Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of AmpC -Lactamases among Gram Negative Clinical Isolates

Background and Objectives: AmpC �-lactamases confer resistance to a wide variety of �-lactam antibiotics including cephamycins such as cefoxitin and cefotetan, narrow and broad spectrum cephalosporins, aztreonam and are poorly inhibited by �- lactamase inhibitors such as clavulanic acid. The present study was undertaken to determine the occurrence of AmpC enzyme producing Gram negative clinical isolates at Navodaya Medical College, Raichur. Materials and Methods: 200 non-repeat Gram negative clinical isolates from various samples were screened for AmpC �- lactamases by using Modified disc Approximation method. The "Screen positive" isolates were detected for AmpC �- lactamase by Modified three-dimensional enzyme extract test, AmpC disk test, and phenyl boronic acid test. Results: Out of the 200 Gram negative isolates, 87 (43.5%) isolates were screened to be positive and 10 (5%) isolates were inducible AmpC producers. Of these 97 isolates subjected to confirmatory tests, 74 (37%) were harbouring AmpC enzymes. Majority of AmpC positive isolates were E.coli (20.5%), K.pneumoniae (5.5%) and Acinetobacter spp. (3.5%). Conclusion: Phenyl boronic acid test is the simple and practical method for the detection of AmpC in routine clinical microbiology laboratories. Plasmid-mediated AmpC �-lactamases have been associated with false in vitro susceptibility to cephalosporins. Thus, the type of �-lactamase produced by the organism should be detected along with the antibiogram for appropriate treatment of the patient.
Alcohol Dehydrogenase from Bacillus subtilis: Cloning and Expression Gene in HD34 Beer Yeast

Alcohol Dehydrogenase (ADH) gene was isolated from Bacillus subtilis by PCR amplification. The 1.1kb amplified fragment was confirmed to be the ADH gene by DNA sequencing. The gene was inserted into expression plasmid pYC6/C7, transformation HD34 beer yeast, as well as some transformants with ADH activity were obtained. (Nature and Science, 2004,2(2):64-66)
Biochemistry Concept Level of Difficulty Profile of Prospective Biology Teachers’ Perception

This descriptive study deals with the prospective teachers’ difficulties in understanding the biochemistry concepts to obtain a figure of biochemistry difficulty profile. The subjects of this research are 42 2nd semester biology students in at LPTK in Aceh Province. The data needed for this study are collected by using an open and closed questionnaire referring to the Likert scale. The data are statistically processed. The results showed that the most difficult biochemistry topics include the topics on the catabolism of carbohydrates (27.3%), catabolism of lipids (16.8%), and catabolism of protein (14.5%). The difficulties in mastering the concepts are sought to be due to their using a lot of chemical formulas and chain reactions that hindered the students to fully understand them. These concepts will be easier to understand and attractive by using computer technology. The results show that biochemistry is important for the prospective teachers. In terms of this, it is highly recommended to prepare good material, learning, and authentic assessment that provide challenges and improve students’ capabilities that can be applied in real life situations. Besides, it is important to do continuous and periodic assessment on this matter
On the taxonomy of the first record of rare deep-water rough shark species of Oxynotidae (Chondrichthyes: Squaliformes) in the western Indian Ocean

An immature female specimen of rough shark was collected south of Reunion Island in the Madagascar Basin in 2009 aboard R/V Dr. Fridtjof Nansen, representing the first official record of the family Oxynotidae in the western Indian Ocean. The specimen is herein identified as Oxynotus sp. due to morphological differences with its closely similar congeners O. centrina and O. bruniensis regarding morphometrics, shape of dorsal, pectoral and caudal fins, shape of the head and colouration, refuting the hypothesis of occurrence of these two species in the region. These results indicate that Oxynotus sp. is possibly an undescribed species. A general description of the external morphology, external morphometrics and photographs of Oxynotus sp. are provided. The specimen has a hepatosomatic index of 36.33% which reveals that it was possibly approaching maturation, suggesting that a viable population of Oxynotus sp. exists in the western Indian Ocean. Intraspecific variations in O. centrina from the Mediterranean Sea and eastern Atlantic Ocean are also noticed, requiring further taxonomic scrutiny.
Set-based Tests for Genetic Association and Gene-Environment Interaction.

Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Since these traits are likely influenced by the joint effect of multiple variants in a gene/region, a joint analysis of these variants considering linkage disequilibrium (LD) may help to explain additional phenotypic variation. In this dissertation, we present several set-based tests for genetic association/gene-environment interaction in both cross-sectional and longitudinal studies. In the first project, we propose a new statistical model based on the random field theory, referred to as a genetic random field model (GenRF), for gene/region based association analysis in a cross-sectional study. Using a pseudo-likelihood approach, a GenRF test for the joint association of multiple genetic variants is developed, which has the following advantages: 1. accommodating complex interactions for improved performance; 2. natural dimension reduction; 3. boosting power in the presence of LD; 4. computationally efficient. Simulation studies are conducted under various scenarios. Compared with the sequence kernel association test (SKAT), as well as other more standard methods, GenRF shows overall comparable performance and better performance in the presence of complex interactions. The method is further illustrated by an application to the Dallas Heart Study. In the second project, we propose a longitudinal genetic random field model (LGRF), to test the association between a phenotype measured repeatedly during the course of an observational study and a set of genetic variants. Generalized score type tests are developed, which we show are robust to misspecification of within-subject correlation. In addition,
Evolutionary history of the flora of Mexico: Dry forests cradles and museums of endemism

Mexico is considered an exceptional biogeographic area with a varied endemic flora, however spatial phylogenetic measures of biodiversity have not yet been estimated to understand how its flora assembled to form the current vegetation. Patterns of species richness, endemism, phylogenetic diversity, phylogenetic endemism and centers of neo‐ and paleo‐endemism were determined to examine differences and congruence among these measures, and their implications for conservation. Of 24 360 vascular plant species 10 235 (42%) are endemic. Areas of endemism and phylogenetic endemism were associated with dry forests in zones of topographic complexity in mountain systems, in deserts, and in isolated xeric vegetation. Every single locality where seasonally tropical dry forests have been reported in Mexico was identified as an area of endemism. Significant phylogenetic diversity was the most restricted and occurred in the Trans‐Mexican Volcanic Belt and in the Sierra de Chiapas. Notably, the highest degree of phylogenetic clustering comprising neo‐, paleo‐, and super‐endemism was identified in southernmost Mexico. Most vascular plant lineages diverged in the Miocene (5–20 mya) when arid environments expanded across the world. The location of Mexico between two very large landmasses and the fact that more than fifty percent of its surface is arid favored the establishment of tropical lineages adapted to extreme seasonality and aridity. These lineages were able to migrate from both North and South America across Central America presumably during the Miocene and to diversify, illustrating the signature of the flora of Mexico of areas of endemism with a mixture of neo‐ and paleo‐endemism.
Towards incorporating asexual fungi in a natural classification: checklist and notes 2012–2016

Incorporating asexual genera in a natural classification system and proposing one name for pleomorphic genera are important topics in the current era of mycology. Recently, several polyphyletic genera have been restricted to a single family, linked with a single sexual morph or spilt into several unrelated genera. Thus, updating existing data bases and check lists is essential to stay abreast of these recent advanes. In this paper, we update the existing outline of asexual genera and provide taxonomic notes for asexual genera which have been introduced since 2012. Approximately, 320 genera have been reported or linked with a sexual morph, but most genera lack sexual morphs.
Genetic variability of wheat germplasm represented in the south Pannonian region

Genetic variability of wheat germplasm represented in the south Pannonian region. -Genetika, Vol 49, No.3, 831-842. In this study, genetic variability was investigated among 50 winter wheat varieties ( Triticum aestivum L.) which are grown in parts of Croatia, Hungary, Serbia and Slovenia according to 22 morphological characteristics used for DUS (distinctness, uniformity and stability) testing. The average Dice similarity coefficient was 0.371. The determined similarity coefficient was in range 0.083 – 0.776. A significant variability of 6.21% in the breeding programs according to period was determined as well as significant variability of 3.10% between breeding programs. The UPGMA clustering divided investigated varieties into four main clusters. Based on data analysis, most distant varieties with best morphological characteristics were found which will provide valuable resource of new parent's combinations in future breeding programs. This paper also provided valuable assessment of morphological characteristics to define distinctness criteria in the DUS examination of wheat.
Genetic and taxonomic relationships of five species of Rallidae (Aves: Gruiformes) based on mitochondrial cytochrome oxidase subunit I sequences

This is the first study to detection the genetic relationship between Porphyrio alleni and four Rallidae species: Fulica atra , Gallinulla angulata , Gallinulla chloropus and Porphyrio porphyrio . Mitochondrial cytochrome oxidase subunit I (COI) sequences were used as an effective marker in this study. DNA of Rallidae species were extracted, amplified using polymerase chain reaction (PCR) and then sequenced. The results obtained from information based on COI sequences revealed that Gallinulla angulata and Gallinulla chloropus fall into two separate clades and they are not monophyletic. This suggests that, two moorhens could not be laid into the same genus. In addition, Porphyrio porphyrio was included in the same genus with Porphyrio alleni but they were situated in two different clades. Porphyrio alleni was more related to Gallinulla angulate , Gallinulla chloropus and Fulica atra than Porphyrio porphyrio. It was concluded that, the mitochondrial gene COI can aid in the differentiation of studied species and finding genetic relationships between them.
Inhibition of DNA Topoisomerases by a Series of Benzoxazoles and their Possible Metabolites

: Background : A series of 2-substituted benzoxazoles and their possible metabolites, N-(2-hydroxy-4(or 5)-nitrophenyl)benzamides and phenylacetamides, which were previously synthesized by our group, were investigated for their inhibitory activities on both eukaryotic DNA topoisomerase I (Topo I) and II (Topo II). Methods : DNA topoisomerase I and II inhibitory activity of compounds were determined by relaxation assay which could measure the conversion of supercoiled pBR322 plasmid DNA to its relaxed form. Results : According to DNA topoisomerase relaxation assay results, four derivatives ( 1c, 1f, 2b, 2e) among tested 21 compounds inhibited human Topo I, whereas three compounds ( 1c, 1e, 1f ) inhibited human Topo IIα. 2-(4’-bromophenyl)-6-nitrobenzoxazole ( 1f ) was observed to be the most effective Topo II inhibitor with the lowest IC 50 value of 71 µM and 2-(4’-tert-butyl-phenyl)-6- nitrobenzoxazole ( 1c ) with the IC 50 value of 104 µM was considered the most effective Topo I inhibitor. However, it is noteworthy that these two compounds affected both Topo I and II enzymes. When the relationship between chemical structures and biological activities of the compounds were examined, the following two results were obtained: (i) CH 2 bridge seems to decrease the Topo I and II inhibitions and (ii) bulky groups at R 1 position increased both Topo I and II inhibitions for ben-zoxazole derivatives while small groups at R1 position increased the Topo I inhibition for ben-zamide derivatives. Conclusion : Biological activity and SAR results of tested derivatives may provide some predictions in order to design novel topoisomerase inhibitors.
Sensitivity of functional diversity metrics to sampling intensity

Functional diversity (FD) metrics are increasingly used in ecological research, particularly in the studies of community assembly and ecosystem functioning. However, studies using the FD metrics vary greatly in the intensity by which ecological communities were sampled and it is largely unknown how sensitive these metrics are to low sampling intensity (undersampling). In this study, we used a combination of simulations with theoretically assembled communities and three comprehensive, independent, empirical datasets on plant, ground beetle, and bird communities to investigate the sensitivity of nine commonly used FD metrics to undersampling. Simulations with both theoretical communities and empirical data showed that in a wide range of contexts, the measurement of various FD metrics requires a much higher sampling effort to reach an ‘adequate’ precision (defined as an r2 of at least 0·7 between different subsets of the same population), than that required for commonly used taxonomic diversity metrics (e.g. species richness), although the ‘accuracy’ (their deviation from the diversity value of a completely sampled community) of their measurements is not more sensitive to undersampling than species richness. We also found that some FD metrics (e.g. Functional Dispersion) are consistently less sensitive to undersampling than others (e.g. nearest neighbour distance‐metrics). Problems of undersampling were generally most severe in datasets with high overall species richness and low overall abundances. We found that the precision of many FD metrics is highly sensitive to undersampling, and more so than commonly used taxonomic diversity metrics. Therefore, to ensure reproducible results in functional biodiversity research, we recommend that thorough sampling designs are used to sample communities and that datasets originally collected for studying taxonomic diversity should only be used for FD when it can be shown that undersampling is not a major issue. In cases where undersampling is suspected or logistically unavoidable, the FD metrics that are relatively insensitive to its effects (e.g. Functional Dispersion) should be prioritized.
AVALIAÇÃO DOS MARCADORES DO ESTRESSE OXIDATIVO EM INDIVÍDUOS SUPLEMENTADOS COM FERRO E ÁCIDO ASCÓRBICO

O ferro e um nutriente essencial para atividades das celulas incluindo transporte de oxigenio, transferencia de eletrons e regulacao genetica. Entretanto, esse mineral e potencialmente toxico por participar de reacoes de oxido-reducao, que favorecem a formacao de especies reativas ao oxigenio (ERO). O dano oxidativo nas biomoleculas pode ser modulado por antioxidantes como o acido ascorbico (AA). Entretanto, sabe-se que na presenca de ferro, o acido ascorbico pode atuar como um pro-oxidante in vitro e contribuir para formacao de radicais hidroxila. Baseado na possibilidade pro-oxidante da interacao entre o ferro e o acido ascorbico, for avaliados as manifestacoes da suplementacao do ferro associado com o acido ascorbico. O estudo foi delineado por 9 voluntarios saudaveis, nao tabagistas, entre 20 e 31 anos. Os voluntarios foram suplementados com uma dose unica contendo 2g de acido ascorbico (primeiro grupo), 150mg de ferro (segundo grupo) e 2g de acido ascorbico mais 150mg de ferro (terceiro grupo). Os 9 individuos foram submetidos a todos os tratamentos, os quais foram alternados a cada 15 dias. Os voluntarios foram submetidos a coletas sanguineas antes da suplementacao e 2, 5 e 24 horas apos a suplementacao. Foram avaliados os niveis de ferro e ferritina, a atividade das enzimas antioxidantes catalase (CAT), glutationa peroxidase (GPx), superoxido dismutase (SOD), os niveis dos antioxidantes nao-enzimaticos: acido ascorbico, tiois nao proteicos (NPSH), bem como os marcadores do estresse oxidativo: especies reativas ao acido tiobarbiturico (TBARS), oxidacao da diclorifluoresceina e a atividade da delta aminolevulinato desidratase (ALA-D) . Os resultados encontrados mostraram que os niveis plasmaticos de acido ascorbico aumentaram significativamente em 2, 5 e 24 horas apos a ingestao de acido ascorbico mais ferro ou somente acido ascorbico. Os niveis plasmaticos de ferro aumentaram significativamente 2 horas apos a ingestao de ferro e 2 e 5 horas no grupo ferro mais acido ascorbico. Os niveis de TBARS eritrocitario diminuiram significativamente em 5 e 24 horas apos a ingestao de ferro, bem como, em 5 horas apos a ingestao de ferro mais acido ascorbico. A atividade da CAT eritrocitaria aumentou significativamente em 5 horas apos a ingestao de acido ascorbico mais ferro. Os demais parâmetros avaliados nao mostraram diferencas significativas. Com isso, o presente estudo nao confirma a hipotese que a combinacao de altas doses de acido ascorbico e ferro, ou apenas ferro causam dano oxidativo in vivo. Entretanto, mais estudos sao necessarios para determinar se a interacao entre o ferro e o acido ascorbico pode causar efeito pro-oxidante in vivo.
Allelopathic activity of the picocyanobacterium Synechococcus sp. on unicellular eukaryote planktonic microalgae

The production and release of allelopathic compounds is an important adaptation by which some species of cyanobacteria can achieve a competitive advantage over other primary producers. In the present study we tested the allelopathic activity of the picocyanobacterium Synechococcus sp. against the following coexisting unicellular eukaryote microalgae: Porphyridium purpureum, Stichococcus bacillaris, Prymnesium parvum and Nitzschia dissipata. With these species, we covered a wide range of taxonomic groups. We demonstrated that both the addition of Synechococcus sp. cell-free filtrate and coculture inhibited the growth, chlorophyll content and photosynthetic rate of P. purpureum and S. bacillaris. Conversely, P. parvum, a well-known mixotroph, was positively affected by both Synechococcus sp. treatments. In contrast, N. dissipata was not affected by either the picocyanobacterial filtrate or coculture. These results suggest that the negative allelopathic effect is related to a reduction in the photosynthetic rate, and that Synechococcus sp. allelopathy should be taken into account in the interactions between picocyanobacteria and eukaryote competitors coexisting in a planktonic system.
A systems genetics study of seed quality and seedling vigour in Brassica rapa

1. A systems genetics study is only possible if knowledge-driven and data-driven approaches are combined. (this thesis) 2. Proper experimental design and phenotyping methods are the most crucial steps in genetic studies. (this thesis) 3. Without phenotypic data, next generation sequencing results do not increase insight into biological processes, but merely use hard-disk memory. 4. The shift from public research funding to public-private partnership funding will be at the expense of fundamental research. 5. Political stability in the current developing world is a pre-requisite for food security. 6. Unlike Dutch communication, Dutch language is very indirect and confusing.
Canopy‐forming macroalgal beds (Sargassum) on coral reefs are resilient to physical disturbance

Disturbances to ecosystems are often considered in terms of their potential to disrupt the feedbacks maintaining a particular ecosystem regime. The likelihood of doing so, however, will be dependent on the nature of the regime and its resilience to disturbance. Within coral reef ecosystems, shifts from coral‐ to macroalgal dominance are becoming increasingly common and, once established, are difficult to reverse. Most studies to date have focused on the biological removal of macroalgae by herbivores, however, none have considered the resilience of macroalgal beds to physical removal by storms. We simulated the physical removal of macroalgal biomass from Sargassum beds on an inshore coral reef on Australia's Great Barrier Reef, and monitored recovery for 11 months. Trimming Sargassum biomass but leaving the holdfast intact had no detectable effect on the density, height or biomass of Sargassum compared to adjacent intact, or control, areas after 5 months. In areas where holdfasts were also removed, Sargassum biomass recovered to 50% of control biomass after 11 months. Given the importance of holdfasts to the resilience of Sargassum beds, we also investigated the ability of herbivores to remove and/or damage holdfasts. Exposing pieces of dead coral with attached Sargassum holdfasts to local herbivore assemblages resulted in a 70% decline in the number of holdfasts over 4 months compared to those protected from herbivores. Synthesis. Beds of Sargassum are extremely resilient to the physical removal of algal biomass, and as such, storms alone are unlikely to lead to permanent reductions in Sargassum abundance. Persistent reductions in the abundance of macroalgae on degraded coral reefs will not only require the physical or biological removal of algal biomass, but critically, sufficient densities of herbivores capable of removing holdfasts.
Genetic Architecture for Pod Yield and its components in Okra (Abelmoschus esculentsus (L.) Moench

Genetic a n al ysis us i ng si x genera t i o ns • 1 . e . P l' P 2' F 1 , F2' BCl and BC2 of si x different cross es o f ok r a was carried out with a v iew to study heterosis, i n breed i ng d e pression, heritability and gene effects . gov ernl.ng d i fferent characters. The e x periment was conducted i n random iz ed bloc k design with four replication at College Farm , N.M. Co l lege of Agriculture, Navsari during Kharif 199 0. Significant difference among v arious gen e r at i o n me a n s was observed for all the characters. It was rev ealed that the degree and direction of he terotic effects var ied fr o m cross to cross so as with characters. Cross P u n j abpa dmi ni x Padra 18-6 recorded highest significan t a v erage hete r osi s and heterobeltiosis for pod yieJd. Heterot i c e ff ect . 1n number of pods per plant mainl y contributed t o wa rd s heterosis in pod yield in all the crosses. Mar ked r educti on