. krusei.
Electronic Counting in Growth Studies of Mycobacterium avium

Metabolically uniform cells of Mycobacterium avium were obtained by selective filtration. The life cycle of these cells was followed by photomicrographs, electronic enumeration, and sizing and by viability and protein determinations. The cells elongate to form filaments several times their initial length; the increase in mass is reflected by a five- to sixfold increase of total protein in the culture. The filaments then fragment causing the production of viable coccobacilli. The techniques employed to obtain this form of growth are described and comparisons with nocardial growth are noted.
Early events in cell-animal virus interactions

INTRODUCTION . 103 INTERPRETATION OF ELECTRON MICROSCOPE IMAGES AND THE PROBLEM OF ARTIFACTS.104 Specimen Preservation 104 Interpretation of Images from Sections 104 Nature of the Inoculum 104 Quantitation of the Process 105 FUSION, LYSIS, AND REPAIR OF CELLULAR MEMBRANES . 105 ATTACHMENT.109 MECHANISMS FOR INTERNALIZATION OF THE INOCULUM: PHAGOCY-
Improved agar gradient-plate technique

MIC of antimicrobial compounds, it is essential to have uniform microbial growth on the agar medium; otherwise, it is difficult to determine a sharply defined area of growth inhibition. The conventional agar gradient-plate method has been found to be unsatisfactory for determining the MIC of chemotherapeutic compounds or antibiotics which inhibit filamentous fungi because the latter frequently do not grow uniformly when streaked on the surface of agar plates. This problem can be circumvented somewhat by seeding the top layer of conventional agar gradient-plates with the test organism; however, the nonuniform depth of the seeded agar layer precludes the determination of a sharply defined area of fungal inhibition. A modification of the original gradient-plate method has been devised and found to improve the utility and accuracy of this technique when