Miracle-dz/UniFAR-FTUs huggingface dataset:
tion and Identification of Microorganisms in Environmental Research

A Text Book of Biotechnology | www.smgebooks. com Copyright  Sun L. This book chapter is open access distributed under the Creative Commons Attribution 4.0 International License, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited. Gr up SM New Techniques for the Detection, Separation and Identification of Microorganisms in Environmental Research
PCR-based Identification of Microorganisms in a Kefir Grain

Nowadays many people are concerned about being healthy, and many dairy products are taken as health supplementary foods. Among dairy products, kefir, also called as Tibet mushroom, is a yogurt fermented by kefir grain, which is a mixture of lactic acid bacteria and yeasts. Although there are many empirical evidences that kefir is very influential for human body, the exact reason is not definitively discovered. Therefore, it would be useful to understand characteristics of a kefir grain and to categorize bacteria in a kefir grain. In this paper, molecular biological apparatus such as PCR, electrophoresis, PCR purification, DNA sequencing were used to identify and classify the species of lactic acid bacteria and yeast in a kefir grain. We used PCR-based identification method using 16S rRNA primer and Internal Transcribed Spacer (ITS) primer. We identified 6 different species which were selected on different medium. In addition, observation with scanning electron microscope (SEM) enabled us to grasp an external shape of the kefir grain. Although we found a limited number of microbial species, more intensive research are needed for extensive identification of microorganism species in Korean kefir grain.
The Role of Elyc Protein in Protection Against Oxidative Stress in E. Coli Cells

Bacteria are covered by a complex envelope that delimits the cell and protects it against variations in osmotic pressure and environmental stresses. The goal of our study was the characterization of the importance role of Conserved inner membrane protein ycbC (elyC) gene in cell wall assembly and oxidative stress response in Escherichia coli. E. coli WT cells, ΔelyC and ΔmrcB mutants were grown in LB medium 37°C and 22°C. After that, the hydroxyl radical level was measured by the Flow cytometry (FACS). RNA extraction and purification was achieved and transcriptional analysis by RT-PCR was performed. Our results demonstrate the increase of Hydroxyl radical (oxidative stress) in ΔelyC mutant compared to WT and ΔmrcB mutant. Our data show the up-regulation of genes encoding for ycbC gene, the genes encoded for the enzymes implicated in PG synthesis and oxidative stress response in WT cells grown at 22°C. Furthermore, ΔelyC and ΔmrcB mutants grown at 37°C and 22°C revealed the overexpression of genes encoding enzymes involved in PG synthesis compared to WT cells. Moreover, gene expression of genes encoded for enzymes implicated in oxidative stress response in ΔelyC mutant was over-expressed but not changed in ΔmrcB mutant. These results approve the significant role of ElyC protein in Gram-negative bacterial envelope assembly and report a possible connection between cell wall biogenesis by ElyC factor and oxidative stress defense in Escherichia coli.
Hyperbolicity and the number of components for random link ランダム絡み目の最頻成分数と双曲性

In recent Low-dimensional topology, to study 3-manifolds and/or knot via random methods could be a hot topic now. As a pioneering work, in [1], Dunfield and W.Thurston introduced a random model of 3-manifolds by using random walks on the mapping class group of a surface, and a theory of random 3-manifolds has started. Actually they considered random Heegaard splittings by gluing a pair of handlebodies by the result of a random walk in the mapping class group. In view of this, the second author introduced and studied two models of random links in [4]. We here report two recent results based on joint works Ichihara-Yoshida [3] and Ichihara-Ma [2]. One model of random link introduced in [4] is defined as the braid closures of the randomly chosen braids via random walks on the braid groups. Suppose that a random walk on the braid group Bn of n-strings induces a uniform distribution on the symmetric group Sn on n letters via the natural projection Bn → Sn (n ≥ 3). Then, the second author showed in [4, Theorem 1.1] that, for the random link coming from a random walk of k-step on Bn (n ≥ 3), the expected value of the number of components converges to 1 + 1 2 + 1 3 + · · ·+ 1 n when k diverges to ∞. Then it is natural to ask what is the most expected number of components for such a random link. We first answer to this question as follows in [3].
A Revision of Syzygium and Allied Genera (Myrtaceae) in Australia

This study shows that [I ve genera are represented in Australia. Acmena: seven species and one subspecies, including two new species, A. mackinnoniana and A. resa, and one new subspecies, A. hemilampra subsp. orophila. Acmenosperma: two species, including one new species, A. pringlei. Eugenia: one species. Syzygium: 52 species and three subspecies, including 16 new species, S. alatoramulum, S. alliiligneum, S. argyropedicum, S. bamagense, S. boonjee, S. canicortex, S. dansiei, S. endophloium, S. macilwraithianum, S. papyraceum, S. pseudoJastigiatum, S. rubrimolle, S. sharonae, S. velae, S. wesa, S. xerampelinum, and one new subspecies, S. forte subsp. potamophilum; 23 new combinations also made. Waterhousea gen. nov.: four species, including two new species, W. mulgraveana and W. unipunctata; two new combinations also made.
Population Dynamics of Rotifers in the Floodplain of River Ravi, Pakistan

A B S T R A C T The population dynamics of Rotifers of a flood plain ecosystem are supposed to change with mixing of flood water from riverine system, during floods. With respect to biodiversity, floodplain ecosystem remained ignored and no work has been done in Pakistan. With the aim to identify monthly changes in the population of rotifer communities in a flood plain, rotifers were estimated through studying the monthly variations of density and diversity of rotifers, from January to December 2012, in the floodplain of River Ravi near Balloki Headworks, Pakistan. A total of 101 species belonging to 32 genera, 15 families and 3 orders were identified from 15 different sites. Family Brachionidae dominated among all (56%) with the Brachionus, Anuraeopsis and Keratella being the most important genera in family Brachionidae. Rotifer density was highest from April to June 2012. Rotifer density showed a positive correlation with air and water temperature, pH, turbidity and total hardness and strong positive correlation with electrical conductivity, total dissolved solids (TDS) and total alkalinity. Similarly a negative correlation existed between rotifer density and visibility and chlorides and strong negative correlations with dissolved oxygen. Analysis of variance showed a significant difference in rotifers between different months and sites. Shannon diversity index (H) showed high species diversity in August and lowest diversity in November. Simpson index of dominance showed lowest diversity in November. Species richness was highest in August and lowest in April. Species evenness was highest in April and lowest in November. It is summarized that density of Rotifers remain highest during summer, when plenty of food is available where as diversity of Rotifers reaches to its maximum when riverine water, carries variety of Rotifers, mixes with the stagnant and isolated flood plain water.
Plexin expression in axotomized rubrospinal and facial motoneurons

Injuries to the central nervous system (CNS) are characterized by the inability of most axons to regenerate to their respective target tissues leading to permanent loss of sensory/motor function, while following peripheral nervous system (PNS) injuries, regeneration can occur. The failure of CNS nerve regeneration is partly attributed to the inhibitory nature of the CNS injury site. Apart from their roles in nervous system patterning during development, inhibitory guidance molecules present at the spinal cord injury site, such as semaphorins, have been suggested to contribute to the inhibitory nature of the CNS injury site. Secreted class 3 semaphorins bind to a receptor complex composed of neuropilins, the ligand binding subunit, and plexins, the signal transducing component. Although injured CNS and PNS neurons continue to express neuropilins, little is known about the expression patterns of plexins by axotomized neurons. This study analyzes class-A plexins and plexin-Bl expression in injured CNS (rubrospinal) and PNS (facial) neurons. Plexin mRNA and protein expression were analyzed over a period of 2 weeks in injured mouse rubrospinal and facial motoneurons after cervical spinal cord hemisection and facial nerve resection, respectively. In rubrospinal neurons, Plxn-Al mRNA and protein and Plxn-A4 mRNA expression did not differ between injured and uninjured neurons while Plxn-A2 mRNA expression increased in injured compared to uninjured rubrospinal neurons. Plxn-A3 mRNA was not detected in rubrospinal neurons. In facial motoneurons, Plxn-Al, -A3 and -A4 mRNA expression was higher in injured compared to uninjured motoneurons, although Plxn-Al protein expression did not change between injured and uninjured neurons. Plxn-A2 mRNA, on the other hand, decreased in injured facial motoneurons. Plxn-Bl mRNA expression was absent from both rubrospinal and facial neurons. Therefore, most class-A plexins continue to be expressed in both rubrospinal and facial motoneurons after injury, suggesting that these neuronal populations will remain responsive to semaphorins present at the injury site. This study provides a crucial step in understanding how injured neurons may respond to semaphorins and which components of the semaphorin response; either plexins, neuropilins or semaphorins, may be targeted to promote successful CNS nerve regeneration.
Mesospheric noctilucent clouds

The current problems of the study of mesospheric Noctilucent Clouds (NLCs) and possible their solutions, based on a large literary survey, are described in an accessible form in this book. Since the authors were repeatedly partaking in expeditions to North Kazakhstan for NLC observations, they present the results of their personal photographic and spectral observations, as well as methods and results of their processing. Because obtaining NLC "pure" spectra on a background of the twilight segment is difficult, the authors made a spectrometer for extended sky objects and carefully researched it. In order to answer the controversial question of the possible luminescence of NLCs, the authors conducted a spacious literature search, hoping to find likely candidates for the role of luminophores to explain an unusual bluish-silvery glow of this atmospheric phenomenon. It seems they are a success to find such an answer. The book is offered to not only a wide range of readers, enthusiasts-observers of Noctilucent Clouds and students, but it also can be useful for the scientists engaged in atmospheric optics.
Nutrient, chlorophyll and zooplankton seasonal variations on the southern coast of a subtropical saline lake (Mar Chiquita, Córdoba, Argentina)

Mar Chiquita is the largest salt lake in South America. Because of its rich and diverse biodiversity, it has been designated a world site of the Ramsar Convention on Wetlands. Despite its importance, its limnological characteristics are poorly documented. Here we report a baseline assessment of the seasonal variations of several limnological parameters on the southern coast of the lake. Samples were obtained at two lake sites (pelagic and coastal) and an additional site in the Laguna del Plata estuary lagoon. We found that Mar Chiquita is a well-mixed eutrophic shallow lake with significant spatial and seasonal variations in its limnological parameters. Of particular relevance are the spring turnover and the clear water phase in summer, being characterized by nutrient peaks (total nitrogen, total phosphorus (P) and soluble reactive P) in early spring, followed by peaks in zooplankton and ammonia in late spring and summer, together with a decrease in chlorophyll and pH. These events appear related to seasonal variations in water temperature and the shallowness of the lake that allows strong biochemical interactions with sediments. Correlations among the studied parameters indicate a significant role of zooplankton (particularly the brine shrimp) in controlling phytoplankton abundance. Laguna del Plata has typical estuary characteristics, including high variability in salt concentrations (13–63 g.L−1 ), high nutrient levels (0.48 mg P.L−1 ) (hypereutrophic) and higher phytoplankton biomass than the main lake. Mar Chiquita characteristics show interesting similarities with those recorded in the Great Salt Lake in the USA.
Mass of agricultural tractors available in the brazilian market

Currently, manufacturers of agricultural tractors offer to farmers a diversity of brands, models, and settings for the most diverse agricultural operations. In this sense, the relation mass/power of tractor influences directly in the performance of these operations. The objective of this research was to study the agricultural wheel tractors marketed in Brazil in relation to their mass, in order to obtain current data to help their selection and proper use. The research involved 145 agricultural tractors models of eight different brands, including 2WD, MFWD and 4WD versions. The variables mass without ballast, relation mass/power for the different brands, type of traction and tractor power were analyzed separately. Tractor power was classified in: Class I ( 150kW), according to the rated engine power declared by the manufacturer. Statistical analyses used were the t-Student and Tukey tests. The most number of tractors belongs to Class II and are considered versatile due to their mass/power relation, and can be used in the most diverse agricultural operations. From these analyses it was detected the mass/power relation decreases when the rated engine power increases.
Food Item Use by Three Sympatric Canids in Southern Illinois

I investigated use of food resources among coyotes (Canis latrans), red foxes (Vulpes vulpes), and gray foxes (Urocyon cinereoargenteus) in southern Illinois. All three species used similar food items; coyote and red fox diets were most similar while coyote and gray fox diets were least similar. Gray fox diets also exhibited greater diversity and omnivory. The high dietary overlap among species results in the potential for resource competition. Competition with coyotes may have reduced red fox abundance in southern Illinois. Despite competition for food resources, gray foxes appear able to coexist with coyotes possibly through habitat segregation and avoidance of antagonistic encounters by climbing trees.
Hormonal effects of several chemicals in recombinant yeast, MCF-7 cells and uterotrophic assays in mice

Many methods have been developed for screening chemicals with hormonal activity. Using recombinant yeasts expressing either human estrogen receptor [Saccharomyces cerevisiae ER + LYS 8127 (YER)] or androgen receptor [S. cerevisiae AR + 8320 (YAR)], we evaluated the hormonal activities of several chemicals by induction of β-galactosidase activity. The chemicals were 17β-estradiol (E2), testosterone (T), p-nonylphenol (NP), bisphenol A (BPA), genistein (GEN), 2-bromopropane (2-BP), dibutyl phthalate (DBP), di-(2-ethylhexyl) phthalate (DEHP), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and butylparaben (BP). To assess the estrogenicity of NP, the result of the in vitro recombinant yeast assay was compared with an E-screen assay using MCF-7 human breast cancer cells and an uterotrophic assay using ovariectomized mice. In the YER yeast cells, E2, NP, BPA, GEN, and BP exhibited estrogenicity in a dose-response manner, while TCDD did not. All the chemicals tested, except T, did not show androgenicity in the YAR yeast cells. The sensitivity of the yeast (YER) assay system to the estrogenic effect of NP was similar to that of the E-screen assay. NP was also estrogenic in the uterotrophic assay. However, in terms of convenience and costs, the yeast assay was superior to the E-screen assay or uterotrophic assay. These results suggest that the recombinant yeast assay can be used as a rapid tool for detecting chemicals with hormonal activities.
Carbohydrate-active enzyme (CAZy) database and its new prospect

The carbohydrate-active enzyme( CAZy) database is a knowledge-based resource specialized in enzymes that synthesis and degrade complex carbohydrates and glycoconjugates. CAZymes were classified into several distinct families based on amino-acid sequence similarity. The information about GenBank accession number,EC designation,family,organism could be accessed in CAZy database and it has been linked with other bioinformatics databases. With the development of metagenomics,the number of sequences in CAZy database increased rapidly,making better opportunity for the refinement of CAZy families into subfamilies. The possibility of function prediction and molecular engineering of CAZymes were improved,thus promoting the rapid development of the conversion of biomass.
Development of multiple gene construct with regulatory genes and their functional validation

Rice is widely cultivated under irrigated condition and its water requirement is very newlinehigh. Due to dwindling water resources, to save irrigation water growing rice under newlinesemi-irrigated aerobic condition has phenomenal relevance. In this ecosystem decreased water availability, high VPD affects crop growth and productivity. From this context it is important to improve adaptation of rice under aerobic condition by improving water relations and cellular level tolerance mechanisms. Stress adaptation at cellular level involves activation of stress responsive genes which are regulated by transcription factors. Hence, under stress, co-ordinated expression of multiple transcription factors is crucial to increase cellular level tolerance. As a first step a multigene construct coexpressing GUS, AtbHLH17 and AtWRKY28 was developed using modified multisite gateway technology and developed transgenics in Arabidopsis. These transgenics showed improved tolerance to diverse stresses like drought, salinity and oxidative stress by upregulation of large number of downstream genes. Further, three stress responsive TFs from different families i.e EcNAC1, EcMYC57, EcbZIP60 were cloned from fingermillet and validated their relevance in stress tolerance in tobacco. Tobacco transgenics co-expressing all the three TFs showed superior phenotype under stress compared to single TFs expressing transgenics signifying the importance of co newlineexpression of relevant stress specific TFs. To improve adaptation of rice under semiirrigated aerobic conditions rice transgenics were developed co-expressing EcNAC1, EcMYC57 and EcbZIP60 in the background of genotype having superior water relations. Desirable transformants were identified based on dessication response. Molecular characterization of transformants showed the integration and expression of all three genes. The transgenics showed improved tolerance to salinity and oxidative stress. %%%Summary p. 140-146, References p. 147-187, Appendix included
Population structure of the traditionally exploited holothurian Holothuria tubulosa in the south Aegean Sea

Structure de la population traditionellement exploitee d'Holothurie Holothuria tubulosa dans le sud de la Mer Egee. La structure de la population traditionellement exploitee d'Holothurie, Holothuria tubulosa, a ete etudiee dans le sud de la Mer Egee pendant deux annees consecutives. Des populations remarquables de l'espece ont ete detectees sur quatre des huit iles examinees, avec une abondance moyenne, evaluee par l'effort de peche a 75 ± 101 ind.h -1 en plongee. Les distributions de frequence de taille etaient unimodales a chaque ile examinee accueillant des populations remarquables. Les Holothuries de taille moyenne et l'indice de gonade ont des valeurs plus petites a l'Ile Pserimos, tandis que les differences temporelles appropriees n'etaient pas significatives. Le statut oligotrophique du complex Dodecanese combine avec l'effet de peche non controle peut expliquer les resultats observes.
A stochastic modelling for LES of a two-phase combusting flow

This current investigation attempts to conduct Large Eddy Simulation (LES) of a turbulent particle-laden combusting experiment where methanol liquid fuel is injected using a Research Simplex Atomizer (RSA), i.e. a type of pressureswirl atomizers. The quality of the computational grid and the set-up of inlet/boundary conditions are validated by simulating an isothermal test case. However, non-reacting and reacting cases with a stochastic breakup model are to be carried out in the future as the reproduction of spray properties using Rosin-Rammler distribution was found to be poor.
Comprehensive Genetic Analysis by Integration of Conventional Karyotyping and Interphase FISH Helps Refinement of Biological Subclasses with Clinical Impact in Chronic Lymphocytic Leukemia

Background: Various genetic technologies have been employed in the identification of genomic complexity and refinement of prognostic classification of clinically heterogeneous disease of chronic lymphocytic leukemia (CLL). Objective: The present study of interphase cytogenetics and conventional karyotyping was undertaken to perform comprehensive analysis of CLL genetics with an approach to refine early prognostication of disease. Material & Methods: Retrospective analysis by fluorescence in situ hybridization (FISH) was carried out on total 671 patients of CLL at diagnosis between 2008 and 2015. Conventional cytogenetics studies were performed in 50 of 671 patients using CPG Oligonucleotide + IL-2 and TPA (12-O-Tetradecanyl Phorbol 13-acetate) for stimulation of lymphocytes cultures. Results: Interphase cytogenetics could detect recurrent abnormalities such as del(13q14), +12, del(17p13), del(11q22), del(6q23) in 71% of cases. The incidence of del(13q) was higher in Rai stage 0, I, II (p = 0.0005); whereas patients with ≥2 aberrations were more common in advance stage III, IV (p = 0.001). Frequency of IgH translocation was 7%. Morphology and immunophenotypic analysis revealed atypical CLL with higher frequency of t(14;19) than t(14;18). Conventional karyotype could detect abnormal karyotype in 97% of cases which displayed targeted FISH abnormalities along with additional non-targeted chromosomal abnormalities. Patients with negative FISH markers showed clonal non-recurrent numerical and structural changes. The complex karyotype was identified in 24% cases which included targeted FISH aberrations as well as non-targeted numerical and structural abnormalities like deletions, and unbalanced translocations. A significant association was observed between complex karyotype and coexistence of ≥2 FISH markers (p = 0.009) and del(11q22) &/or del(17p) (p = 0.03). Conclusion: Our data of interphase FISH with integration of conventional karyotyping revealed genomic complexity that helped identification of biological subclasses with clinical impact at diagnosis. Further, these cytogenetic subclasses along with molecular markers are likely to evolve more refined prognostic groups, which will help design risk-adapted therapies in B-CLL.