Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence, Detection, Characterization and Description of Selected Beer-Spoilage Lactic Acid Bacteria

The present study provides a current overview about the spectrum of beer-spoiling bacteria which was obtained by evaluating routine analysis samples in terms of contaminating species and brewing-related questions. A new beer-spoiling species was demarcated from known species and subsequently newly described. The phenotypic and genotypic variability of beer-spoiling L. rossiae isolates was determined. Furthermore, the optimization of a routine analysis method used for the detection of beer-spoiling bacteria in process samples containing yeast was described.
Amelioration of genetic diversity and its assessment in Brassica napus - carinata introgression lines

One of the breeding goals in Brassica napus has been to facilitate introgression of novel traits from wild or closely related species through inter- and intra-specific crosses. The present study is based on the evaluation of B. napus – carinata introgression lines (ILs) for introgressed morphological and genetic diversity in comparison to the parental B. napus lines. A set of 81 Brassica napus – carinata ILs, developed previously following a back cross strategy, was assessed for introgressed genetic diversity by comparing them with the 15 B. napus recipient parents under two environments (E1: timely sown and E2: late sown) for phenotypic expression of 13 morpho-physiological traits. Trait averages as well as trait variations were generally higher for ILs, indicating introgression of variability in the desired direction. In comparison to the parents, the ILs were observed to be early to flower, early to mature, higher yielding, had more siliquae on the main axis and the siliquae were longer. ANOVA revealed highly significant differences amongst genotypes for 10 traits of which 4 traits, viz., days to 50% flowering, days to 100% flowering, plant height and pod length were highly significant in both the environments. SNP-based chromosome-wise gene diversity, as estimated using software SELECTIONTOOL, indicated high estimates for individual chromosomes in ILs as compared to the parental lines. The phenotypic variability estimated for majority of the traits in ILs is being utilized for developing new high yielding rapeseed varieties.
N-terminal protein acetylation by NatB modulates the levels of Nmnats, the NAD+ biosynthetic enzymes in Saccharomyces cerevisiae

NAD+ is an essential metabolite participating in cellular biochemical processes and signaling. The regulation and interconnection among multiple NAD+ biosynthesis pathways are not completely understood. We previously identified the N-terminal (Nt) protein acetyltransferase complex NatB as a NAD+ homeostasis factor. Cells lacking NatB show an approximate 50% reduction in the NAD+ level and aberrant metabolism of NAD+ precursors, which are associated with a decrease of nicotinamide mononucleotide adenylyltransferases (Nmnat) protein levels. Here we show this decrease in NAD+ and Nmnat protein levels is specifically due to the absence of Nt-acetylation of Nmnat (Nma1 and Nma2) proteins, and not other NatB substrates. Nt-acetylation is a critical regulator of protein degradation by the N-end rule pathways, indicating absence of Nt-acetylation may alter Nmnat protein stability. Interestingly, the rate of protein turnover (t1/2) of non-Nt-acetylated Nmnats does not significantly differ from Nt-acetylated Nmnats, suggesting reduced Nmnat levels in NmatB mutants are not due to increased post-translational degradation of non-Nt-acetylated Nmnats. In line with these observations, deletion or depletion of N-rule pathway ubiquitin E3 ligases in NatB mutants is not sufficient to restore NAD+ levels. Moreover, the status of Nt-acetylation does not alter the rate of translation initiation of Nmnats. Collectively our studies suggest absence of Nt-acetylation may increase co-translational degradation of nascent Nmnat polypeptides, which results in reduced Nmnat levels in NatB mutants. Nmnat activities are essential for all routes of NAD+ biosynthesis. Understanding the regulation of Nmnat protein homeostasis will facilitate our understanding of the molecular basis and regulation of NAD+ metabolism.
Quality assessment of potted petunia based on a probabilistic neural network classifier

Quality of ornamental plants relies on foliage and flower appearance and evaluation of such characteristics depends on people experience; therefore, more reliable scoring methods are needed. The objective of this research was to explore the usefulness of digital image segmentation with a probabilistic neural network (PNN) classifier from which quality indicators can be obtained for quantifying time-dependent ornamental characteristics. A petunia variety (Petunia multiflora cv. F1 ‘Glistering Pearls mixed’) grown in pots in the Central High Valleys of Mexico was used as model. The variety includes a mixture of genotypes with flowers in many colors. The PNN classifier was trained and tested on six color classes (four flower classes, one foliage class and one background class). From image segmentation, six quality indicators were calculated. For the test sets, the best classification scenario whose inputs were a combination of some of the channels of RGB, CIE-Lab, CIEL*uv, HSV, and CMY color models reached an overall accuracy (OA) of 98% while it was 96% when using the RGB color model alone. The quality indicators identified differences on tends of plant quality associated to flower color. White-flowered plants had larger ground cover per plant and greater ratio of flower area to total plant area, as well as a lower roundness index. Pinkflowered plants had the lowest ground cover per plant and plant perimeter, while they had the largest roundness index. This approach allowed to identify different behaviors of the genotypes based on quality indicators, and it might be used for estimating the period this species keeps its exhibition quality.
Bioprospecting study of cultivable prokaryotic fraction from Manaure solar saltern, La Guajira, Colombia

III LIST OF FIGURES . VII LIST OF TABLES . IX LIST OF ABBREVIATIONS . X INTRODUCTION . 1 REFERENCES . 3 OBJECTIVES . 5 General objective . 5 Specific objectives . 5 CHAPTER I: Use of a mixed culture strategy to isolate halophilic bacteria with antibacterial and cytotoxic activity from the Manaure Solar Saltern in Colombia 1. ABSTRACT . 6 2. BACKGROUND . 7 3. METHODS . 9 3.1. Sampling . 9 3.2. Growth and enrichment of mixed cultures . 9 3.3. Extraction and characterization of crude extracts . 10 3.4. Antibacterial activity . 10 3.5. Cytotoxic activity . 11 3.6. Enrichment, isolation and characterization of bacteria from mixed cultures . 11 3.7. Amplification and sequencing of the 16S rRNA gene . 12 3.8. MALDI-TOF MS analysis . 13 3.9. Bioautography of a bioactive extract of Vibrio sp. A1SM3-36-8 . 13 3.10. Isolation and identification analysis . 14 4. RESULTS . 14 4.1. Bioactivity of mixed cultures . 14 4.2. Isolation of microorganisms from mixed cultures and bioactivity assays . 15 4.3. Identification of isolates . 16 4.4. Characterization of Vibrio sp. A1SM3-36-8 . 18 4.5. Isolation and identification of a bioactive fraction from Vibrio sp. A1SM3-36-8 . 19
Global transcriptome profiling uncovers footprints of root and shoot development in crop models barley and tomato

Land plants establish their forms at two development hotspots- root and shoots apices. In this study, we dissected and compared the global transcriptome of these developmental zones in crop models barley and tomato. We employed a state of the art transcriptome analysis technique for deep profiling of expressed genes. This analysis resulted in highly reproducible quantitative expression profiles of 19,441 and 23,388 genes in barley and tomato, respectively. In barley, 16,834 genes were expressed both in root and shoot apices, whereas 1,081 genes were specific to root apex and 1,526 genes were active in shoot apex. With significant variations 20,154 genes were expressed in root and shoot apices of tomato of which 1,858 and 1,376 genes showed root and shoot specificities. Systematic analyses of these genes revealed distinct commonalties and divergence among the active genes for root and shoot development. A deeper insight in these data uncover tissue- and species specific genes, unique footprints of gene ontologies and divergence of auxins pathway genes in root and shoot apices of barley and tomato. These data provide a primary resource to understand intra- and inter-species genetic networks of root and shoot development as well as the evolution of genes in crop plants.
Shifting spaces: which disparity or dissimilarity metrics best summarise occupancy in multidimensional spaces?

Multidimensional analysis of traits are now a common toolkit in ecology and evolution and are based on trait-spaces in which each dimension summarise the observed trait combination (a morphospace or an ecospace). Observations of interest will typically occupy a subset of this trait-space, and researchers will apply one or more metrics to quantify the way in which organisms “inhabit” that trait-space. In macroevolution and ecology these metrics are referred to as disparity or dissimilarity metrics and can be generalised as space occupancy metrics. Researchers use these metrics to investigate how space occupancy changes through time, in relation to other groups of organisms, and in response to global environmental changes, such as global warming events or mass extinctions. However, the mathematical and biological meaning of most space occupancy metrics is vague with the majority of widely-used metrics lacking formal description. Here we propose a broad classification of space occupancy metrics into three categories that capture changes in volume, density, or position. We analyse the behaviour of 25 metrics to study changes in trait-space volume, density and position on a series of simulated and empirical datasets. We find no one metric describes all of trait-space but that some metrics are better at capturing certain aspects compared to other approaches and that their performance depends on both the trait-space and the hypothesis analysed. However, our results confirm the three broad categories (volume, density and position) and allow to relate changes in any of these categories to biological phenomena. Since the choice of space occupancy metric should be specific to the data and question at had, we introduced moms, a user-friendly tool based on a graphical interface that allows users to both visualise and measure changes space occupancy for any metric in simulated or imported trait-spaces. Users are also provided with tools to transform their data in space (e.g. contraction, displacement, etc.). This tool is designed to help researchers choose the right space occupancy metrics, given the properties of their trait-space and their biological question.
Integrative Multi-Omics Analysis of Barley Genotypes Shows Differential Salt-Induced Osmotic Barriers and Response Phases Among Rootzones

The mechanisms underlying rootzone-localised responses to salinity stress during early stage of barley development remains fragmentary and elusive. Here, we performed a comprehensive detection of the multi-root-omes (transcriptomes, metabolomes, lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) with seedling root growth maintained and restricted in response to salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEG) or abundant metabolites (DAM) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, maturation Z3). Based on pathway over-representation of the DEG and DAM, phenylpropanoid biosynthesis is the most statistically over-represented biological pathways among all salinity responses observed. Together with the histological evidence, an intense salt-induced lignin impregnation was found only at the stelic cell wall of Clipper Z2, comparing to a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on global correlation network construction of the DEG and DAM, callose deposition that potentially adjusted the symplastic flow in roots was almost independent of salinity in rootzones of Clipper, but was markedly decreased in that of Sahara. Through closer examinations of molecular and hormonal clues, we further demonstrate that the salinity response in rootzones of Clipper were mostly at recovery phase, comparing to Sahara with rootzones retained at quiescence. Taken together, we propose that two distinctive salt tolerance mechanisms could exist in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with the deteriorating global salinization of soil.
The complete mitochondrial genome of Archamia macropterus (Perciformes; Apogonidae) and phylogenetic studies of Perciformes

Abstract The complete mitochondrial genome sequence of Archamia macropterus was determined. The complete mitochondrial genome was 16,513 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 non-coding region (the control region and the origin of light strand replication). The overall base composition was A 26.37%, T 25.61%, C 30.80%, and G 17.22%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6, all other genes were encoded on the heavy strand, the NJ tree demonstrated that A. macropterus has a closest relationship with Cheilodipterus quinquelineatus and Apogon semilineatus.
The brain of a nocturnal migratory insect, the Australian Bogong moth

Every year, millions of Australian Bogong moths (Agrotis infusa) complete an astonishing journey: in spring, they migrate from their breeding grounds to the alpine regions of the Snowy Mountains, where they endure the hot summer in the cool climate of alpine caves. In autumn, the moths return to their breeding grounds, where they mate, lay eggs and die. Each journey can be over 1000 km long and each moth generation completes the entire roundtrip. Without being able to learn any aspect of this journey from experienced individuals, these moths can use visual cues in combination with the geomagnetic field to guide their flight. How these cues are processed and integrated in the brain to drive migratory behaviour is as yet unknown. Equally unanswered is the question of how these insects identify their targets, i.e. specific alpine caves used as aestivation sites over many generations. To generate an access point for functional studies aiming at understanding the neural basis of these insect’s nocturnal migrations, we provide a detailed description of the Bogong moth’s brain. Based on immunohistochemical stainings against synapsin and serotonin (5HT), we describe the overall layout as well as the fine structure of all major neuropils, including all regions that have previously been implicated in compass-based navigation. The resulting average brain atlas consists of 3D reconstructions of 25 separate neuropils, comprising the most detailed account of a moth brain to date. Our results show that the Bogong moth brain follows the typical lepidopteran ground pattern, with no major specializations that can be attributed to their spectacular migratory lifestyle. Comparison to the brain of the migratory Monarch butterfly revealed nocturnal versus diurnal lifestyle and phylogenetic identity as the dominant parameters determining large-scale neuroarchitecture. These findings suggest that migratory behaviour does not require widespread modifications of brain structure, but might be achievable via small adjustments of neural circuitry in key brain areas. Locating these subtle changes will be a challenging task for the future, for which our study provides an essential anatomical framework.
PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment

Kaposi’s sarcoma (KS) is an AIDS-defining cancer caused by the KS-associated herpesvirus (KSHV). Unanswered questions regarding KS are its cellular ontology and the conditions conducive to viral oncogenesis. We identify PDGFRA(+)/SCA-1(+) bone marrow-derived mesenchymal stem cells (Pα(+)S MSCs) as KS spindle-cell progenitors and found that pro-angiogenic environmental conditions typical of KS are critical for KSHV sarcomagenesis. This is because growth in KS-like conditions generates a de-repressed KSHV epigenome allowing oncogenic KSHV gene expression in infected Pα(+)S MSCs. Furthermore, these growth conditions allow KSHV-infected Pα(+)S MSCs to overcome KSHV-driven oncogene-induced senescence and cell cycle arrest via a PDGFRA-signaling mechanism; thus identifying PDGFRA not only as a phenotypic determinant for KS-progenitors but also as a critical enabler for viral oncogenesis. AUTHOR SUMMARY Identification of the KS progenitor cell creates the possibility of studying viral oncogenesis and its determinants from its initial steps as a continuum. It also increases our understanding of pathogenic mechanisms and disease preferential tropism. Hereby we identify Pα(+)S-MSCs as KS progenitors, in which KSHV infection has oncogenic consequences; only when these cells are in a pro-angiogenic environment in which PDGFRA activation enables an oncogenic de-repressed KSHV epigenome. These results identify a KS-progenitor population in the Pα(+)S-MSCs and point to pro-angiogenic environmental conditions as essential for oncogenic viral gene expression and transformation. We designed a novel model of KSHV oncogenesis, creating a very robust platform to identify KSHV oncogenic pathways and their relationship with cellular lineages and extracellular growth environments.
Evaluation of nutritional profile and total antioxidant capacity of the Mediterranean diet of southern Spain

Abstract The objective of this study was to determine the antioxidant capacity of a Mediterranean diet consisting typical dishes from southern Spain. For that, a 5‐day diet was developed with typical dishes of Murcia. The antioxidant capacity of the diet was measured using ORACHF, FRAP, and DPPH methods, and the total phenolic compound content of this diet was estimated by Folin–Ciocalteu. About 50% of the antioxidant capacity and 29% of the phenolic compounds per day came from sample 14 (artichokes with ham), whereas only 1% and a 4%, respectively, proceed from sample 16 (gypsy pot). The total antioxidant capacity of the diet was estimated as 9,506.33 ET/100 g/person/day by the ORACHF method, and the total phenolic consume was estimated as 1,839.05 mg GAE/person/day. The proposed diet can be considered an excellent strategy for improving the nutritional status of the population because of its high antioxidant activity and phenolic compound content.
Functional traits explain amphibian distribution in the Brazilian Atlantic Forest

Species distributions are one of the most important ways to understand how communities interact through macroecological relationships. The functional abilities of a species, such as its plasticity in various environments, can determine its distribution, species richness and beta diversity patterns. In this study, we evaluate how functional traits influence the distribution of amphibians, and hypothesize which functional traits explain the current pattern of amphibian species composition.
A physico - chemical characterization of oil from Camelina sativa seeds grown in Romania

It is well-known that camelina oil, obtained from Camelina sativa seeds is rich in fatty acids, predominantly linolenic acid and is used successfully in pharmaceutical and cosmetic therapies. It is remarkable that this species has a great adaptability to environmental conditions, being able to cultivate it on agricultural parcels and polluted soils. The goal of this work is to evaluate the quantitative and qualitative differences of three types of camelina oils, obtained from varieties grown in Romania: GP 202-Spanish provenance, Camelia and Mădălina, both Romanian provenance. The effect of soil fertilization on the quality of the seeds /oil obtained from 3 varieties of camelina was tested, the control being the unfertilized Camelina variety. The following parameters have been evaluated: seed moisture, cold oil extraction yield, certain physico-chemical oil indicators and percent quantitative composition of individual and total fatty acids. Remarkable is the total fatty acid content of the oil that varies between 75.87 g% for the unfertilized Mădălina variant and 81 g% for the fertilized GP-202 variant. Taking in consideration the results for all the studied parameters, it can be concluded that the Mădălina variety is very similar to the other two, and fertilization contributes insignificantly to the improvement of the quality of the
Cockroaches Show Individuality in Learning and Memory During Classical and Operant Conditioning

Animal personality and individuality are intensively researched in vertebrates and both concepts are increasingly applied to behavioral science in insects. However, only few studies have looked into individuality with respect to performance in learning and memory tasks. In vertebrates individual learning capabilities vary considerably with respect to learning speed and learning rate. Likewise, honeybees express individual learning abilities in a wide range of classical conditioning protocols. Here, we study individuality in the learning and memory performance of cockroaches, both in classical and operant conditioning tasks. We implemented a novel classical (olfactory) conditioning paradigm where the conditioned response is established in the maxilla-labia response (MLR). Operant spatial learning was investigated in a forced two-choice task using a T-maze. Our results confirm individual learning abilities in classical conditioning of cockroaches that was reported for honeybees and vertebrates but contrast long-standing reports on stochastic learning behavior in fruit flies. In our experiments, most learners expressed a correct behavior after only a single learning trial showing a consistent high performance during training and test. We can further show that individual learning differences in insects are not limited to classical conditioning but equally appear in operant conditioning of the cockroach.
The complete chloroplast genome sequence of Dendrobium zhenghuoense (Orchidaceae)

Abstract Dendrobium zhenghuoense is very distinctive among Orchidaceae species with yellowish-green flowers and short peduncle. In this study, we reported the complete chloroplast genome of D. zhenghuoense. Present study suggests that genomic information of D. zhenghuoense would have special importance in conservation and molecular phylogenetic studies on Orchidaceae. The circle genome of D. zhenghuoense was 148,431 bp in length with 37.0% GC content and a large single-copy (LSC) region of 84,167 bp, a small single-copy (SSC) region of 12,588 bp, which were separated by a pair of inverted repeat (IR) region of 25,838 bp. The genome contained 130 genes, including 75 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The maximum likelihood phylogenetic analysis indicated that D. zhenghuoense was the sister to the rest 11 species of Dendrobium tested.