Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of physical activity in the molecular regulation of colon cancer risk

A strong body of observational evidence supports the notion that physical activity (PA) is inversely associated with colon cancer (CC) risk. Epigenetic alterations, such as aberrant DNA methylation, are apparent in the early stages of carcinogenesis. Recent evidence has suggested that PA can alter DNA methylation patterns in a variety of tissues. It is not known whether PA can affect DNA methylation patterns in genes implicated in CC risk. Study 1 was a longitudinal investigation of 253 females (70.7 ± 4.0 yrs) and 137 males (71.4 ± 4.3 yrs) for whom DNA from peripheral blood leukocytes were available. Participants showed differential DNA methylation of relevant genes depending on whether they had increased, decreased, or maintained their PA level over eight years. Study 2 was a randomised controlled trial of sedentary colon adenoma patients (n = 31; 68.5 ± 3.2 yrs) who were randomised to a 6-12 month Active Lifestyle Programme or Usual Care. DNA methylation patterns of CC risk genes in buccal cells were unaffected by taking part in the Active Lifestyle Programme. Low recruitment probably resulted in the study being underpowered, and buccal cells may not have been a suitable surrogate marker of colon DNA methylation. A lack of colon biopsies prevented any analysis of changes in methylation in this tissue. Due to the absence of colon biopsies, Study 3 tested whether serum from physically active or inactive volunteers affected the proliferation of in vitro models of colon epithelia, in the fasted state and after a single bout of treadmill running. A randomised controlled trial with a crossover design was conducted in 20 male participants (59 ± 6.0 yrs) free of metabolic or cardiovascular disease, and data pooled together with 20 male colon adenoma patients from the previous investigation. This study showed that male adenoma patients’ cardiorespiratory fitness was inversely correlated with serum-stimulated growth of the colorectal cancer cell line Caco-2 in vitro, but no relationship was observed in disease-free volunteers at rest or after exercise. In conclusion, this series of studies demonstrated that whilst PA is associated with beneficial changes in DNA methylation longitudinally, this might not be realised in a trial setting with sedentary older persons. It remains unclear whether increasing PA is an effective strategy for reducing CC risk via changes to DNA methylation patterns. Furthermore, it has suggested that cardiorespiratory fitness might be important in modulating the growth of the Caco-2 cell line, but more investigation is needed.
BMP4 signaling pathways progenitor cells by combined modulation of the MEK/ERK and + CD34 Efficient differentiation of human pluripotent stem cells into functional

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Interaction of Tolaasin I Lipodepsipeptides of Pseudomonas and WLIP, tolaasii and P. "reactans ", with Biological and Model Membranes

The activity of tolaasin I and White . Line ! nducing £rinciple (WLIP), produced in vitro by virulent strains of Pseudomonas tolaasii and P. "reactans", respectively, was comparatively evaluated on red blood cells and large unilamellar vesicles. Tolaasin I and WLIP caused red blood cell haemolysis through a colloid-osmotic shock apparently caused by transmembrane pores formation. Both lipodepsipeptides were able to form channels in lipid vesicles. Their activity was dependent on the toxin concentration and liposomes composition, and independent on the pH. Studies of dynamic light scattering suggested a detergent-like activity for WLIP at high concentration (higher than 27 /lM). This effect was not detected for tolaasin I at the concentrations tested (up to 28.2 1lM).
De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research

Reference quality genomes are expected to provide a resource for studying gene structure and function. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution to this problem is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna’s hummingbird reference, two vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range (N50s of 5.4 and 7.7 Mb, respectively), and representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read assemblies corrected and resolved what we discovered to be misassemblies, including due to erroneous sequences flanking gaps, complex repeat structure errors in the references, base call errors in difficult to sequence regions, and inaccurate resolution of allelic differences between the two haplotypes. We analyzed protein-coding genes widely studied in neuroscience and specialized in vocal learning species, and found numerous assembly and sequence errors in the reference genes that the PacBio-based assemblies resolved completely, validated by single long genomic reads and transcriptome reads. These findings demonstrate, for the first time in non-human vocal learning species, the impact of higher quality, phased and gap-less assemblies for understanding gene structure and function.
The Effects of a Hydroalcoholic Extract of Terfezia boudieri on serum level of Estrogene and Progesterone in female Rats

BACKGROUND AND OBJECTIVE: Terfezia Boudieri (TB), has flavonoids and antioxidant compounds. The aim of this study was to investigate the possible effects of ethanol extracts of TB on serum levels of estrogen and progesterone in adult female rat. METHODS: 35 female Wistar rats were used in this experimental study. Animals weighing 180 ± 20 g were divided into 5 groups (each group consisted of7 rats. normal control group with no treatment, sham group received normal saline and experimental groups (1,2,3groups) were injected i.p. with 110, 220 and 330 mg/kg of TB for 14 days respectively. All groups at the end of the 14th day were bled and the sex hormones estrogen and progesterone hormone levels were measured. FINDINGS: According to the results of serum levels of progesterone and estrogen, 220 mg/kg extract of TB (16±0.75), estrogen concentrations increased compared with the control group (12.2±0.98) and sham (12±1.14) (p<0.01). Also 220 mg/kg of TB (39.1±1.55) compared to controls (15±0.83) and sham (15.1±1.2) increased significantly (p<0.01). CONCLUSION: The results of this study showed that TB can increase significantly the serum levels of estrogen and
Confirming a plant‐mediated “Biological Tide” in an aridland constructed treatment wetland

As urban populations grow and the need for sustainable water treatment increases, urban constructed treatment wetlands (CTWs) are increasingly being used and studied. However, less is known about the effectiveness of this “turquoise infrastructure” in arid climates. In a recent publication, we presented evidence of plant-mediated control of surface hydrology, using a water budget approach, in a CTW in Phoenix, Arizona, USA. We also demonstrated how this transpiration-driven wetland surface flow made this treatment marsh more effective at pollutant removal than its counterparts in cooler or more mesic environments. Water budget-based calculations estimated that nearly 20% of the water overlying the marsh was transpired daily by the plants (40–60 L·m−2·d−1) during the hottest summer months. We estimated the associated water velocity to be about 40 cm/h. In this paper, we report on hydrodynamic experiments that confirmed the existence of this phenomenon that we refer to as the “Biological Tide,” and verified the rate at which transpiration by the marsh vegetation moves surface water into the biogeochemically active marsh. We combined a water budget-based approach and dye tracer experiments to quantify and confirm this phenomenon. Because of the low velocities estimated from our water budget approach (a few cm/h), we used a fixed-wall flowthrough marsh flume to limit the lateral dye movement during the tracer experiments. We measured actual flow rates of 7–50 cm/h (with 5–8% precision) during these experiments, which closely conformed to the values estimated from our water budget-based approaches. The flow was largely dispersive due to the extensive impedance imparted by dense plant stems in the marsh. From these summer flow rates, we calculated that residence time of the water overlying the marsh in this CTW averaged about 13 d, but could be as low as four days. Again, these values were reasonably close to the 15–20% replacement rate for marsh water we estimated using the water budget approach. This is the first time, to our knowledge, that plant-mediated biological control of surface hydrology in a wetland, without connection to groundwater, has been reported.
HIV-1 transactivator of transcription (TAT) protein causes neurotoxicity via astrocyte activation.

HIV is most well-known for its negative effects on the immune system and the resulting development of AIDS, however it also has severe damaging effects on the central nervous system. Many infected individuals exhibit neuropsychological and behavioral dysfunctions which are collectively referred to as HIV-associated dementia (HAD). One of the worrying aspects of HAD is the fact that current anti-retroviral therapy, while being effective in managing the onslaughts of HIV on the immune system, is less efficient in addressing the impact of HIV on the CNS. The HIV-1 regulatory protein, transactivator of transcription (Tat), is responsible for the transactivation of viral transcription, and has been identified as a possible etiological factor of HAD. Neurotoxicity caused by HIV-1 is an indirect effect since the virus is unable to infect neurons directly. We subsequently hypothesized that HIV-1 infects non-neuronal cells in the CNS which leads to their activation, resulting in the release of cytokines that are detrimental to neurons. The aims of this study was therefore to (i) determine whether Tat activates astrocytes, (ii) establish whether astrocytes exposed to Tat result in the release of IL-6 and TNF-α, and to (iii) assess whether these cytokines can induce apoptosis of neuronal cells. Our study has shown that Tat does activate astrocytes and that activated astrocytes do indeed release cytokines IL-6 and TNF-α into their growth medium. Tat treated cells release more than double the amount of IL-6 than the control group of untreated astrocytes. We also observed that exogenous administration of these cytokines (individually or collectively) to neurons has the ability to cause neuronal apoptosis. Interestingly in combination, these cytokines show no cooperative effect. Our data also showed that neurons, when exposed to the culture medium of astrocytes that were subjected to Tat, exhibit hallmarks of apoptosis similar to that induced by IL-6 and TNF-α. Our findings led us to conclude that in individuals with HIV-infection, the virus activates astrocytes possibly via the production and release of Tat. This causes the astrocytes to secrete pro-inflammatory cytokines (e.g. TNFα and IL-6) that may induce apoptotic cell death of neurons. This mechanism may explain the development of HAD.
Stacked species distribution and macroecological models provide incongruent predictions of species richness for Drosophilidae in the Brazilian savanna

We tested the adequacy of two richness‐modelling approaches within the ‘spatially explicit species assemblage modelling’ (SESAM) framework for drosophilid flies in a tropical biome. The pattern of drosophilid species richness throughout the Brazilian savanna was investigated by comparing richness estimates from macroecological models (MEM) and stacked species distribution models (S‐SDM). We used occurrence records for macroecological modelling and to generate geographic ranges by modelling species’ niches, which were stacked to generate SDM richness. Richness predictions were compared between models and with empirical data from well‐sampled areas. The spatial variation in drosophilid richness for both estimates revealed more species in the central and south‐eastern regions of the biome. Nonetheless, MEM generated a more fragmented pattern than S‐SDM, with scattered patches of high richness. S‐SDM produced richness estimates nearer to the empirical values than MEM, which in turn strongly underestimated richness. The correlation between S‐SDM and observed richness suggests that climate is the major (indirect) driver of drosophilid richness in the Brazilian savanna. Richness estimates based on macroecological modelling are, however, almost certainly affected by inventory incompleteness and sampling bias. We emphasise that S‐SDM can be a valuable approach to explore species richness patterns in poorly sampled regions.
Characterization ofPlasmids inErwinia stewartiit

Plasmids in39strains ofErwiniastewartii were examinedby agarose gel electrophoresis. Mostvirulent strains hadfrom11to13plasmids rangingin molecular mass from2.8to210megadaltons andcontained plasmids of210,70, 49,43,29.5, 16.8, 8.8, and2.8megadaltons. Plasmids instrains SW2 andSS104 were characterized bybothelectron microscopy andagarose gelelectrophoresis andmay beuseful asconvenient references forsizing plasmids byelectrophoresis. Specific size classes ofplasmids could notbeassociated withantibiotic andheavy metal resistance, carbohydrate utilization, bacteriocin production, orpathogenicitytocorn.However, avirulent strains tendedtohavefewerplasmids than virulent strains. Erwinia stewartii (E.F.Smith) Dyecancause adevastating disease ofbothsweetandfield com.Thebacterium growsintheintercellular spaces ofleaves, causing localized lesions, andin thexylem vessels, causing systemic wilting. Duringthesummer, E.stewartii istransmitted by thecornflea beetle (Chaetocnema pulicularia Melch) andcanoverwinter inthebeetle's alimentary tract. Wehavebeenusing E.stewartii asamodelsystem forstudying mechanisms of virulence andhostresistance andhavepreviously demonstrated thatitreadily exchanges Rfactors withEscherichia coli(5)andcontains several derepressed conjugative plasmids which canmobilize pCR1between E.stewartii andE. coli (6). Thepurpose ofthis study wastoverify thattheDNA species previously observed in strains SW2andSS104byagarose gelelectrophoresis (AGE)(5,6)areplasmid DNAs,to showthatmultiple plasmids arecharacteristic ofthis species, andtoidentify, forfuture study, sizeclasses ofplasmids commoninvirulent strains.
Antibiotic Resistance in Non-humans and its Impact on Human Health.

Antimicrobial drugs are magic bullets which are used in humans, animals and plants to treat and prevent bacterial infections. The inevitable side effects of the use of antibiotics are the emergence and dissemination of resistant bacteria. Their level of resistance is considered to be a good indicator for selection pressure by antibiotic use and for resistance problems to be expected in pathogens. At least twelve classes of antimicrobials namely arsenicals, polypeptides, glycolipids, tetracyclines, elfamycins, macrolides, lincosamides, polyethers, beta-lactams, quinoxalines, streptogramins, and sulfonamides have been used in veterinary practice. The effect of this selection pressure has been the appearance of numerous resistant strains of Escherichia coli, Salmonella species, Staphylococcus aureus, Pasteurella hemolytica, Pseudomonas aeruginosa, Klebsiella pneumoniae, Clostridium perfringens and many other bacterial species. Bacteria also acquire genes conferring resistance by a variety of mechanisms including acquisition of extrachromosomal plasmids that replicate apart from the chromosomal DNA. Damage caused by antibiotic resistant bacteria is a kind of pollution. The precise effect of agricultural antibiotic use on resistance levels in the general population is not known, but the evidence points to a link. Considerable attention has been focussed on a very small minority of bacteria that cause disease but a vast sea of commensal and environmental bacteria continuously and promiscuously exchange genes totally unnoticed. Immediate action has to be taken to prevent the antibiotic resistance in bacteria by judicious and rational use of antibiotics, effective hospital infection control programs and research for the development of new antibiotics or by combination therapy.
Genetic structure and diversity of the black-throated finch (Poephila cincta) across its current range

Abstract. Understanding the patterns of population connectivity and level of genetic diversity can facilitate the identification of both ecologically relevant populations and the spatial scales at which conservation management may need to focus. We quantified genetic variation within and among populations of black-throated finches across their current distribution. To quantify genetic structure and diversity, we genotyped 242 individuals from four populations using 14 polymorphic microsatellite markers and sequenced 25 individuals based on a 302-base-pair segment of mitochondrial control region. We found modest levels of genetic diversity (average allelic richness r = 4.37 ± 0.41 (standard error) and average heterozygosity HO = 0.42 ± 0.040 (standard error)) with no bottleneck signature among sampled populations. We identified two genetic groups that represent populations of two subspecies based on Bayesian clustering analysis and low levels of genetic differentiation based on pairwise genetic differentiation statistics (all FST, RST and Nei’s unbiased D values < 0.1). Our data suggest that genetic exchange occurs among sampled populations despite recent population declines. Conservation efforts that focus on maintaining habitat connectivity and increasing habitat quality to ensure a high level of gene flow on a larger scale will improve the species’ ability to persist in changing landscapes. Conservation management should also support continuous monitoring of the bird to identify any rapid population declines as land-use intensification occurs throughout the species’ range.
Effects of dietary methionine on feed utilization, plasma amino acid profiles and gene expression in rainbow trout (Oncorhynchus mykiss)

The use of aquafeeds formulated with plant protein sources supplemented with crystalline amino acids (CAAs) is believed to influence amino acid (AA) uptake patterns and AA metabolic fate. Oxygen consumption and ammonia excretion rates were measured in rainbow trout (468.5 ± 86.5 g) force fed 0.75% of their body mass with a diet based on either i) fish meal (FM), ii) pea protein concentrate (PPC), or iii) pea protein concentrate supplemented with histidine, lysine, methionine and threonine (PPC+) to mimic FM AA profile. The specific dynamic action and nitrogen quotient (NQ) were calculated for 48 h of the postprandial period. In parallel, plasma AA concentrations were measured in blood samples withdrawn from the caudal vein before and then 2, 4, 6, 8, 12, 20, 32 and 48 h after feed administration. The unbalanced diet PPC had a significantly higher NQ compare to FM (0.29±0.09 and 0.18±0.04, respectively) and plasma profiles of essential AAs reflected the dietary deficiencies. Supplementation with CAA in diet PPC+ resulted in an intermediary NQ (0.21±0.04) and significantly affected plasma AA profiles; presenting greater and faster rises followed by sharp decreases compare to FM. The strongest effect was observed for methionine, presenting 3-fold higher concentrations at peak time for PPC+ compared to FM (297.0±77.0 and 131.8±39.0 nmol ml, respectively). The differences in AA availability and metabolic profile in the pea diets compared to the FM diet were believed to be caused by an unbalanced dietary AA profile and CAA supplementation, rather than inclusion of plant protein concentrate.
Antioxidant activity of polyphenol rich fruits on human erythrocytes

Diets rich in fruit and vegetables promote health and delay the onset of diseases associated with oxidative stress. The benefit, especially of different berries, has been largely attributed to their content of numerous phytochemicals, and their effects in terms of antioxidant capacity are often evaluated chemically by different methods. We have instead used a highly relevant biological model, a modified CAP-e assay (Cell-based Antioxidant Protection in erythrocytes), to evaluate bioefficacy of antioxidants in Swedish berries. Extracts of twelve fruit and berries were analysed both by chemical and biological analyses: apple (Malus domestica, peel), bilberry (Vaccinium myrtillus), black currant (Ribes nigrum), purple chokeberry (Aronia x prunifolia), cranberry (Vaccinium macrocarpon), elderberry (Sambucus nigra), lingonberry (Vaccinium vitis-idaea), raspberry (Rubus idaeus), rose hips (Rosa spp.), sea buckthorn (Hippohae rhamnoides), sloe (Prunus spinosa) and strawberry (Fragaria x ananassa). Purple chokeberry, sloe and rose hips showed high antioxidant capacity in the chemical assays. Rose hips showed the highest degree of antioxidant protection also in the biological model, however, chokeberry and sloe showed medium or low protection. Furthermore, strawberry showed overall high protection in the biological assay but low antioxidant capacity in the chemical assays. The chemical and biological models showed different results and future studies of the biological model and in vivo situations are necessary.
Evaluation of cytotoxic activity of various extracts of sweet cherry ( Prunus avium ) against human colorectal adenocarcinoma HT-29 cell line

HT-29 is a human colorectal adenocarcinoma cell line with epithelial morphology. These cells are sensitive to the chemotherapeutic drugs 5-fluorouracil and oxaliplatin, which are standard treatment options for colorectal cancer. In addition to being a xenograft tumor model for colorectal cancer, the HT29 cell line is also used as an in-vitro model to study absorption, transport, and secretion by intestinal cells. Under standard culture conditions, these cells grow as a nonpolarized, undifferentiated multilayer. Altering culture conditions or treating the cells with various inducers, however, results in a differentiated and polarized morphology, characterized by the redistribution of membrane antigens and development of an apical brush-border membrane. The main objective of the present research work is to isolate the bioactive molecules and evaluate the in vitro cytotoxic activity of methanolic and chloroform extracts of sweet cherry (MEC and CEC) of Prunus avium. The in vitro cytotoxic activity was carried out against human colorectal adenocarcinoma cell line HT-29 by SRB assay. The results obtained from the in-vitro studies performed by SRB assay by using human colorectal adenocarcinoma cell line HT 29 displayed that the various extracts of sweet cherry (MEC and CEC) possessed a very good anticancer activity. From the present studied it had been concluded that MEC and CEC, all were exhibiting the potential capability to kill the cancer cell when compared with standard drug 5-FU and the cell growth inhibition of MEC and CEC was found to be the highest 93.91% at 10 μg (IC50 = 2.5 μg/ml) and 94.25% % at 10 μg (IC50 = 2.1 μg/ml.