Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Mycoplasma synoviae by PCR and Culture Methods and Determination of the Prevalence of P1, P30, and P116 Virulence Genes in the Isolates

C I T A T I O N L I N K S A R T I C L E I N F O Article Type Original Research Authors Najmeh Salmani zadeh korani1, MSc Babak Kheirkhah*2 , PhD How to cite this article Salmani zadeh korani N, Kheirkhah B. Identification of Mycoplasma synoviae by PCR and Culture Methods and Determination of the Prevalence of P1, P30, and P116 Virulence Genes in the Isolates. Infection Epidemiology and Microbiology. 2019;5(3):19-26 1Department of Microbiology, Shiraz branch, Islamic Azad University, Shiraz, Iran 2Department of Microbiology, Shiraz branch, Islamic Azad University, Shiraz, Iran * Correspondence Address: Department of Microbiology, Shiraz branch, Islamic Azad University, Shiraz, Iran Babakkheirkhah@yahoo.com Article History Received: July 7 ,2019 Accepted: September 8 ,2019 Published: October 12 ,2019 Aims: Mycoplasma synoviae, as one of the main pathogens of birds, causes a lot of economic losses to the poultry industry. This study aimed to identify M. synoviae strains in clinical samples by PCR and culture methods. Materials & Methods: A total of 135 samples were randomly collected from the respiratory tracts of female broilers in industrial poultry farms in Kerman, Iran during the first six months of 2016. Samples were cultured on Frey and PPLO broth media. Then PCR method was performed to identify Mycoplasma genus and synoviae species. Finally, multiplex PCR was performed to determine the prevalence of P1, P30, and P116 virulence genes. Findings: In this study, 17 (32%) out of 53 poultry samples were positive for the presence of Mycoplasma genus by culture method, whereas according to the PCR results, 25 (47%) out of 53 samples were confirmed as Mycoplasma genus, among which 13 samples (25%) were identified as M. synoviae species. Among the strains confirmed as M. synoviae, the prevalence rate of P1, P30, and P116 genes was 7 (53.8%), 6 46.1%), and 5 (38.46%), respectively. Conclusion: According to the PCR and culture methods results, the prevalence of M. synoviae strains was high in industrial poultry farms, Kerman, Iran. The PCR results revealed a higher prevalence rate for this bacterium, suggesting that this method may be more reliable than culture method.
Image Quality and Reliability of a Novel Dark-Blood Late Gadolinium Enhancement Sequence in Ischemic Cardiomyopathy

Purpose: The aim of this study was to assess the reliability of a 2D dark-blood phase-sensitive late gadolinium enhancement sequence (2D-DBPSLGE) compared with 2D phase-sensitive inversion recovery late gadolinium enhancement sequence (2D-BBPSLGE) in patients with ischemic cardiomyopathy (ICM). Materials and Methods: A total of 73 patients with a clinical history of ICM were prospectively enrolled. The following endpoints were evaluated: (a) comparison of image quality between 2D-BBPSLGE and 2D-DBPSLGE for differentiation between blood pool-late gadolinium enhancement (LGE), remote myocardium-LGE, and blood pool-remote myocardium; (b) diagnostic accuracy of 2D-DBPSLGE compared with gold standard 2D-BBPSLGE for the evaluation of infarcted segments; (c) diagnostic accuracy of 2D-DBPSLGE for the evaluation of microvascular obstruction (MVO); (d) comparison of transmurality index between 2D-BBPSLGE and 2D-DBPSLGE; (e) comparison of papillary muscle hyperenhancement between 2D-BBPSLGE and 2D-DBPSLGE; inter-reader agreement for depiction of hyperenhanced segments in both LGE sequences. Data were analyzed using paired t test, Wilcoxon test, and McNemar test, and η2 coefficient and intercorrelation coefficient (ICC). Results: Image quality was superior for 2D-DBPSLGE for differentiation of blood pool-LGE (P<0.001). 2D-DBPSLGE, compared with 2D-BBPSLGE, showed a sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of 96.93%, 99.89%, 99.71%, 98.78, and 99.04%, respectively. Concerning MVO detection, 2D-DBPSLGE showed a sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of 66.67%, 100.00%, 100.00%, 80.95%, and 86.21%, respectively. 2D-DBPSLGE underestimated the transmurality (P=0.007) and identified papillary muscle hyperenhancement (P<0.001). Both LGE sequences showed comparable interobserver agreement for the evaluation of infarcted areas (2D-BBPSLGE: ICC 0.99;2D-DBPSLGE: ICC 0.99). Conclusions: Compared with 2D-BBPSLGE, 2D-DBPSLGE sequences provide better differentiation between LGE and blood-pool, while underestimating LGE trasmurality and the presence of MVO.
Illness perception and sense of well-being in breast cancer patients

Purpose The objective of the study was to explore breast cancer patients’ illness perception, its relationship to perceived sense of well-being, and the role of perceived social support. Methods Women with diagnosed breast cancer were recruited from the two university hospitals in South Korea between January and April 2018. The questionnaires included the Illness Perception Questionnaire-Revised (IPQ-R) and the Functional Assessment of Cancer Therapy for Breast cancer (FACT-B). A total of 321 participants’ data was analyzed using descriptive analyses, multiple regression, and structural equation modeling. Results Negative illness perception was greater in participants currently receiving chemotherapy (p=0.044) or had received chemotherapy in the past (p=0.006). Positive illness perception was lower in older participants (p=0.001) or those who had received chemotherapy (p=0.018). Negative illness perception had a direct effect on a low sense of well-being (p<0.001). Perceived social support had a significant mediation effect on the relationship between negative/positive illness perception and sense of well-being (p<0.001). Conclusion Significant relationships between illness perception and sense of well-being were observed in breast cancer patients. Strengthening patients’ perceived social support would be helpful in improving their sense of well-being.
Current affinity approaches for purification of recombinant proteins

Abstract Recombinant proteins have wide applications in the development of pharmaceutical compounds, industrial applications of enzymes, and basic proteomics research. In this way, efficient production of recombinant proteins with high purity needs efficient purification methods. Various strategies have been devised to improve these proteins purification such as affinity purification and physicochemical purification methods which the affinity purification has some advantages over the others. Affinity strategies especially fusion strategies have been devised as indispensable tools for the massive parallel production, identification and purification of recombinant proteins from the host systems. These strategies facilitate commercial and industrial formulations of recombinant proteins, improve the study of protein interactions at the molecular level, and develop highly sensitive and specific bioassays. Recently, various surface-modified nanoparticles have been widely developed to enhance recovery and purification of recombinant proteins such as Hydrophobic polymer nanoparticles and Oleosin nanoparticles. In this review, we aim to discuss affinity purification technologies and address the principles, advantages, limitations and potential applications of them.
Foraging plasticity of Atta cephalotes (Hymenoptera: Formicidae) in response to temperature differences between forest and pasture

Introduction: Changes in microclimatic conditions due to land cover transformations influence variations in population life histories and the developmental patterns of organisms. These variations can have either a genetic basis, an environmental basis, or both. Objective: To determine the differences between habitats in the foraging activity of Atta cephalotes in response to changes in temperature and the extent to which any such differences are due to phenotypic plasticity, genetic variability, or both. Methods: We performed foraging experiments; each colony (4 colonies sourced from pasture and 3 colonies sourced from forest) underwent eight temperature treatments from 10 to 45 ºC (± 1 ºC) at 5 ºC intervals, using common garden and reciprocal transplant experiments. Results: We found high plasticity in the foraging activity of Atta cephalotes in response to temperature, with the foraging activity gradually increasing from 15 ºC to 35 ºC. Additionally, we found no significant differences in the foraging activity between the colonies sourced from the pasture and forest. Conclusions: The foraging activity of A. cephalotes was directly proportional to temperature, with ants exhibiting thermophilic behaviors and high plasticity, and there were no differences in the foraging activity between colonies sourced from both habitats.
Evidence that vertical transmission of the vaginal microbiota can persist into adolescence

Abstract Background Factors that influence vaginal microbiota composition, including its source, are not well understood. To determine if vaginal microbiota transmission from mother to daughter at birth influences the human vaginal microbiota composition in adolescence, we investigated the relationship between the vaginal microbiota of 13 mother/daughter pairs and the daughter’s birth mode. Results Based on analysis of bacterial 16S rRNA gene sequences, the vaginal microbiotas of mother/daughter pairs were more similar to each other if the daughter was born by vaginal delivery rather than by C-section. Additionally, genome sequences from an important member of the vaginal microbiota, Lactobacillus crispatus, isolated from one mother/daughter pair in which the daughter was born by vaginal delivery, were highly similar. Conclusions Both community-level analysis and isolate genome sequence analysis provide evidence of birth-mode dependent transmission and persistence of at least some members of the vaginal microbiota. Importance The composition of the human vaginal microbiota is related to many aspects of health from infection susceptibility to preterm birth. Our study provides evidence that transmission of vaginal bacteria from mother to daughter at birth is an important factor influencing vaginal microbiota composition into adolescence.
Recoding of viral mRNAs by –1 programmed ribosome frameshifting

–1 programmed ribosome frameshifting (–1PRF) is commonly used in many viruses and cellular genes. The current study focuses on the –1PRF in two human viruses, human immunodeficiency virus type 1 (HIV-1) and Semliki Forest virus (SFV), which share the same slippery site (SS) sequence, but have different mRNA secondary structures. –1PRF on the gag-pol mRNA of HIV-1 results in the production of structural proteins of the capsid (Gag, 0-frame) and viral enzymes (Gag-Pol, –1-frame), and its dysregulation is detrimental for the structural integrity of the virion and its infectivity. In SFV –1PRF is responsible for the synthesis of the structural proteins 6K and TransFrame (TF), which contribute to the virus pathogenicity. Here we show that –1PRF in both viruses operates via two conserved kinetic pathways: tRNA dual-slippage during translocation under saturated translation conditions and single P-site tRNA slippage when the A site is vacant due to the limited supply of tRNAs. –1PRF is modulated by the abundance of Leu-tRNALeu that reads the rare UUA codon at the mRNA SS. In HIV-1 the Gag to Gag-Pol ratio is maintained by switching between two frameshifting mechanisms depending on the tRNALeu(UUA) availability. Leu-tRNALeu(UUA) is rare in human cell lines derived from CD4+ T-lymphocytes – a natural target of HIV-1 infection. –1PRF in HIV-1 is additionally stimulated by a downstream enhancer sequence located within the first 12 nt after the SS. Finally, a second potential SS downstream of the first one is normally inefficient but can also support –1-frameshifting when altered by a compensatory resistance mutation in response to current anti-HIV drug therapy. With regard to SFV, we determined that its frameshifting site contains an extended stem-loop (SL) following the SS, which could act as a modulator of frameshifting under the limited supply of Leu-tRNALeu(UUA). The previously predicted enhancer sequence does not seem to play a role in –1PRF in SFV. Described different frameshifting regimes and stimulators allow the viruses to maintain a constant –1PRF efficiency regardless of environmental or therapeutical influence to ensure high viral load and successful virus propagation.
The complete mitochondrial genome of Neritina violacea

Abstract Neritina violacea is a common and important component of mangrove ecosystem. In this study, the mitogenome of N. violacea was determined for the first time using next-generation sequencing; the overall base components of mitogenome consisting of 15,710 bp was 31.37% for A, 34.91% for T, 19.47% for G, 14.25% for C, and its GC content was 33.72%. The mitogenome was composed of 13 protein-coding genes, 22 tranfer RNAs, and 2 ribosomal RNAs. Polygenetic analysis showed that the N. violacea was more close to N. Usnea and Theodoxus fluviatilis. We speculated that the N. violacea was evolved from freshwater species.
Population genetic structure, migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae)

Abstract Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST‐SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long‐term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.
Taxonomic revision of the genus Hyperaulax Pilsbry, 1897 (Gastropoda, Stylommatophora, Odontostomidae)

The genus Hyperaulax Pilsbry, 1897 comprises two living species endemic to the oceanic Fernando de Noronha Archipelago, off north-eastern Brazil. They are currently allocated in two subgenera, Hyperaulax s. str. and Bonnanius Jousseaume, 1900, belonging to the family Odontostomidae. Herein we present a taxonomic revision of these species, assessing their familiar allocation within Orthalicoidea, offering updated diagnoses and descriptions, figuring the type materials and further relevant specimens, and providing barcoding DNA sequences. We conclude that Bonnanius is a junior synonym of Hyperaulax, which is classified in Odontostomidae. The genus contains two valid species, H. ridleyi and H. ramagei, both endemic to Fernando de Noronha.
Enhancing temperature tolerance of Pyropia tenera (Bangiales) by inducing mutation

ABSTRACT We induced a mutation in Pyropia tenera using gamma irradiation to obtain strains with improved tolerance to high temperatures. We selected a mutant Pt1k with improved heat tolerance and different blade colour at high temperatures (20 °C) after an irradiation dose of 1 kGy. We observed physiological changes and responses in the wild-type (WT) and Pt1k blades under high-temperature stress. The selected Pt1k mutant blades were dark green, which was different from the natural red of the WT. At 12 °C, Pt1k blade growth rate and biomass were four times higher than those of the WT, and phycocyanin (PC) content also increased. When cultured at 20 and 25 °C, blade shapes and growth rates of Pt1k were maintained; however, WT blades were considerably decayed and growth rate was inhibited. When cultured at 25 °C for 3 weeks, chlorophyll a and PC contents were higher in Pt1k than in WT strains, whereas the phycoerythrin (PE) level was constant. Changes in hydrogen peroxide (H2O2) and malondialdehyde (MDA) content after 3 weeks at 25 °C Pt1k showed a slow increase; however, activities in the WT strain were highly increased. Under these conditions, activities of the antioxidant enzymes (superoxide dismutase and ascorbate peroxidase) of the two strains similarly increased when subjected to high-temperature stress for 1 week; however, the WT enzymes decreased rapidly during long-term exposure. Conversely, the Pt1k mutant had constant activities even when exposed to long-term high temperatures. These results indicate that the isolated mutant Pt1k had improved growth and tolerance to higher temperatures than the WT. In conlusion, we suggest that antioxidant enzyme activity, which is more abundant in the mutant Pt1k than in WT at high temperatures, is involved in the tolerance mechanism against temperature.
Quorum sensing in Bacillus subtilis slows down biofilm formation by enabling sporulation bet hedging

The ComQXPA quorum sensing (QS) system of Bacillus subtilis, a Gram-positive, industrially relevant, endospore forming bacterium, promotes surfactin production. This lipopeptide increases transcription of several genes involved in biofilm matrix synthesis via the Spo0A-P master regulator. We hypothesized that the inactivation of the QS system will therefore result in decreased rates of floating biofilm formation. We find that this is not the case and that the QS deficient mutant forms pellicles with a faster rate and produces more biofilm matrix components than the wild type. As Spo0A-P is the master regulator of sporulation initiation we hypothesized that the ComQXPA dependent signaling promotes sporulation and consequently slows the growth rate of the wild type strain. Indeed, our results confirm that cells with the inactive QS initiate endospore formation in biofilms later and more synchronously than the wild type, as evidenced by spore frequencies and the PspoIIQ promoter activity. We argue, that the QS system acts as a switch that promotes stochastic sporulation initiation and consequently bet hedging behavior. By committing a subpopulation of cells to sporulation early during growth, wild type population grows slower and produces thinner biofilms but also assures better survival under stressful conditions. 1.1 IMPORTANCE Bacillus subtilis is widely employed model organism to study biofilm formation and sporulation in Gram-positive bacteria. The ComQXPA quorum sensing (QS) system indirectly increases the transcription of genes involved in biofilm matrix formation, which predicts a positive role of this QS in biofilm development Here we show that QS mutants actually form more matrix components per pellicle than the wild type and that their pellicles are thicker and form with a faster rate. We explain this, by showing that cells with an inactive QS exhibit a delay in sporulation entry, which is also more synchronous relative to the wild type. We argue, that the ComQXPA QS system acts as a switch that contributes to the stochastic sporulation initiation and though this path promotes bet hedging behavior. This finding is important in terms of “quorum quenching” strategies aiming to down modulate biofilm development through inhibition of QS signaling and underscores the richness of QS regulated phenotypic outcomes among bacterial species.
Transmission Chains or Independent Solvers? A Comparative Study of Two Collective Problem-Solving Methods

Groups can be very successful problem-solvers. This collective achievement crucially depends on how the group is structured, that is, how information flows between members and how individual contributions are merged. Numerous methods have been proposed, which can be divided into two major categories: those that involve an exchange of information between the group members, and those that do not. Here we compare two instances of such methods for solving complex problems: (1) transmission chains, where individuals tackle the problem one after the other, each one building on the solution of the predecessor and (2) groups of independent solvers, where individuals tackle the problem independently, and the best solution found in the group is selected afterwards. By means of numerical simulations and experimental observations, we show that the best performing method is determined by the interplay between two key factors: the skills of the individuals and the difficulty of the problem. We find that transmission chains are superior either when the problem is rather easy, or when the group is composed of rather unskilled individuals. On the contrary, groups of independent solvers are preferable for harder problems or for groups of rather skillful individuals. Finally, we deepen the comparison by studying the impact of the group size and diversity. Our research stresses that efficient collective problem-solving requires a good matching between the nature of the problem and the structure of the group.
The impact of Relative Language Distance on Bilingual Language Control – a functional imaging study

Cross-linguistic activation is unavoidable in bilinguals and they require language control to manage it. In this study, it is posited that Relative Language Distance (RLD; the extent of lexical feature-similarity between bilinguals’ languages) can affect the extent of cross-linguistic activation and hence influence bilingual language control. This was investigated via an er-fMRI word-translation task on three similar bilingual groups but with varying RLDs: Dutch-English (low-RLD), Hindi-English (intermediate-RLD) and Cantonese-English (high-RLD). Cross-linguistic conflict and the degree of conflict monitoring/control necessary to manage it were expected to increase with decreasing RLD across groups and be appropriately reflected in the activity of conflict monitoring/control neural regions, such as the ACC (anterior cingulate cortex). Analysis revealed a significantly differential ACC response across the groups, reflecting its adaptation to differential conflict monitoring/control demands generated by RLD. The findings provide emerging evidence for RLD as a dimension of bilingualism impacting bilingual language control processes and neurobiology.
Aromatic Compounds Valuable in Identifying Local Varieties of Kefir

This paper attempts to analyze the range of five types of kefir aromatic presence in Romania, particularly aiming at the concentration of higher alcohols, aldehydes, ketones, esters and carboxylic acids. GC-MS methods used have led to results which gives the aromatic characteristics of these products vary according to the manufacturer, the resulting values being situated between 230.4567 mg / L and 345.2267 mg / L higher alcohol, 235.6722 mg / L and 398.9604 mg / L to aldehydes, 130.9861 mg / L and 162.2452 mg / L ketones, 439.0863 mg / L and 463.2015 mg / L esters and 291.7619 mg / L and 333 1917 mg / L for carboxylic acids. Flavorings results in these samples are conferred majority of the metabolic activity of the microorganisms involved in the production of Kefir and the recipe used by the manufacturer default fat concentration of the product.