Miracle-dz/UniFAR-FTUs huggingface dataset:
The CURE for Cultivating Fastidious Microbes

Course-based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.
Sensing Plant Physiology and Environmental Stress by Automatically Tracking Fj and Fi Features in PSII Chlorophyll Fluorescence Induction

Following a step excitation, chlorophyll fluorescence (ChlF) from photosystem II of a dark-adapted plant leaf exhibits the well-known OJIP pattern. The OJIP induction has been widely applied in plant science, agriculture engineering, and environmental engineering. While the J and I phases are related to transitions of photochemical reaction redox states, characteristic fluorescence intensities for the two phases (Fj and Fi) are often treated as fixed time points in routine measurement and thus do not account for variations in plant and experimental conditions, which (1) neglects the time differences, potentially useful information for characterizing plant status and environmental factors, and (2) leads to errors in measured Fj and Fi values. In this work, a method for consistent measurement of Fj and Fi was developed through polynomial fitting and curvature analysis. The method measures the curvatures in the OJIP curve and automatically tracks the characteristic transition points under variable sample and experimental conditions. Experiments were carried out to demonstrate the concept and classification capabilities of the developed method. This research established a new framework to analyze ChlF and enhanced the applications of ChlF.
INFLUENCE OF AUXIN ON BIOMASS PRODUCTION AND WITHANOLIDE ACCUMULATION IN ADVENTITIOUS ROOT CULTURE OF INDIAN RENNET: WITHANIA COAGULANS

Objective: Withanolides are the biologically active, principle compound present in Withania coagulans , which is having a high medicinal value and possesses potent therapeutic activity. The present study was attempted with an objective to investigate a biomass growth and withanolide production in in vitro root tissues of W. coagulans . Methods: High-performance thin layer chromatography (HPTLC) often serves as a method for quantification of major withanolides. In the present study, methanolic withanolide extract of in vitro cultured W. coagulans root tissue were carried out using HPTLC. The HPTLC analysis was performed using precoated silica gel aluminum plate (20 cm × 20 cm) 60F254 (E.MERCK, Germany) with mobile phase toluene: ethyl acetate: formic acid (5:5:1). Results: The optimization of different combination and concentration of plant growth regulators (indole-3-butyric acid [IBA] and indole-acetic acid) was used to stimulate the biomass growth and withanolide production. The maximum biomass growth (7.48±0.25 g/dL) was observed in medium with 4.93 μM−1 IBA. The higher amount of withanolide A (204.98±0.87 μg/L DW) and withaferin A (227.15±0.57 μg/L DW) accumulation was recorded in culture grown on half Murashiga-Skoog media supplemented with 4.93 μM−1 and 2.46 μM−1 IBA. Conclusion: We concluded that in vitro -cultured system could provide unique opportunities for large-scale production of pharmaceutically important compound than field grown plants.
Comprehensive SNP Analysis of Genes in Cholestrol Metabolism (PGC 1 Alpha), Insulin Signaling (IRS1), Potassium Channel (KCNJ11) and Glucose Homeostasis (PI3K) in Three Diversified Groups

Objective: Type 2 Diabetes is an increasingly common serious, metabolic disorder with a substantial inherited component. We examined 4 SNPs in 4 candidate genes for association with diabetes status and related phenotype in 800 individuals in a case control study. Research design and methodology: We examined SNPs of 4 candidate genes predicted to have their major role in T2DM. A total of 800 subjects were enrolled (400 patients and 400 controls) from North Indian Population of Jammu and Kashmir from three ethnic groups (Brahmins 200, Khatris 100, Guptas 100). Genotypic analysis was followed by DNA extraction and PCR RFLP technique. Results: The results confirmed the genetic complexity of Type 2 Diabetes and provide evidence that PGC 1 Alpha (Gly482Ser) and PI3K (Met 326 Ile) polymorphisms have altered the cholesterol pathway and glucose homeostasis and signified the risk of T2DM.
Rhizosphere mediated nutrient management in Allium hookeri Thwaites by using phosphate solubilizing rhizobacteria and tricalcium phosphate amended soil

ABSTRACT This work describes integrated nutrient management for cultivation of Allium hookeri by using phosphate solubilizing bacteria (PSB) applied in rhizosphere, along with tricalcium phosphate (TCP). Arthrobacter luteolus S4C7, Enterobacter asburiae S5C7, Klebsiella pneumoniae S4C9, S4C10 and S6C1, and K. quasipneumoniae S6C2, were isolated from rhizosphere of Allium hookeri Thwaites, and were found to release substantial amount of soluble phosphate (124.8–266.4 μg/mL) from TCP in vitro conditions. These isolates were experimented for plant growth promoting attributes, including IAA, siderophore, and nitrogen-fixation. Treatment with PSB resulted in enhanced growth of A. hookeri Th. , which was even better with TCP amendment with PSB. K.quasipneumoniae S6C2 resulted in 39.1% and 533.3% increase (p ≤ 0.05) of root length and weight respectively. The treatment with these isolates, in TCP amended soil also resulted in 200–250% increase in available P in soil, which was maximum for K. quasipneumoniae (1.866 mg/g).
Heparin Synergistically Enhances Interleukin-11 Signaling through Upregulation of the Map Kinase Pathway.

Using an animal model of heparin-induced osteoporosis we previously demonstrated that heparin causes bone loss, in part, by increasing osteoclast number and activity. In an effort to account for these findings, we examined the effect of heparin on osteoclast formation in vitro. We found that while heparin alone had no effect, it was able to synergistically enhance Interleukin-11 (IL-11) - induced STAT3 (Signal Transducer and Activator of Transcription) activation and thus, increase both gp130 expression and osteoclast formation. In the present study, we examine the effect of various serine kinase inhibitors on heparin’s ability to synergistically enhance both STAT3 activation and gp130 expression. As assessed by electrophoretic mobility shift assays (EMSAs), treatment of murine calvaria cells with heparin was found to increase IL-11-induced STAT3-DNA complex formation by 2 fold. Inhibition of the c-Jun N-terminal kinase (JNK), p38 mitogen-activated protein (MAP) kinase, or the phosphatidylinositol 3-kinase (PI3-K) pathway had no effect on heparin’s ability to promote STAT3-DNA complex formation. In contrast, the mitogen-activated protein kinase kinase (MEK) inhibitor, PD098059, completely abolished the ability of heparin to act synergistically with IL-11. Similar results were obtained when northern blot analysis was used to assess heparin’s ability to enhance IL-11-induced gp130 expression. In an attempt to resolve the mechanism by which this was occurring, we examined the ability of heparin to influence STAT3 Ser727 phosphorylation in the presence or absence of IL-11. Heparin alone was found to have no effect on Ser727 phosphorylation, nor did heparin alter the phosphorylation status of Ser727 in the presence of IL-11. Heparin was, however, found to increase ERK1/2 (extracellular signal regulated kinase) activation in both a time and dose-dependent manner. When taken together, these findings suggest that heparin enhances IL-11-induced STAT3 activation and thus, gp130 expression, by a mechanism that is independent of STAT3 Ser727 phosphorylation, but which involves upregulation of the MAP Kinase pathway.
cAMP mediated regulation of fibroblast to myofibroblast differentiation in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a fibrotic lung disease with no effective treatment. Myofibroblasts contribute to the pathology of IPF by secreting large amounts of extracellular matrix proteins such as alpha smooth muscle actin (α-SMA) and Collagen I (Col 1). Myofibroblasts have reduced Prostaglandin E2 (PGE2), a key anti-fibrotic mediator, due to diminished cyclooxygenase-2 (COX-2) expression. Primary fibroblasts isolated from lungs of IPF patients (F-IPF) expressed significantly less COX-2 in response to IL-1β and increased α-SMA and Col I compared with fibroblasts isolated from lungs of non-fibrotic patients (F-NL). COX-2 was gradually lost in F-NL treated with transforming growth factor-β (TGF-β1), a pro-fibrotic cytokine, whereas PGE2, and cAMP elevating agents increased IL-1β-induced COX-2 expression in F-IPF. Ras, a small G protein, has been shown to have a role in several fibrotic conditions. Farnesylthiosalicylic acid (FTS), a Ras inhibitor, increased IL-1β-induced COX-2 and prevented TGF-β1-induced reduction of COX-2. Previous studies suggest that COX-2 is epigenetically repressed. LBH589, a HDAC inhibitor, prevented TGF-β1-induced repressed COX-2 whereas BIX01294, a DNA lysine methyltransferase inhibitor, and RG108, a G9a histone methyltransferase inhibitor, both increased IL-1β-induced COX-2 in F-IPF. In conclusion, the gradual loss of PGE2/COX-2 anti-fibrotic mechanism during myofibroblast differentiation may contribute to the pathophysiology of pulmonary fibrosis and agents that increase cAMP levels, inhibit Ras or inhibit epigenetic repression of COX-2, may compensate for the lack of endogenous PGE2.
Beta-Lactamase Genes in Soil Bacteria Isolated from the Banks of the Niangua River in Missouri

approved: Beta-lactam antibiotics are among the most widely prescribed antibiotics in clinical settings. As a result, it is not uncommon to encounter clinically isolated bacteria that produce beta-lactamase as a means of resistance to these antibiotics. Among the many beta-lactamases currently known, TEM-type beta-lactamase is the most widespread beta-lactamase observed in clinical settings. However, less is known regarding its prevalence among bacteria in natural settings. To determine how widespread the TEM-type beta-lactamase gene is in the environment, experiments were designed to detect this and other beta-lactamase genes from environmentally isolated bacteria. Briefly, soil was collected along the banks of the Niangua River located in west-central Missouri. Diluted soil preparations were plated onto tryptic soy agar plates containing ampicillin and allowed to incubate at room temperate for up to 14 days. Colonies (n = 58) growing on the plates were selected and total DNA isolated from each strain. Using 7 groups of beta-lactamase specific DNA primers, the polymerase chain reaction was employed to amplify beta-lactamase genes, if present. In total, 58 isolates were positive for an 800 base pair amplicon indicative of a TEM-type beta-lactamase. DNA sequencing of the amplified fragment from each strain was sequenced to identify the TEM variant present. The data indicated that TEM-116 beta-lactamases are widespread among natural populations of bacteria from this location. In total, 56 of the genes were TEM-116, 1 was TEM-1, and 1 was TEM-118. These genes were most predominate in the genera Bacillus and Pseudomonas. Attempts to transfer the resistance genes via transformation and conjugation were unsuccessful. BETA-LACTAMASE GENES IN SOIL BACTERIA ISOLATED FROM THE BANKS OF THE NIANGUA RIVER IN MISSOURI A Thesis Presented to The Department of Biological Sciences EMPORIA STATE UNIVERSITY In Partial Fulfillment of the Requirements for the Degree
Identification of a Novel Mutant pAMT Allele Responsible for Low-pungency and Capsinoid Production in Chili Pepper: Accession ‘No. 4034’ (Capsicum chinense)

Capsinoids are low-pungent capsaicinoid analogues in chili pepper fruits. They exhibit various bioactivities in humans similar to capsaicinoids, but do not produce a nasty burning sensation, encouraging their application in foods and supplements. Previous reports demonstrated that loss-of-function of putative aminotransferase ( pAMT ) leads to low-pungency and capsinoid accumulation. Therefore, the pamt allele is a useful gene in chili pepper breeding programs to enhance health-promoting properties. Eight loss-of-function alleles have been identified in the Capsicum genus, but the variation in pamt alleles remains to be fully elucidated. In this study, we identified one novel loss-of-function allele from the analysis of low-pungent chili pepper ‘No. 4034’ ( C. chinense ). ‘No. 4034’ contained mainly capsinoid with an undetectable level of capsaicinoid. A genetic complementation test was conducted by crossing ‘No. 4034’ with other accessions. The results indicated that ‘No. 4034’ possessed a loss-of-function pamt allele. Sequence analysis showed that the novel mutant allele contained a 7-bp insertion (TCGGTAC) in the 16th exon region, which we designated as pamt 9 . The insertion caused a frameshift mutation and resulted in a truncated protein. Gene expression analysis showed that the expression level of pAMT specifically decreased among biosynthetic genes tested here in ‘No. 4034’, compared with that of pungent accession. pamt 9 will be useful for low-pungency and capsinoid breeding, and will provide additional information for variations in pAMT mutants.
Flame Atomic Absorption Spectrometric Determination of Cadmium in Vegetable and Water Samples After Preconcentration Using Magnetic Solid-Phase Extraction

ABSTRACT Accurate and reliable determination of cadmium (Cd) in vegetables is often difficult due to low concentrations and matrix effects. Magnetic solid-phase extraction (MSPE) was developed for preconcentration and determination of trace amounts of Cd in vegetables and water samples prior to flame atomic absorption spectrometry (FAAS) analysis. Cobalt magnetic nanoparticles were synthesized and modified by sodium dodecyl sulfate (SDS) and 2-(5-bromo-2-pyridylazo)-5-diethyl aminophenol ligand (5-Br-PADAP) through a chemical precipitation method so that the nanoparticles (NPs) could be used as a new sorbent. The NPs bearing the Cd ions were easily separated from the aqueous solution by applying an external magnetic field and the complexed metals were desorbed using dilute HNO3. Extraction conditions including pH, amount of sorbent, contact time, desorption solvent, breakthrough volume, and sorption capacity were optimized. Under optimal conditions, the calibration curve was linear from 1.0–500 ng·mL−1 of Cd, R2 = 0.997. The detection limit was 0.6 ng·mL−1 in the original solution (3 Sb·m−1) and the relative standard deviation for eight replicates determination of 0.1 μg·mL−1 Cd was ±2.2%. Cadmium is easily aggregated in edible parts of leafy vegetables. Heavy metals analysis of vegetables is essential for protection of human health and to comply with regulatory controls.
Impact of Mdm2-p53 on the proteasome assembly and disassembly Role of the ubiquitination of some 19S subunits

The ubiquitin proteasome system is a fundamental actor for the proteolysis of cellular proteins. My results demonstrated that the E3 ligase Mdm2 and its substrate p53 might be implied in the formation of the fully-assembled proteasome. Mdm2 promotes also the ubiquitination of some 19S subunits of the proteasome via a non-conventional chain and it is not a signal for self-degradation. Moreover, this ubiqitination seemed to play a role in the formation of the proteasome.
Urease Test Protocol

Production of the enzyme urease is characteristic of the Proteeae and a few other members of the Enterobacteriaceae among others. Urease is a constitutively produced enzyme that hydrolyzes urea with the resultant release of ammonia and carbon dioxide. The use of urea agar and urea broth for the detection of urease activity is described in this protocol.
Incompatibilité interspécifique chez Populus : effet Mentor

L'incompatibilite interspecifique chez les peupliers resulte d'un arret passif des tubes polliniques dans les tissus femelles, se produisant a l'issue de leur phase autotrophique de croissance. Plusieurs proteines et glycoproteines polliniques diffusibles sont associees au groupe d'incompatibilite. Certaines beta -galactosidases seraient des effecteurs metaboliques impliques dans la reprise de la croissance heterotrophique. Les observations cytologiques demontrent que la pollinisation mentor (pollen compatible sterilise+pollen incompatible) provoque une stimulation de croissance des tubes polliniques incompatibles. Toutefois aucun individu hybride n'a ete obtenue de cette maniere. Cependant, celle-ci a induit le developpement d'individus probablement parthenogenetique
Isolation and Characterization of Lytic Coliphages from Sewage Water

The goal of this study was to isolate and characterize phages that might be used in transport and treatment of potential E.coli pathogen in water sources. E.coli KP005067 was especially targeted because this is the dominant strain obtained from the sewage canal. The abundance of phage and its host directly from the sewage water was analysed using Epifluorescence Microscopy. The morphological characterization of the bacteriophages was studied using transmission electronic microscopy (TEM) and the genomic studies using Agarose Gel Electrophoresis. Studies on phage growth curve and its survival rate with respect to UV irradiation was also carried out. Almost 64% of the phages produced large, clear plaques indicating lytic activity. Phages had long noncontractile tail and icosahedral capsid head and therefore belonged to the Siphoviridae. Their estimated genome sizes was about 31 kb. One-step growth kinetics of the phage showed the latent period 15 min, rise period 20 min, and the average burst size 35 phage particles/infected cell. Also a clear downward trend in lytic activity was observed in phage groups exposed to longer than 30 minutes of UV. The characterization of the phages will be helpful in its future application as microbial tracers and bio-disinfectants in water sources.
Specific Virus-Host Genome Interactions Revealed by Tethered Chromosome Conformation Capture

Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1–3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.
Impatiens galactica (Balsaminaceae), a new spurless species of section Trimorphopetalum from Madagascar

Impatiens galactica, a new species from lowland rainforest in Marojejy National Park, NE Madagascar, is described and illustrated. It belongs to Impatiens section Trimorphopetalum and is related to I. messmerae , also known from Mt. Marojejy. Impatiens galactica differs from the latter species in the shape of the lateral sepals, and in the dorsal petal and the lateral united petals being entirely glabrous and lacking small white scales. Furthermore, I. galactica has a distinct flower morphology with strongly reduced upper lobes of the lateral united petals. The lateral petals are thus resembling the lower case letter “b” or “d”, respectively. Additionally, it has unusually coloured yellowish white, semi-transparent flowers with an orange-yellow, shiny line along the midrib of the lower sepal, all of which are lacking in I. messmerae .
Detecting phytoplankton diatom fraction based on the spectral shape of satellite‐derived algal light absorption coefficient

Knowledge about phytoplankton composition is important for biological and biogeochemical research as well as for ecological applications (e.g., water quality) in coastal and inland waters. Satellite remote sensing can potentially map the baseline patterns, anomalies, and trends of phytoplankton composition on a synoptic basis. A prominent challenge is the attribution of the total optical signal to phytoplankton amid interference from minerals and humus. Here, we obtained the phytoplankton light absorption coefficient, aph(λ), in the Chesapeake Bay by partitioning satellite‐derived total light absorption coefficient of water using the generalized stacked‐constraints model (GSCM). We show that the red‐to‐blue band ratio of GSCM‐derived aph(670)/aph(440) can be associated with diatom fraction in Chesapeake Bay. Further, the spatial‐temporal patterns shown in the satellite‐derived diatom fraction data agree well with field studies conducted previously around this region, including low diatom dominance in summer, high diatom dominance in the lower bay in winter, diatom‐dominated spring blooms in coastal waters outside of the bay, and increasing seasonal variability of diatom fraction from the upper to the lower bay. We also found that in the middle bay the summer diatom fraction correlates strongly with spring streamflow on an annual basis, which can be explained because sediment deposited by spring freshets is the main source of silicate supply during summer. These results suggest that the satellite‐derived diatom fraction maps can serve as a baseline for detecting phytoplankton composition anomalies, and highlight the effectiveness of using absorption‐based approach to extract phytoplankton composition information for optically complex waters.