Miracle-dz/UniFAR-FTUs huggingface dataset:
A functional msbB acyltransferase of Photorhabdus luminescens, required for secondary lipid a acylation in gram-negative bacteria, confers resistance to anti-microbial peptides

Abi Khattar Z. , S. Gaudriault and A. Givaudan. 2016. A functional msbB acyltransferase of Photorhabdus luminescens, required for secondary lipid a acylation in gram-negative bacteria, confers resistance to anti-microbial peptides. Lebanese Science Journal, 17(1): 45-56. Lipid A is a potent endotoxin, and its fatty acids (lauric, myristic, and sometimes palmitic acid) anchors lipopolysaccharide (LPS) into the outer leaflet of the outer membrane of most Gram-negative bacteria. The highly anionic charge of the glucosamine lipid A moiety makes the LPS a powerful attractant for cationic antimicrobial peptides (AMPs). AMPs are major component of innate immunity that kill bacteria by permeabilization of lipid bilayers. Secondary lipid A acylation of Klebsiella pneumoniae, involving the acyltransferase LpxM (formally, msbB or WaaN) that acylates (KDO)2-(lauroyl)-lipid IV-A with myristate during lipid A biosynthesis, has been associated with bacterial resistance to AMPs contributing to virulence in animal models. We investigated here the role of the msbB gene of the entomopathogenic bacterium Photorhabdus luminescens in AMP resistance, by functional complementation of the AMP susceptible K. pneumoniae lpxM mutant with the P. luminescens msbB gene. We showed that msbB (lpxM) gene of P. luminescens is able to enhance polymyxin B, colistin and cecropin A resistance of K. pneumoniae lpxM mutant, compared to the non-complemented mutant. However, we could not obtain any msbB mutant of Photorhabdus by performing allelic exchange experiments based on positive selection of sucrose highly resistant mutants. We thus suggest that msbB-mediated Photorhabdus lipid A acylation is essential for outer membrane low-permeability and that modification of lipid A composition, fluidity and osmosis-resistance have an important role in the ability of Photorhabdus to grow in sucrose at high concentrations.
Peach Fruit Set and Buttoning after Spring Frost

Peach fruit set is affected by cumulative chill and spring frost. A spring frost occurred on 29 Mar. 2015 at the U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS) Byron station after 3 weeks of bloom, reducing fruit set and resulting in many buttons (abnormally small fruit with dead embryos). Fruit set was rated in 2014, 2015, and 2016 and button set rated in 2015 using the same scale (0 = no fruit/button to 9 = 1–2 fruit/button at every node). The overall fruit set rating was substantially different in the 3 years, averaging 5.61 in 2014, 2.61 in 2015, and 6.04 in 2016. Buttons and skin-damaged fruit in 2015 varied among peach genotypes. Compar- ison of fruit and button set ratings showed that there was no difference between cultivars and selections, but some signiﬁcant differences in fruit set for four ripening months, among the 3 years, and among the nine chilling classes, respectively. Among the cultivars, the most common button set rating was 0–3. For example, ‘Sunprince’, ‘Loring’, and ‘Carored’ trees had a high button set rating, whereas ‘Flameprince’, ‘Julyprince’, and ‘Contender’ trees were low. As for peach selections, BY04P1690n was among those with the highest button set rating. In the population derived from a cross of button-prone BY04P1690n and button-free BY99P3866w, fruit and button counts from 10 long fruiting shoots ranged from 4 to 53 fruit (21.63 on average) and 2 to 27 buttons (10.39 on average). The peach button rate ranged from 5.36% to 87.10% (30.70% on
Morphological changes of the hippocampal astrocytes at different phases of the estrous cycle in female mice

Background: Usual fluctuations of sex hormones during the estrous cycle in female mice affect the hippocampal neurogenesis. The hippocampus also comprises many steroid receptors suggesting the modulatory effects of gonadal hormones on the hippocampal plasticity. Sex differences at the level of structure and function of the hippocampus are mostly due to the fluctuations of steroid hormones during the estrous cycle. The purpose of this study was to investigate the morphological changes in hippocampal astrocytes and also the expression of glial fibrillary acidic protein (GFAP) at different phases of the estrous cycle. Materials and Methods: In this study, different stages of the estrous cycle were determined in 6-8 week NMRI female mice by methylene blue-stained vaginal smears. The morphological changes of astrocytes in the hippocampus were investigated using GFAP immunohistochemistry. In addition to the morphological study, the expression of astrocytic marker was quantitatively evaluated. Results: GFAP immunostaining showed the changes in the morphology of astrocytes and also in the serum level of estrogen during the estrous cycle. The highest concentrations of estrogen and GFAP reactivity were observed in the proestrus stage. Conclusion: Different stages of the estrous cycle in female mice were associated with morphological changes of hippocampal astrocytes and the alternation in the serum level of estrogen.
Cultura organizacional e os fatores críticos de qualidade de vida no trabalho, na percepção dos policiais da terceira companhia independente da polícia militar de pernambuco.

Recent social changes are provoking new demands to the working world, triggering more emphatic discussions about Quality of Work Life (QWL) and organizational culture as a way to provide balance between the demands for performance in organizations and welfare of the employee. Although being recurrent themes in the organizational literature, there are few attempts to treat them so associated. The aim of this study is to characterize the relationship between values and practices of Organizational Culture, highlighted by pelo Instrumento Brasileiro de Avaliacao da Cultura Organizacional (IBACO), and the critical factors of Quality of Work Life in the Third Independent Company of Military Police of Pernambuco (3rd CIPM .) The study in question is of an explanatory nature, relied primarily on the dimensions of quality of life proposed by Walton (1973) and the values and practices proposed by Ferreira and Assmar (2008) through the IBACO. The strategy used in this research was quantitative, using for collecting data the survey method. To analyze and interpret the data was used descriptive statistics, and rank-order correlation of Spearman, for comparison of two variables. The survey results revealed seven variables critical to QVT. About the values and practices measured: the values of professional cooperativism, stiffness in the hierarchical structure of power and external integration practices were considered moderate; practices promote interpersonal relationships, practices and reward training, and values professionalism competitive and individualistic, were considered only slightly present in the organization, and the values associated with satisfaction and well-being of employees were considered the least in the organizational culture. After the analysis of the correlation matrix among the critical factors of Quality of Work Life and practices and measured values, it was concluded that organizational culture significantly influences the Quality of Work Life in the 3rd CIPM.
Predation on parasites and its consequences for transmission

Understanding pathogen transmission is crucial for predicting disease impacts, yet few studies test alternative functional forms of transmission and, among those that do, “classical” forms such frequency and density dependent transmission receive surprisingly little empirical support. Using interactions between amphibian hosts and trematode parasites as a model system, we used a novel experimental approach in which we varied four factors—duration of exposure, numbers of parasites, numbers of hosts, and parasite density—to differentiate among seven candidate transmission functions using a maximum likelihood approach. Our results indicated that, among the candidate models considered, non-linear forms of transmission involving either a power law or negative binomial function were the best fitting models and consistently outperformed density and frequency dependent functions. Across host-pathogen systems, non-linear functions may more accurately represent transmission dynamics thus providing more realistic predictions for infection and highlighting important potential mechanisms in addition to parasite depletion. Introduction Understanding the functional form of transmission has important implications for modeling disease impacts on host population dynamics, forecasting disease persistence in host populations and establishment in new populations, and understanding the evolution of virulence (McCallum et al. 2001, Fenton et al. 2002, Boots and Sasaki 2003, Holt et al. 2003, de Castro and Bolker 2005). An almost universal assumption in contemporary disease ecology is that the form of
The microenvironment is essential for OTSCC progression

The tumor microenvironment (TME) is critically important for tumor development. The microenvironment consists of fibroblasts, endothelial and immune cells as well as extracellular matrix (ECM), proteases and various other soluble factors produced by the cells. It is challenging to develop methods that appropriately mimic the human microenvironment, but this effort is essential in order to reliably elucidate the properties of potential anti-tumor drugs. The aim of this study was to create new 3D organotypic invasion models based on human tissue that would be used to study the effects of the anti-angiogenic molecules arresten and endostatin on tongue squamous carcinoma cells. The classic way to study cancer invasion has been to use a collagen invasion model that is created by mixing rat type I collagen, matrix produced by mouse EHS tumor cells and human fibroblasts. Our research group has developed a novel human myoma tissue based invasion model, which is composed of several different cell types and molecules that are normally present in the human TME. We show how this model is suitable for invasion studies, not only for oral cancer, but for other invasive cell lines as well. There are several matrix-derived fragments that have been shown to possess anti-angiogenic activity. Arresten is a 26 kDa fragment that is cleaved from type IV collagen and is known to inhibit angiogenesis, the formation of new capillaries and tumor growth in vivo. However, its effect on the tumor microenvironment in addition to endothelial cells has not been studied. We show that arresten also directly affects oral cancer cells by decreasing their migration and invasion as well as tumor size, invasion and angiogenesis in in vivo mouse xenografts. Another inhibitor of angiogenesis, endostatin, is cleaved from type XVIII collagen. It has been shown to suppress angiogenesis and tumor growth without toxicity or side effects in mouse models. Our studies show that endostatin directly affects tongue squamous carcinoma cells by reducing their invasion and spreading in organotypic 3D assays and mouse tumor models. In summary, arresten and endostatin are anti-angiogenic as well as anti-invasive molecules and therefore potential cancer drugs. They seem to have a direct effect on carcinoma cells making the cells less invasive. The myoma model allows us to study the effects of anti-cancer molecules with a new prospective.
Realizing the potential of trait‐based aquatic ecology: New tools and collaborative approaches

Trait‐based ecology, which focuses on using the traits of species and individuals to understand ecology (from populations to ecosystems), is becoming an increasingly productive and widely employed paradigm. To date, trait‐based approaches have been used to study taxa from microbes to megafauna in every major area of aquatic ecology yielding exciting results. However, this promising field faces a number of significant obstacles, including: (1) identifying and measuring ecologically relevant traits, (2) integrating inter‐ and intra‐specific trait variation, (3) detecting and quantifying trait correlations and trade‐offs, and (4) accounting for the context dependency of traits. These issues are often particularly acute for specific taxa or systems. This paper highlights these looming challenges, as well as ways to address them. Proposed solutions center around using new technologies to collect trait data, coordinating research efforts, and curating and sharing data. Throughout, we take an interdisciplinary approach, sharing examples spanning a wide range of aquatic taxa and systems. It is our hope that this paper will stimulate frank discussions and help the growing field of trait‐based aquatic ecology maximize its potential.
Estimation of ascorbic acid, ß carotene, total chlorophyll, phenolics and antioxidant activity of some European vegetables grown in mid hill conditions of western Himalaya

Seven European vegetables viz: Chinese Cabbage (Brassicca pekinensis), Black Lai (Brassicca rugossa), Broccoil (Brassicca oleracea var italica), Brussel’s Sprout (Brassicca oleracea var germifera), Cauliflower (Brassicca oleracea var botrytis), Red Cabbage (Brassicca oleracea var rubra) and Lettuce (Lectuca sativa) were grown and estimated for antioxidant phytonutrients. Maximum ascorbic acid content (175.99 mg/100g), ß carotene (52.34 μg/g), antioxidant activity (1.38 IC50) phenol content (13.59 mg/g) and total chlorophyll content (16.92 mg/g) was recorded in Brussels’s Sprout. Linear regressions were performed with collected data in order to know which phytonutrients are contributing to antioxidant activity. Results revealed that ascorbic acid, ß carotene, total phenols and total chlorophyll contents were highly correlated with antioxidant activity for European vegetables. It is revealed from the results that European vegetables are rich source of abundant antioxidants and there is significant variation among the different species for antioxidant phytochemicals.
Palaeoecological record of local fire history from a peat deposit in SW Finland

The stratigraphical variation of charcoal abundance in a postglacial peat deposit, together with palynoiogical and sedimentological data, was used for a reconstruction of vegetation changes in Paimio, SW Finland. The in situ fires were differentiated from those which occurred outside the basin. The charcoal profile was correlated with changes in coniferous tree pollen, "sprouter" pollen and anthropogenic pollen. Natural forest fires, man-induced fires and the history of land use were inferred and related to a time scale consisting of inferred ages based on various models. The mean forest fire frequency during the last 3 000 years (after Picea migration) has been one fire every 80 to 85 years. Prior to 2 000 years B.P., forest fires were primarily natural, but later when slash-and-burn cultivation spread to the area, the interpretation of the data became complex. The vegetation succession was determined by a combination of climatic and edaphic change, species migration and competition, and natural and man-induced forest fires. Three progressive stages of human interference were revealed, viz. temporary slash-and-burn clearance (from about A.D. 300 to 700), intensive, continual slash-and-burn practice (from about A.D. 700/900 till the Middle Ages and modern times) and predominantly arable cultivation (from about A.D. 1700).
Étude des mécanismes non-conventionnels de traduction chez le virus de l'immunodéficience humaine de type 1 et le virus de l'hépatite C

Human immunodeficiency virus type 1 (HIV-1) and Hepatitis C virus (HCV) are responsible for two major viral pandernics and around 40 and 200 million people, respectively, are infected with these viruses worldwide. During the course of my Ph.D. studies, I investigated unconventional translation mechanisms used by these two viruses. One of these unconventional translation mechanisrns is a programmed —1 ribosornal frameshift that is used by HIV1. In HIV1, Gag, the precursor of the viral structural proteins, and Pol, the precursor of the viral enzymes, are synthesized from the saine RNA, i.e. the full-length viral RNA, but the coding sequence of Pol is in a —1 reading frame relative to the coding sequence of Gag. The majority of ribosornes translate the viral RNA according to conventional rules and synthesize Gag, but a minority of ribosomes that initiated translation at the initiation codon of Gag shifi the reading frame at a specific sequence before they encounter the stop codon of Gag and extend the translation to the pot gene, synthesizing Gag-Pol. The expression of Pol is thus regulated by a —1 frameshifi and the efficiency of this —l frameshifi event controls the Gag-Pol to Gag ratio, which is critical for particle assembly, replication and viral infectivity. This —Ï frameshifi requires two cis acting elements in the viral mRNA: a slippery sequence, where ribosomes slip by one nucleotide in the 5’ direction, and a downstrearn stimulatory signal, which is a specific structure that controls the —1 frarneshifi efficiency. Our group had previously dernonstrated that the —l frameshifi stirnulatory signal ofthe subtype B of group M ofHIV-1 (the group M is predorninant worldwide and the subtype B is the rnost widespread in America and Europe) is a two-stem helix, in which a three-purine bulge interrupts the two stems. Our studies showed that the —1 frameshifi stimulatory signal of all the other subtypes of group M can be folded into the same structure as in subtype B, despite sequence variations. Wc also showed that the efficiency of the —1 frameshifi of every subtype of group M falis within a nanow window, the maximal deviation from the mean value of the efficiency of these subtypes being 35%. Our results confirmed the importance of the Gag-Pol to Gag
In vitro Growth of Dwarf Cavendish Banana Plantlets in Different Culture Vessels and Light Intensities

The growth and multiplication of a local Cavendish banana called “Kwadu Pa” was investigated under three different light intensities and three types of culture vessels. The light intensities were 4000, 5000 and 6000 Lux with glass, plastic bottles and conical flask as the vessel types. Each of the treatments for light intensity and vessel type were replicated 50 times and cultures were arranged in a completely randomized fashion. They were cultured for 16 weeks and data was taken on mean shoot fresh weight, number of shoots per plantlet, shoot dry weight, leaf chlorophyll content and shoot height. Plantlets that were cultured in conical flask under the three different light intensities had higher values for all the parameters measured under the different light intensities. Among the light intensities, plantlets that were cultured under 5000 Lux showed superior growth and multiplication compared to those cultured under 4000 and 6000 Lux. At light intensities above 5000 Lux, growth characteristics and chlorophyll content declined significantly. Conical flask as a culture vessel and photon flux of 5000 Lux were optimal for the in vitro growth and multiplication of banana.
Azadirachta indica A. Juss Induced Changes in Spermatogenic Pattern in Albino Rats

Objective: The leaves of Azadirachta indica A. Juss was tested to find the antispermatogenicity in seminiferious epithelium of rats. Materials and methods: Male albino rats were administered orally (by gavage), 100 mg/ body weight Azadirachta indica leaf powder with or without testosterone (IM). Suitable controls were maintained. Results: Damaged seminiferous tubules and abundance of vacuoles of varying size were observed in Azadirachta indica treated rats. The germ cells showed overall decrease in cytoplasmic ground substance. Leydig cells exhibited characteristics of degeneration with condensed nuclei. Total count of spermatocytes, spermatids and Leydig cells were reduced. The cell and nuclear diameter of spermatogonia, spermatocytes, spermatids and Leydig cells were also reduced. Conclusion: From the results obtained, it can be observed that Azadirachta indica effects on the testis are possibly due to gonadotrophic hormone deficiency, caused directly or indirectly. The probable mode of antiandrogenic and antispermatogenic actions of the medicinal plant is discussed.
MERS Coronavirus in Dromedary Camel Herd

A prospective study of a dromedary camel herd during the 2013–14 calving season showed Middle East respira-tory syndrome coronavirus infection of calves and adults. Virus was isolated from the nose and feces but more fre-quently from the nose. Preexisting neutralizing antibody did not appear to protect against infection.
Type VI secretion systems of Bradyhizobium nodulating lupines

The Rhizobium-legume symbiosis is highly specific and depends on several molecular signals produced by both partners. Some of these signals are bacterial proteins named effectors that are translocated into the plant cells by secretion systems similar to contractile nanomachines also called injectisomes (Deakin and Broughton, 2009). The injectisomes puncture and deliver the effectors into the target cell. One of these nanomachines, known as type VI secretion system (T6SS), was discovered recently and is reminiscent of phage injection machinery (Records, 2011). The role of these systems in legume endosymbiotic bacteria is mostly unknown, and this work presents the initial study of T6SSs from different bradyrhizobia. T6SSs have been identified in draft genomic sequences from Bradyrhizobium strains isolated from Lupinus spp. thriving in the Iberian Peninsula. In all cases, the genes encoding T6SSs were grouped and showed, in most cases, a high degree of conservation among genes encoding the structural components of the system. Bradyrhizobium sp. strain ISLU101 isolated from L. angustifolius, contains two clusters of genes involved in the formation of T6SS. One of such systems, designated as T6SS-1, contains 17 genes and shows a high degree of conservation regarding genes of B. diazoefficiens USDA110. The other one, T6SS-2, contains 16 genes flanked by insertion element sequences. Amino acid similarity between equivalent proteins encoded in both clusters is only about 40-50 %. A phylogenetic analysis based on the concatenation of sequences of several T6SS proteins was performed, and results indicate a clear separation of T6SS-2 from most rhizobial T6SSs. ISLU101 T6SS mutant derivatives in genes impO, impC1 and impC2 were generated by single homologous recombination of amplified internal fragments from the respective genes cloned into the suicide vector pK18mobsac. The symbiotic behaviour of mutants was examined with L. angustifolius. Results showed no effect of impC1 and impC2 mutations, while the impO mutant generated smaller plants with a mixture of white/red nodules. These results suggest that T6SSs may play a role in the Bradyrhizobium-lupines symbioses
Isolation, characterization and discovery of new alleles of sHsp genes in durum wheat (Triticum durum Desf.)

5 Riassunto . 6 List of abbreviations . 8 List of figures . 9 List of tables . 10 Chapter 1. General introduction . 12 1.1 The Wheat . 12 1.1.1 Importance of wheat . 12 1.1.2 The today’s challenges of the wheat production . 12 1.1.3 Domestication evolution in wheat . 15 1.1. 4 Wheat genetics and genomics . 17 1.1. 5 Generalities and developmental stages . 19 1.2 Abiotic stress in plants . 21 1.2. 1 Plant responses to abiotic stresses . 21 1.2. 2 The Heat Stress Response (HSR) . 23 1.2. 3 Transcription factors and stress responsive elements in abiotic stress tolerance . 25 1.2. 4 Effect of heat stress on chloroplast and photosynthesis . 27 1.2. 5 The Heat Shock Proteins (HSPs) . 28 1.2. 6 The small Heat Shock Proteins (sHSPs) . 34 1.3 Functional genomics in crop improvement . 39 1.3. 1 TILLING in functional genomics . 39 1.3. 1.1 Creation of the mutagenized population . 41 1.3. 1.2 Mutation detection methods . 43 1.3. 2 TILLING by sequencing and online TILLING . 46 1.3. 3 EcoTILLING . 48 1.3. 4 SNP-based functional markers . 49 1.3. 4.1 KASP genotyping applied in TILLING . 53 Objectives . 55 Chapter 2. Identification and characterization of the T. durum chloroplastic sHsps genes (TdHsp26) and promoters . 56 2.