Miracle-dz/UniFAR-FTUs huggingface dataset:
Aislamiento e identificación de genes de Opuntia streptacantha inducidos en condiciones de estrés abiótico

Proline (Pro) is one of the most accumulated osmolytes in salinity and water deficit conditions in plants. In the present study, we measured the Pro content, the activity and the expression level of delta 1-pyrroline-5-carboxylate synthetase (P5CS: g-glutamyl kinase, EC 2.7.2.11 and glutamate-5-semialdehyde dehydrogenase, EC 1.2.1.41), a key regulatory enzyme involved in the biosynthesis of Pro, in cactus pear (Opuntia streptacantha) subjected to 6, 9 and 11 days of salt stress. Treatment with NaCl of O. streptacantha young plants resulted in a decrease in the cladode thickness and root length, and in a significant and gradual accumulation of Pro in young cladodes, in a timeand concentration-dependent manner. P5CS activity, studied as g-glutamyl kinase, was reduced at all times as a consequence of salt treatment, except at the sixth day at 75 and 150 mM of NaCl, where a slight increase was observed. We isolated an open reading frame (ORF) fragment of p5cs gene. The deduced amino acid sequence of the P5CS protein exhibited 90.4% of identity with the P5CS protein from Mesembryanthemum crystallinum. RT-PCR analysis revealed that the Osp5cs gene of O. streptacantha was induced by salt stress at 9 and 11 days of treatment. Furthermore, ABA-induced Osp5cs gene expression was observed in cladodes of cactus pear young plants. We observed an evident correlation between the transcript up-regulation and the Pro accumulation under salt stress; however, these results do not parallel with the changes in P5CS enzymatic activity. This Pro accumulation might function as an osmolyte for the intracellular osmotic adjustment and might be playing a critical role in protecting photosynthetic activity in O. streptacantha plants under salt stress. 2007 Elsevier Masson SAS. All rights reserved.
Identification of Streptococcus agalactiae isolated from pregnant women by 16srRNA gene

The main goal of the current study is to isolate and diagnose of Streptococcus agalactiae by using the diagnostic 16 SrRNA gene. S.agalactiae was isolated from 850 samples including (425) vaginal swabs, (425) rectal swabs and identified by studying the morphological characteristics of colonies on culture, microscopic characteristics of bacterial cells, biochemical methods, Vitek 2 system, API-20 Strep, and then confirmed the identification by detection of 16SrRNA gene by Polymerase Chain reaction (PCR) followed by DNA Sequence analysis for this gene. A total of 16 isolates of S.agalactiae were isolated from 12 (2.82%) vaginal swabs, 4 (0.99%) rectal swabs, and 16SrRNA was detected in 100% of the S.agalactiae isolates.
Decision making support geo-informational system for managing socio-economical sphere of region

For the management of social or educational resources of a region for different levels of managers multidimensional information is needed. For effective analyses of this information and for decision making the geo-informational system (GIS) was developed. It offers the geo-informational features for a wide range of Internet users in their work with information for social sphere description. The GIS combines the advantages of Web and GIS technologies, such as a large amount of potential users, common interface and advanced features of information visualization including cartographical. For work with the GIS only a Web browser is needed. Several features of the system are: multi-user data access; operation with spatially-attached information; metadata actualization; data input (load); and using the data warehouse concept. On the present implementation phase the information of the National Statistics Committee of the Tomsk region is taken as basic data.
Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate

Cys-loop receptors are vital for controlling neuronal excitability in the brain and their dysfunction results in numerous neurological disorders. Recently, six de novo missense variants in GABRA2 gene, a member of this family, have been associated with early infantile epileptic encephalopathy (EIEE) and intellectual disability with seizures. Here, using whole-genome sequencing we identified a de novo missense variant in GABRA2 gene in a patient with EIEE and developmental delay. We perform protein structural analysis of the seven variants and show that all the mutations are in the transmembrane domain, either close to the desensitization gate, the activation gate or in inter-subunit interfaces. Further investigations demonstrated that the majority of pathogenic variants reported are at equivalent positions in other Cys-loop receptors, emphasizing the importance of these residues for the adequate function of the receptor. Also, a comparison of the distribution of the mutations in all the Cys-loop receptors showed that pathogenic variants are more common in the transmembrane helices, more specifically in the M2 helix, highlighting the importance of this segment. Our study expands the clinical spectrum of individuals with pathogenic missense mutations in GABRA2, defines the regions where pathogenic mutations are in the protein structure, and highlights the value of considering sequence, evolutionary, and structural information from other Cys-loop receptors as a strategy for variant interpretation of novel missense mutations in GABRA2.
Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif

Pathogens infecting plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen, Bremia lactucae, using comparative genomics and bioinformatics to search for the WY domain. This conserved structural element is found in Phytophthora effectors and some other oomycete pathogens; it has been implicated in the immune-suppressing function of these effectors as well as their recognition by host resistance proteins. We predicted 54 WY domain containing proteins in isolate SF5 of B. lactucae that have substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis effectors containing WY domains revealed eleven out of 21 that triggered necrosis, which is characteristic of the immune response on wild accessions and domesticated lettuce lines containing resistance genes. Only two of the eleven recognized effectors contained a canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens. Author Summary There is a microscopic battle that takes place at the molecular level during infection of plants and animals by pathogens. Some of the weapons that pathogens battle with are known as “effectors,” which are secreted proteins that enter host cells to alter physiology and suppress the immune system. Effectors can also be a liability for plant pathogens because plants have evolved ways to recognize these effectors, triggering a defense response leading to localized cell death, which prevents the spread of the pathogen. Here we used computer models to predict effectors from the genome of Bremia lactucae, the causal agent of lettuce downy mildew. Three effectors were demonstrated to suppress the basal immune system of lettuce. Eleven effectors were recognized by one or more resistant lines of lettuce. In addition to contributing to our understanding of the mechanisms of pathogenesis, this study of effectors is useful for breeding disease resistant lettuce, decreasing agricultural reliance on fungicides.
Inventory of European Sea Bass (Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development

During early animal ontogenesis, a plethora of small non-coding RNAs (sncRNAs) are greatly expressed and have been shown to be involved in several regulatory pathways vital to proper development. The rapid advancements in sequencing and computing methodologies in the last decade have paved the way for the production of sequencing data in a broad range of organisms, including teleost species. Consequently, this has led to the discovery of sncRNAs as well as the potentially novel roles of sncRNA in gene regulation. Among the several classes of sncRNAs, microRNAs (miRNAs) have, in particular, been shown to play a key role in development. The present work aims to identify the miRNAs that play important roles during early European sea bass (Dicentrarchus labrax) development. The European sea bass is a species of high commercial impact in European and especially Mediterranean aquaculture. This study reports, for the first time, the identification and characterization of small RNAs that play a part in the 10 developmental stages (from morula to all fins) of the European sea bass. From 10 developmental stages, more than 135 million reads, generated by next-generation sequencing, were retrieved from publicly available databases as well as newly generated. The analysis resulted in about 2,000 sample grouped reads, and their subsequently annotation revealed that the majority of transcripts belonged to the class of miRNAs followed by small nuclear RNAs and small nucleolar RNAs. The analysis of small RNA expression among the developmental stages under study revealed that miRNAs are active throughout development, with the main activity occurring after the earlier stages (morula and 50% epiboly) and at the later stages (first feeding, flexion, and all fins). Furthermore, investigating miRNAs exclusively expressed in one of the stages unraveled five miRNAs with a higher abundance only in the morula stage (miR-155, miR-430a, d1, d2, and miR-458), indicating possible important key roles of those miRNAs in further embryonic development. An additional target search showed putative miRNA-mRNA interactions with possible direct and indirect regulatory functions of the identified miRNAs.
University of Birmingham Replay of Stimulus Specific Temporal Patterns during Associative Memory Formation

Forming a memory often entails the association of recent experience with present events. This recent experience is usually an information rich and dynamic representation of the world around us. We here show that associating a static cue with a previously shown dynamic stimulus, yields a detectable, dynamic representation of this stimulus. We further implicate this representation in the decrease of low-frequency power (~4-30 Hz) in the ongoing electroencephalogram (EEG), which is a well-known correlate of successful memory formation. The reappearance of content specific patterns in desynchronizing brain oscillations was observed in two sensory domains, i.e. in a visual and in an auditory condition. Together with previous results, these data suggest a mechanism that generalizes across domains and processes, in which the decrease in oscillatory power allows for the dynamic representation of information in ongoing brain oscillations.
Growth Response of Sessile Oak and European Hornbeam to Traditional Coppice-with-Standards Management

Research Highlights: The influence of litter raking and livestock grazing on the development of juvenile sessile oak and European hornbeam sprouts as well as on sessile oak standards were studied. Such experiments are very rare, especially in central Europe where these activities have been prohibited for several decades. Little is known on how these ancient management activities affect tree growth. Background and Objectives: Traditional management practices in coppice forests such as grazing and litter raking have been abandoned, but have recently been studied as to whether these practices can substantially contribute to an increase in the species diversity of coppices. The important question is, however, how these practices influence the growth of coppice-with-standards. Therefore, this study focused on the effect of grazing, litter raking, and their combination on both sprouts and adult trees in a coppice-with-standards system one year after harvest. Materials and Methods: The experiment was carried out in the area of the Training Forest Enterprise Masaryk Forest Křtiny, Czech Republic, in a forest stand dominated by sessile oak and European hornbeam. We analyzed 132 oak polycormons, 132 hornbeam polycormons, and 163 oak standards. Results: The number of sprouts per stump was affected by the stump size and management practice: (A) coppice-with-standards, litter raking, and sheep grazing; (B) coppice-with-standards and sheep grazing; (C) coppice-with-standards and litter raking; and (D) coppice-with-standards), but not by tree species. The number of the sprouts as well as their height increased with the stump size. In contrast, grazing resulted in a smaller height of the sprouts while thinner sprouts were found under a combination of grazing and raking. When comparing the species, the oak sprouts were higher and thicker when compared to the hornbeam sprouts. The increment of standards increased after stand harvest. This, however, was not the result of grazing or raking, but the response to the reduction of tree number and thus of competition between neighboring trees. Conclusions: The results showed that there were rather negative impacts from the implemented traditional management practices on the growth of sprouts. This may lead to the question of whether ecological diversity resulting from the traditional practices may prevail their negative effect on the growth of the coppices.
Sibling competition in Blue Tits (Cyanistes caeruleus) is stronger in homozygous broods

ABSTRACT Heterozygosity affects mate selection and can modulate interactions among family members and their fitness-related decisions. We studied whether nestling heterozygosity affected parent–offspring interactions and sib–sib competition in the Blue Tit (Cyanistes caeruleus) while controlling for the degree of relatedness among nestlings. Demanding environmental conditions might make the detection of heterozygosity-fitness correlations easier. Thus, we also investigated whether the decision rules of family members according to offspring heterozygosity were affected by brood size, as a proxy of the strength of sibling conflict. We found that chick individual heterozygosity was positively although weakly associated with individual body mass. Mean brood heterozygosity did not predict fledging success, but broods that fledged more chicks showed a higher number of less common alleles. Interestingly, fathers, but not mothers, favored heterozygous broods with many nestlings, that is, heterozygous broods with higher potential for sibling conflict. Moreover, the lower the mean brood heterozygosity the stronger the begging intensity when parents were absent, regardless of brood size. Finally, the degree of relatedness among nestlings was not associated with any behavioral parameter, supporting a more prominent role for heterozygosity in shaping intra-family interactions. Our findings suggest that offspring heterozygosity determines sex-specific rules of parental care and that genetic diversity is associated with lower sibling competition.
Assesment of Larvicidal Activities of Essential Oil Extracted from Country Onion ( Afrostyrax lepidophyllus ) Seed on Anopheles Mosquito Larvae

Mosquitoes particularly anopheles are the main vectors for the malaria parasites that causes malaria fever diseases which is the highest killer of human beings in the tropics. There has been exploration of various methods over the centuries to control mosquito borne diseases. Larvicidal activities of essential oil extracted from country onion ( Afrostyrax lepidophyllus ) seed, on anopheles mosquito larvae has been determined in this study. Essential oils were extracted from Afrostyrax lepidophyllus seed by Hydrodistillation method, with a percentage yield of 4.12% and characterized using gas chromatography-mass spectrometry (GC-MS). Eighteen (18) compounds were identified to be Methanamine (1.07%), Dimethyl trisulfide (16.7%), Furan (0.79%), 1,2-Benzenediol (1.53), Disulfide (52.3%), 1,2,4 trithiolane (0.40%), 2,4-dimethyl-3-nitrobicyclo [3.2. 1] (2.85%), 2-pyridinemethanamine (0.66%), Bis (2sulfhydrylethyl (16.7%), Benzenemethanol (0.28%), 2,2-dimethylpropanoic acid (0.50%),1,2 bis (trimethylsily) benzene (0.27%), Cyclotrisiloxane (0.28%), Silane (0.27%), Tetrasiloxane (0.68%), Methyltris (trimethylsiloxane) silane (1.00%), Silicic acid (2.15%), 1,4-phenylenebis[trimethyl (1.53%). The percentage amounts of the components was determined based on their relative abundance and their retention indices. There were significance differences (P Afrostyrax lepidophyllus essential oil activities against anopheles mosquito’s larvae. Results of the larvicidal activity showed that, 200ppm and 400ppm concentration of essential oil induced 100% larval mortality in 24hr. While At lower concentration of 50ppm, 100ppm and 150ppm, induced 45% and 95% and 99% larval mortality within 24hr respectively. This results of larvicidal activity of Essential oil from the Afrostyrax lepidophyllus seed shows that the oil is highly reactive against anopheles mosquito larvae indicating that it could be explored as a more potentially effective, economical and cost effective mosquito control agent for industrial and household usage.
Potential antigenic mismatch of the H3N2 component of the 2019 Southern Hemisphere influenza vaccine

Here, we find that the egg-adapted H3N2 component of the 2019 Southern Hemisphere influenza vaccine elicits an antibody response in ferrets that is highly focused on antigenic site A of hemagglutinin. This is potentially problematic since most H3N2 viruses currently circulating in the Southern Hemisphere possess antigenic site A substitutions.
Variations in morphological traits, agronomic traits and traits related to drought tolerance in indigenous Thai rice varieties

Indigenous rice is worth conserving as it possesses many important traits such as good table quality for consumers, resistance to biotic and abiotic stresses and, especially, quality of starch. The objectives of this study were to evaluate indigenous rice accessions collected in Northeast Thailand and select the superior accessions for further improvement of indigenous rice. Forty indigenous rice accessions were evaluated in a pot experiment in a split-plot design with completely randomized arrangement of the treatments and four replications for two years in 2014 and 2015. Main plots were two water regimes, including well-irrigated treatment and early season drought treatment; the subplots included 40 indigenous rice accessions. Well-irrigated treatment was higher than early season drought condition in terms of plant height, number of tiller per plants, number of ears per plant, number of unfilled grains per ear, grain weight per plant, straw weight per plant and shoot dry weight per plant; drought treatment was higher than irrigated treatment in terms of the number of filled grains per plant, 1000-grain weight and root dry weight; whereas these two types of treatment showed no differences in terms of the number of tillers/plant at 30 days after emergence and harvest index. The superior genotypes for each trait and the genotypes with better drought tolerance index were
Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of small-colony variant Enterobactericeae

Isolation of bacterial small colony variants (SCVs) from clinical specimens is not uncommon and can fundamentally change the outcome of the associated infections. Bacterial SCVs often emerge with their normal colony phenotype (NCV) co-isolates in the same sample. The genetic and biochemical basis of SCV emergence in vivo is not well understood in Gram-negative bacteria. In this study, we interrogated the causal genetic lesions of SCV growth in three pairs of NCV and SCV co-isolates of Escherichia coli, Citrobacter freundii, and Enterobacter hormaechei. We confirmed the isogenic basis of SCV emergence, as there were only 4 single nucleotide variants in SCV for E. coli, 5 in C. freundii, and 8 in E. hormaechei, with respect to their NCV co-isolate. In addition, a 10.2kb chromosomal segment containing 11 genes was deleted in the E. hormaechei SCV isolate. Intriguingly, each SCV had at least one coding change in a gene associated with bacterial oxidative respiration and another involved iron capture. Chemical rescue confirmed the causal role of heme biosynthesis in E. coli and C. freundii and lipoic acid in E. hormaechei SCV isolates. Genetic rescue restored normal growth under aerobic conditions for fes and hemL in C. freundii; hemL in E. coli; and lipA in E. hormaechei SCV isolates. Prototrophic growth in all 3 SCV Enterobacteriaceae species was unaffected under anaerobic culture conditions in vitro, illustrating how SCVs may persist in vivo by abandoning the highly energetic lifestyle in an iron-limiting environment. We propose that the selective loss of functions in oxidative respiration and iron acquisition is indicative of bacterial virulence attenuation for niche specialization and persistence in vivo. Importance Small colony variant (SCV) bacteria are routinely isolated in the clinical microbiology laboratory and can be notoriously difficult to treat. Most studies of the genetic underpinnings of SCV clinical isolates have examined Staphylococcus aureus and few have looked at how SCV emerge in Gram-negative bacteria. Here, we undertook detailed characterization of three clinical isolates of SCV in Escherichia coli, Citrobacter freundii, and Enterobacter hormaechei along with their NCV co-isolates. Genomic sequencing revealed that each SCV had at least one coding change in genes involved in both bacterial oxidative respiration and iron capture. Chemical and genetic rescue revealed that both pathways could be responsible for the small colony variant. Each of the SCV showed no growth defect compared to NCV when incubated under anaerobic conditions, indicating a potential mechanism for SCV survival in vivo. We hypothesize that by retreating to anaerobic environments and avoiding escalating iron competition with the host, SCV have adapted to live to see another day.
Randomness Assessment of an Unpredictable Random Number Generator based on Hardware Performance Counters

Hardware performance counters capture and measure hardware events within the processor, providing a detailed indication on the internal behavior and performance of the various micro-architectural components within the processor while running system or user level programs. We have previously investigated the potential of hardware events captured by performance counters to provide entropy sources for generating unpredictable random number sequences, and now we extend the generator model introduced in [1] by various delay types and simple operations which show high impact on the internal behavior of the processor. The randomness quality of sequences produced by the generator in different conﬁgurations are thoroughly assessed using statistical and visual randomness tests which highlight the characteristics and limitations of the generator and show the improvements achieved by the new design.