Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuropeptide relay between SIFa signaling controls the experience-dependent mating duration of male Drosophila

Drosophila melanogaster is a suitable model for investigating how neuropeptides influence animal behaviours and physiology. We previously reported that two behavioural paradigms control mating duration of male Drosophila, called Longer-Mating-Duration (LMD) and Shorter-Mating-Duration (SMD) that are induced through socio-sexual environment prior to copulation. Understanding the molecular and cellular mechanisms by which males exhibit plasticity to different social cues remains poorly understood. Here, we show that SIFa modulates the neural circuitry for both LMD and SMD. Neuropeptide-to-neuropeptide communication, so called ‘neuropeptide relay’ plays a key role to mediate this control. We identified that 7 neuropeptides expressed in SIFa Receptor-positive cells are functionally important to regulate either LMD and/or SMD. The modulation of two independent mating duration behaviour by the different SIFa-mediated neuropeptide relay will help to further investigate how the neuropeptidergic modulation can control complex behaviours.
Microalgal blooms in a eutrophic estuary (Golden Horn, Sea of Marmara) following a remediation effort

Abstract The present work describes microalgal blooms that occurred in a eutrophic estuary (Golden Horn, Sea of Marmara, Turkey) between October 2013 and September 2014 following a remediation effort. The relationships between bloom-forming microalgal species and environmental factors were investigated during the study period. The changing environmental conditions (e.g. increasing water transparency and salinity) after seawater transfer to the Golden Horn Estuary stimulated phytoplankton growth with dense algal blooms. Annual average values of Secchi depth, salinity and dissolved oxygen increased in comparison with those in an earlier study in 2009–2010. Nine microalgal species, which consisted of four diatoms, two dinoflagellates, one cryptophycean, one raphidophycean and one euglenophycean, formed the blooms with water discolorations during spring and summer. The species that reached the highest bloom density were Plagioselmis prolonga (62.4 × 106 cells l−1) among crytophyceans, Heterocapsa triquetra (21.8 × 106 cells l−1) among dinoflagellates and Skeletonema marinoi (39 × 106 cells l−1) among diatoms. The abundance of dinoflagellates and phytoflagellates increased particularly in the upper estuary when compared to diatoms and their rapid growth and bloom formation revealed that they have a wide range of tolerance to changing environmental conditions and a strong ability to compete with other species in this study area.
Pre-adaptation to climate change through topography-driven evolution of traits and their plasticity

Climate change is expected to increase the level of drought stress experienced by many plant populations, yet the spatial distribution of changes in dryness remains highly uncertain. Species can, to some extent, adapt to climate uncertainty through evolving increased trait plasticity. Biodiversity conservation could capitalize on such natural variation in the ability of populations to cope with climate variability. Yet, disentangling evolution of trait means vs. trait plasticity is challenging, as it requires a sampling design with genetic replicates grown under distinct environmental conditions. Here, we applied different soil moisture treatments to clones of Fragaria vesca plants that were raised from seeds that were sampled in distinct mountainous topographical settings, to study adaptive trait and plasticity divergence in response to drought. We demonstrate that various fitness traits evolved along topographical gradients, including increased specific leaf area (SLA) with increasing slope, and increased growth plasticity with increasing altitude. Our results indicate that traits and their plasticity can evolve independently in response to distinct topographical stressors. We further show that trait heritability varies considerably among traits and topographical settings. Heritability of phenotypic plasticity tended to increase with altitude for all traits, with populations from high altitudes harboring more than twice the heritability for growth and SLA plasticity compared to populations from low altitudes. We conclude that (i) low altitudinal populations, which are expected to be least vulnerable to climate change, may only withstand limited increases in drought stress, while (ii) populations that evolved to thrive under more heterogeneous mountain conditions are pre-adapted to climate change through high plasticity and heritability. Highly heterogeneous landscapes may thus represent invaluable sources of quantitative genetic variation that could support conservation under climate change across the globe.
Performance optimization of aircraft deicing equipment based on genetic algorithm

Using deicing fluids is the main way of aircraft ground deicing, which plays an important role in ensuring flights’ safety. However, most of the airports use deicing fluids excessively to ensure the quality and efficiency of aircraft ground deicing, which will not only cause a large amount of deicing fluids wasted but also pollute water resources and the environment. Finding the optimal solution between deicing efficiency and deicing fluids consumption through effective methods is necessary. This article analyzes the energy conversion process of aircraft ground deicing, establishes multi-parameter optimization model for deicing, and optimizes the consumption of deicing fluids. The physical quantity, including the flow rate and the temperature of deicing fluids, is found as the main influence of the deicing time, which is the most concerned problem in the actual operation. Under the precondition of ensuring the deicing efficiency, the optimized parameters such as different ambient temperature, wing area, and icing thickness are obtained by genetic algorithm. The trend between the parameters with the change of environment has also been analyzed. Finally, the actual using condition in the capital airport and the optimized results are compared, and the results show that the usage of deicing fluids reduced 13% to 24%.
Physiology and nutritional contents of lettuce (Lactuca sativa L.) plants induced by Pseudomonas fluorescens

Sustainable agriculture and the larger scales of production needed to meet the higher demand for food each year have become models for several studies; beneficial microorganisms are one model that has been used as an alternative for greater production of and reductions in the use of chemical fertilizers. Thus, the objective of this work was to study the physiological changes in and nutrient contents of lettuce after inoculation with Pseudomonas fluorescens in combination with chemical fertilization. P. fluorescens had a positive influence on gas exchange, with increases of 41% in A , 44% in Gs , 29% in E , and 100% in A / Ci ; increased ISSN Concentration of chlorophyll a and b , of 220% more chl a and 106% chl b; increased chlorophyll a fluorescence, higher relative water content; and nutrient content increases of 19% for nitrogen, 24% for phosphorus, and 105% for potassium. Plants inoculated with BRM-32111 presented increases for MFT, MFC and FF, in 37%, 34% and 26% respectively. However, when combined with fertilization, antagonism occurred, and the evaluated parameters were negatively affected. potássio. As plantas inoculadas BRM-32111 MFC FF, 37%, 34% e 26%, respectivamente. No quando combinado a fertilização, ocorreu antagonismo e os parâmetros avaliados foram afetados negativamente.
Plant gene expression control using genome- and epigenome-editing technologies

ABSTRACT In this review, we present some specific examples of plant species only where modulation of gene regulation has been achieved via genome-editing and epigenome-editing technologies. Among genome-editing tools used in plants are zinc-finger nucleases in maize (Zea mays L.); transcription activator-like effector nucleases in rice (Oryza sativa L.), sugarcane (Saccharum spp.), and wheat (Triticum aestivum L.); and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) in O. sativa and tomato (Solanum lycopersicum L.). A large number of epigenome-editing tools based on small RNAs have been employed for controlling plant gene expression in thale cress (Arabidopsis thaliana), tobacco (Nicotiana benthamiana), O. sativa, potato (Solanum tuberosum), and Z. mays. RNAi-based tools have been used in A. thaliana; RNA-directed DNA Methylation (RdDM) in A. thaliana; and RdDM involving transgenically produced exogenous small interfering RNAs in O. sativa. Site-specific DNA-binding proteins that have been successfully repurposed to function as DNA-binding domains of epigenome-editing tools include zinc-finger proteins, transcription activator-like effectors, and dead Cas9 complexed with single-guide RNA. Zinc-finger-based epigenome-editing tools have been applied in A. thaliana and O. sativa; and transcription activator-like effector and dead Cas9-based tools in O. sativa and A. thaliana, respectively. Targeting-induced-local-lesions-in-genomes approach has been employed in muskmelon (Cucumis melo). Quantitative trait loci (QTL) were epigenetically modified in A. thaliana and O. sativa. In vitro tissue culture-based epigenome-editing DNA and/or histone modifications have been achieved in Caribbean agave (Agave angustifolia), Henequen (Agave fourcroydes), A. thaliana, common tobacco (Nicotiana tabacum), O. sativa, pine (Pinus radiata), and Z. mays.
Sexually antagonistic coevolution between the sex chromosomes of Drosophila melanogaster

Significance Sex chromosomes are not only involved in genetic sex determination—they are also important factors in sexual conflict and speciation. Using laboratory experiments and population genetic modeling, we show that the sex chromosomes of Drosophila melanogaster can coevolve antagonistically. We found that swapping sex chromosomes between five D. melanogaster populations increased male fitness, apparently at the cost of reduced offspring survival. After 25 generations, these fitness effects had disappeared, consistent with the resolution of conflict after disrupting antagonistically coevolved X- and Y-linked genes. Our population genetic models show that antagonistic coevolution between sex chromosomes is a biologically plausible explanation for our empirical findings. Together, our empirical and theoretical results provide support for a potential path to speciation through sexual conflict. Antagonistic interactions between the sexes are important drivers of evolutionary divergence. Interlocus sexual conflict is generally described as a conflict between alleles at two interacting loci whose identity and genomic location are arbitrary, but with opposite fitness effects in each sex. We build on previous theory by suggesting that when loci under interlocus sexual conflict are located on the sex chromosomes it can lead to cycles of antagonistic coevolution between them and therefore between the sexes. We tested this hypothesis by performing experimental crosses using Drosophila melanogaster where we reciprocally exchanged the sex chromosomes between five allopatric wild-type populations in a round-robin design. Disrupting putatively coevolved sex chromosome pairs resulted in increased male reproductive success in 16 of 20 experimental populations (10 of which were individually significant), but also resulted in lower offspring egg-to-adult viability that affected both male and female fitness. After 25 generations of experimental evolution these sexually antagonistic fitness effects appeared to be resolved. To formalize our hypothesis, we developed population genetic models of antagonistic coevolution using fitness expressions based on our empirical results. Our model predictions support the conclusion that antagonistic coevolution between the sex chromosomes is plausible under the fitness effects observed in our experiments. Together, our results lend both empirical and theoretical support to the idea that cycles of antagonistic coevolution can occur between sex chromosomes and illustrate how this process, in combination with autosomal coadaptation, may drive genetic and phenotypic divergence between populations.
Review on in vitro antioxidant activities of Curcuma species commonly used as herbal components in Indonesia

Free radicals, reactive nitrogen species (RNS) and reactive oxygen species (ROS) have been known to contribute several degenerative diseases such as cardiovascular diseases, aging, certain types of cancers, rheumatoid arthritis, neurodegenerative, and diabetes mellitus. In order to overcome the negative effects of these radicals, some scientists have explored some natural antioxidants from plants and it's by-products. The antioxidant can be defined as any substances or samples capable of inhibiting free radical reactions in the oxidation reaction. Due to curcuminoids contained, Curcuma species such as Curcuma longa, Curcuma heyneana, Curcuma mangga, and Curcuma xanthorriza were commonly used for herbal components in some traditional medicine. Several in vitro tests been introduced and used to measure antioxidant activities, namely radical scavenging assay using 2,2’-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis-(3-ethylbenzothiazoline-6 -sulfonic acid) (ABTS•+), ferric reducing antioxidant power (FRAP), ferric-thiocyanate, phosphomolybdenum method, cupric ion reducing antioxidant capacity, metal chelating power, beta-carotene bleaching linoleic-ferric-thiocyanate, and thiobarbituric acid methods. This review highlighted the antioxidant activities in vitro of C. longa, C. heyneana, C. mangga, and C. xanthorriza through several tests. To perform this review, several repute databases were analyzed and used. From this review, it can be stated that Curcuma species have powerful antioxidant activities, therefore they could be potential sources of natural antioxidants and can be used as food supplements.
Pooled CRISPRi screening of the cyanobacterium Synechocystis sp. PCC 6803 for enhanced growth, tolerance, and chemical production

We developed an inducible CRISPRi gene repression library in the cyanobacterium Synechocystis sp. PCC 6803, where all annotated genes are targeted for repression. We used the library to estimate gene fitness in multiple conditions. The library revealed several mutants with increased specific growth rates (up to 17%), and transcriptomics of these mutants revealed common upregulation of genes within photosynthetic electron flow. We challenged the library with L-lactate stress to find more tolerant mutants. Repression of the peroxiredoxin Bcp2 increased growth rate by 49% in the presence of 0.1 M L-lactate. Finally, the library was transformed into a L-lactate-secreting strain, and droplet microfluidics sorting of top producers enriched sgRNAs targeting nutrient assimilation, redox modulation, and cyclic-electron flow. Several clones showed increased productivity in batch cultivations (up to 75%). In some cases, tolerance or productivity was enhanced by partial repression of essential genes, which are difficult to access by transposon insertion.
Invasive alien plants occurring in Lesotho: Their ethnobotany, potential risks, distribution and origin

Background: Several recent studies have documented the ethnobotanical uses of plants used in Lesotho, in particular those used for medicinal purposes. However, these reports did not make a distinction between indigenous, naturalised or invasive alien plants. Furthermore, the existing records on the status of the occurrence of these plants in the country are not up to date.Objectives: The aim of this article is to present information on the current knowledge regarding the status of invasive alien plant species in Lesotho and to discuss their ethnobotanical uses, distribution in the country, origin and safety. We further assess the existing legislation designed to regulate the spread of such plants and make a comparison with the invasiveness and regulation of such plants in the neighbouring South Africa.Method: This article is based mainly on a literature survey of published information obtained from various databases, such as Google Scholar, Science Direct and Scopus, as well as from unpublished data such as technical reports, dissertations and theses.Results: A total of 57 species, comprising one pteridophyte, one gymnosperm and 56 flowering plants (52 dicotyledons and 4 monocotyledons) are documented. Although these plants are invasive in nature, they are utilised for a variety of purposes including food, treatment of various medical conditions, cosmetics and functional uses. However, some of the species are reported to be poisonous to both animals and humans, with a majority of the plants causing skin irritation. Most of these species are widely distributed throughout the country and most of them originated from America, Europe and Asia. Although a number of reports on the occurrence of invasive alien plants have been generated, the information therein has not yet been published.Conclusion: This study has identified knowledge gaps in terms of safety and distribution of the species, as well as shortfalls in the policies intended to regulate invasive alien species (IAS) in Lesotho. Further research in this regard is therefore recommended.
Manual for Economic Data Collection in Pharmacotherapy Trials for Heroin Dependence

The purpose of the manual is to assist with the data collection necessary for economic evaluation of new opioid withdrawal and substitution therapies within a number of clinical trials in Australia. The trials are designed to evaluate a range of therapies and take place in a number of different settings. Section 1 of the manual provides a brief introduction to the framework of economic evaluation. Sections 2 and 3 discuss the principles underpinning the data collection for outcomes and costs respectively and provide some worked examples. Section 4 provides a number of sample data collection forms, which can be used in a range of settings.
Pan-genomic analyses of Corynebacterium pseudotuberculosis andcharacterization of the biovars ovis and equi through comparative genomics

1 I. Presentation. 2 I.1 Collaborators . 3 II. Preface . 4 II.1 C. pseudotuberculosis state of the art . 5 II.1.1 Biovars of C. pseudotuberculosis . 5 II.1.1. 1 Biovar ovis . 5 II.1.1.2 Biovar equi . 8 II.2 Manuscript Structure and author's contributions . 10 II
Chemical composition of seed and seed oil from Iranian commercial date cultivars

In the present study, the seeds of two date palm (phoenix dactylifera L.) cultivars, Mazafati and Kalutah, were analyzed for their physical properties and chemical composition. Studies were also conducted on properties of oil extracted from the seeds and its fatty acid composition. The seeds constituted about 6-10% of the fruit weight. They, on the average, contained 4.84% protein, 12.22% fat, 27.58% fiber, 80.76% carbohydrates, 1.18% ash and 1.72% moisture. Mineral analysis showed higher concentration of Fe followed by Ca, Cu, Na, Zn and Mn. The seeds were also a rich source of phenolics, which ranged from 1840.93 to 1952.93 mg GAE/100 g. The average chemical characteristics of the date seed oils were: iodine value 55.153, saponification value 228.067 and peroxide value 15.537. The main fatty acids of the seed oils were oleic (48.10-50.50%), lauric (14.00-15.80%), palmitic (10.80-11.70%), myristic (10.60-10.90%), linoleic (7.70-8.20%) and stearic acids (3.00-3.40%).
Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension

The geographically restricted M. africanum lineages (MAF) are primarily found in West Africa, where they account for a significant proportion of tuberculosis. Despite this phenomenon, little is known about the co-evolution of these ancient lineages with West Africans. MAF and M. tuberculosis sensu stricto lineages (MTB) differ in their clinical, in vitro and in vivo characteristics for reasons not fully understood. Therefore, we compared genomes of 289 MAF and 205 MTB clinical isolates from the 6 main human-adapted M. tuberculosis complex lineages, for mutations in their Electron Transport Chain and Central Carbon Metabolic pathway in an attempt to explain these metabolic differences. Furthermore, we determined, in silico, whether each mutation could affect the function of genes encoding enzymes in these pathways. We found more potentially deleterious mutations in these pathways in MAF lineages compared to MTB lineages. Additionally, we found that convergent evolution in these pathways occurred between MAF and some MTB lineages. Generally, our findings show further differences between MAF and MTB lineages that may have contributed to the MAF clinical- and growth phenotype and may indicate potential adaptation of MAF lineages to a distinct ecological niche, that we suggest may include areas characterized by low oxygen tension.
mesenchymal stem cells novel therapeutic option besides their stem cell properties utilizing the niche effect

Mesenchymal StemCells (MSC’s) are multipotent stem cells having diverse l inflammatory, antimicrobial, antimicrobial and regenerative therapeutic efficacy because of which there is effect on damaged tissues and inflammation.MSC’s may be used for direct clinical effects but its manipulation of host response in different occasionsvia cell-cellactions including through production of bioactive secreted factors which include smallproteins, chemokines, cytokines & other cellular regulators. The following factors can induceangiogenesis by chemotactic and induction of cellular recruitment manner.This differential can also be bettered in vitro before in vivo administration potentiating the versatility of the MSC’s => active communication between newly administered cells&host tissue.Various clinical trials are on and studiesconducted on MSC’sability for therapy in human disease.Still controversy existand deeper insight required to bring them into therapeutic arena.
YKL-40 Levels in Rheumatoid Arthritis and Their Correlation with Disease Activity: A Meta-analysis

Objective. To examine the relationship of serum/plasma YKL-40 levels with rheumatoid arthritis (RA) and their correlation with RA activity and rheumatoid factor (RF) level. Methods. We performed a meta-analysis comparing the serum/plasma YKL-40 levels between patients with RA and controls and examined the correlation coefficients of the circulating YKL-40 level with the RF level and RA activity based on the 28-joint disease activity score (DAS28), erythrocyte sedimentation rate (ESR), and C-re-active protein (CRP) level. Results. Nine studies (707 patients with RA and 1,041 controls) were included in the meta-analysis. The YKL-40 levels were significantly higher in the RA group than in the control group (standardized mean difference [SMD]=1.071, 95% confidence interval [CI]=0.726 ∼ 1.417, p ＜ 0.001). Stratification by ethnicity showed significantly ele-vated YKL-40 levels in the RA groups from European, Asian, North American, and Arab populations. The YKL-40 level was significantly higher in the RA group than in the control group in both age- and sex-matched and only age-matched populations (SMD=0.937, 95% CI=0.554 ∼ 1.320, p ＜ 0.001; SMD=2.951, 95% CI=1.389 ∼ 4.512, p ＜ 0.001, respectively). Subgroup analysis by sample size showed significantly increased YKL-40 levels in the RA group in both small (n ＜ 100) and large (n ＞ 100) populations. Meta-analysis of correlation coefficients showed a significant positive correlation between the YKL-40 levels and DAS28, ESR, CRP level, and RF level (DAS28: correlation coefficient=0.381, 95% CI=0.044 ∼ 0.640, p=0.028; RF level: correlation coefficient=0.341, 95% CI=0.176 ∼ 0.487, p ＜ 0.001). Conclusion. The circulating YKL-40 levels are high in patients with RA and positively correlate with RA activity and RF level. (J Rheum Dis 2019;26:257-263)