Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Trait Loci for some of Behavior and Performance Traits on Chromosome 4 of Japanese Quail

The current study was conducted to identify the quantitative trait locus (QTL) for the body weight at age 1, 7, 14, 21 and 28 days and daily gain at age 0-1, 1-2, 2-3 and 3-4 weeks, slighter carcass weight and tonic immobility in Japanese quail. Two divergently lines of wild and white Japanese quail which maintained in the Animal Science Research Center of the Shahid Bahonar University of Kerman was used. Birds in two lines were mated in reciprocal cross for generating F1 generation. The F2 generation was generated by random mating of F1 birds. The half sib and F2 model analysis of QTL express was used for QTL mapping the measured traits. Total F2 individuals (422 birds), their parents (34 F1 birds) and pure lines (16 birds) were genotyped by 2 informative microsatellite markers on chromosomes 4. On this chromosome, with the half sib model, no significant QTL at the 5%, 1% chromosome wide was detected. But, with the F2 model, a significant QTL at the 5% chromosome wide was identified for body weight (BW) at age 21 and 28 days, carcass weight and daily gain traits during 1-2, 2-3 and 3-4 weeks in 54cM position. The all of identified QTLs explain less of 4% of the phenotypic variance, because the traits of growth are complex traits affected by many loci influencing appetite, feed uptake, nutrient allocation, metabolic rate, physical activity and so forth.
Environmental correlates of the Late Quaternary regional extinctions of large and small Palaearctic mammals

Most studies of mammal extinctions during the Pleistocene–Holocene transition explore the relative effects of climate change vs. human impacts on these extinctions, but the relative importance of the different environmental factors involved remains poorly understood. Moreover, these studies are strongly biased towards megafauna, which may have been more influenced by human hunting than species of small body size. We examined the potential environmental causes of Pleistocene–Holocene mammal extinctions by linking regional environmental characteristics with the regional extinction rates of large and small mammals in 14 Palaearctic regions. We found that regional extinction rates were larger for megafauna, but extinction patterns across regions were similar for both size groups, emphasizing the importance of environmental change as an extinction factor as opposed to hunting. Still, the bias towards megafauna extinctions was larger in Southern Europe and smaller in central Eurasia. The loss of suitable habitats, low macroclimatic heterogeneity within regions and an increase in precipitation were identified as the strongest predictors of regional extinction rates. Suitable habitats for many species of the Last Glacial fauna were grassland and desert, but not tundra or forest. The low-extinction regions identified in central Eurasia are characterized by the continuous presence of grasslands and deserts until the present. In contrast, forest expansion associated with an increase in precipitation and temperature was likely the main factor causing habitat loss in the high-extinction regions. The shift of grassland into tundra also contributed to the loss of suitable habitats in northern Eurasia. Habitat loss was more strongly related to the extinctions of megafauna than of small mammals. Ungulate species with low tolerance to deep snow were more likely to go regionally extinct. Thus, the increase in precipitation at the Pleistocene–Holocene transition may have also directly contributed to the extinctions by creating deep snow cover which decreases forage availability in winter. This article is protected by copyright. All rights reserved.
Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans

Susceptibility genes for psychiatric and neurological disorders - including APOE, BDNF, CLU,CNTNAP2, COMT, DISC1, DTNBP1, ErbB4, HFE, NRG1, NTKR3, and ZNF804A - have been reported to affect white matter (WM) microstructure in the healthy human brain, as assessed through diffusion tensor imaging (DTI). However, effects of single nucleotide polymorphisms (SNPs) in these genes explain only a small fraction of the overall variance and are challenging to detect reliably in single cohort studies. To date, few studies have evaluated the reproducibility of these results. As part of the ENIGMA-DTI consortium, we pooled regional fractional anisotropy (FA) measures for 6,165 subjects (CEU ancestry N=4,458) from 11 cohorts worldwide to evaluate effects of 15 candidate SNPs by examining their associations with WM microstructure. Additive association tests were conducted for each SNP. We used several meta-analytic and mega-analytic designs, and we evaluated regions of interest at multiple granularity levels. The ENIGMA-DTI protocol was able to detect single-cohort findings as originally reported. Even so, in this very large sample, no significant associations remained after multiple-testing correction for the 15 SNPs investigated. Suggestive associations (1.3×10-4 < p < 0.05, uncorrected) were found for BDNF, COMT, and ZNF804A in specific tracts. Meta-and mega-analyses revealed similar findings. Regardless of the approach, the previously reported candidate SNPs did not show significant associations with WM microstructure in this largest genetic study of DTI to date; the negative findings are likely not due to insufficient power. Genome-wide studies, involving large-scale meta-analyses, may help to discover SNPs robustly influencing WM microstructure.
Investigating the Relation between miR-31 and RhoA Expressions in Breast Cancer Clinical Samples and Cell Lines: A Controversial Matter

Breast cancer is the most prevalent diagnosed cancer and the second cause of cancer death among women worldwide. There are different mechanisms that play crucial roles in the onset and progression of breast cancer including microRNAs. microRNAs are small noncoding RNAs that regulate gene expression by repressing translation post-transcriptionally. miR-31 is an integrin modulator implicated in different cellular processes such as apoptosis, cell cycle control, and DNA repair. According to the literature, RhoA is one of the genes regulated by miR-31. It has an important role in actin-myosin contraction and subsequently in cell motility and migration in metastasis cascade. Breast cancer cell lines, MCF-7 and MDA-MB-231, as well as normal breast cells, MCF-10A, were cultured. RNA extraction, cDNA synthesis, and SYBR Green I quantitative real-time PCR were used to investigate the expression of miR-31 and RhoA . In addition, 10 metastatic breast cancer clinical samples were analyzed to assess miR-31 and RhoA expression, and normal cells from the same patients were used as controls. Pearson’s correlation co-efficient was applied to find out any probable relation between miR-31 and RhoA expression. Gene expression analyses in MCF-7 cell line showed downregulation of miR-31 while RhoA was upregulated in the cell line (inverse correlation). miR-31 and RhoA were both upregulated in metastatic MDA-MB-231 cell line and downregulated in 90% of clinical samples. Pearson’s correlation co-efficient showed complete positive correlation between miR-31 and RhoA expression. The expression of miR-31 and RhoA is positively correlated, and it is declined in metastatic breast that cancer clinical samples save MDA-MB-231 cells. Unlike previous reports, we found that miR-31 is not the main silencer of RhoA expression. Therefore, more investigation on genes and miRNAs affecting metastasis process can elucidate new biomarkers and therapeutic targets for metastatic breast cancer. Highlights miR-31 is an important miRNA implicated in different cellular processes as well as cancer. The protein product of RhoA gene plays a role in actin-myosin contraction and cell motility in cancer metastasis. We approved bioinformatically and experimentally that RhoA is one of the genes regulated by miR-31
The effects of ethanolic herbal extracts and CuO nanoparticles on catalase, glutathione peroxidase and malondialdehyde in male diabetic rats

Abstract Antioxidants can reduce the occurrence of long-term damages, caused by free radicals. In this study, we aimed to evaluate the effects of CuO nanoparticles and hydroalcoholic extracts of Berberis vulgaris, Descurainia sophia and Silybum marianum on catalase, glutathione peroxidase, and malondialdehyde concentrations in male diabetic rats. In case 50 Wistar rats (250–350 g) were divided in ten groups (five rats per group): healthy controls, healthy rats receiving nanoparticles, healthy rats receiving B. vulgaris, D. sophia, and S. marianum extracts (independently), diabetic controls, diabetic rats receiving CuO nanoparticles, and diabetic rats receiving the extracts independently. In diabetic groups, diabetes was induced in half of the rats, using alloxan at a dose of 120 mg kg−1. In addition to CuO nanoparticles, the control and diabetic groups independently received 0.5 ml of B. vulgaris, D. sophia, and S. marianum extracts via intraperitoneal injection for 30 days. Then, the animals were anesthetized with ketamine and the liver tissues were removed. The concentrations of catalase, glutathione peroxidase, and malondialdehyde were measured and compared. In diabetic groups treated with CuO nanoparticles, a significant increase was reported in the concentration of malondialdehyde (from 4.7 ± 0.44 to 5.05 ± 0.40) (mean ± SD). Moreover, a significant decline was observed in the activity of catalase (from 36.8 ± 1.48 to 36.2 ± 1.48) and glutathione peroxidase enzymes (from 75.4 ± 3.91 to 72.4 ± 4.33). The results show that S. marianum extract was more effective than B. vulgaris and D. sophia extracts in diminishing the effects of CuO nanoparticles.
Effect of Dietary Inclusion of Lemon Balm (Melissa Officinalis L.) Extract on Performance, Gut Microflora, Blood Parameters, Immunity and Carcass Traits of Broilers

The aim of the present study was to evaluate the effects of lemon balm (LB; Melissa officinalis L.) extract as additive on performance, health status and carcass traits of broilers during a 42-days production cycle. One hundred mixed chicks of Ross 308 strain were assigned for five dietary treatments with four replicates per group and five birds per replicate as follows: control diet, 0.5LB, 1.0LB, 1.5LB and 2.0LB with 0.0, 0.5, 1.0, 1.5 or 2.0 mL of LB extract per liter of drinking water, respectively. In overall, at 42nd day, low feed, energy and protein efficiency (P<0.05) were observed in 1.0LB group than in control diet. However, during the 3rd and 5–6th weeks, feed, energy and protein intakes were improved (P<0.05), without any efficiency enhancement (P>0.05) mainly in group on 1.0LB diet. During the 5th week of rearing, daily weight gain was higher (P<0.05) in groups 0.5LB, 1.0LB and 2.0LB compared to control diet. At the end of feeding period, cecal enterococcus bacteria colony count was higher (P<0.05) and left cecum diameter was lower (P<0.05) in 1.0LB group. Hematological parameters and viscera and carcass traits remained unaffected (P>0.05) by dietary treatments. In conclusion, the supplementation with LB as natural feed additive resulted in a potential positive effect on broilers performance mainly during the grower and finisher periods.
Sex differences in morphology and migration timing of Chiffchaff Phylloscopus collybita and Willow Warbler Phylloscopus trochilus in northern Poland

Chiffchaff (Phylloscopus collybita) and Willow Warbler (Phylloscopus trochilus) are two sympatric bird species breeding across most of Europe and a part of Asia. During autumn and spring migration to Africa and southern parts of Europe, north-European populations of these species migrate along the coasts of the Baltic Sea. Both species are monomorphic in plumage, which impedes any research of potential sex differences in their migration behaviour. I collected and analysed blood samples of individuals of both species captured during their migration through the Baltic coast in northern Poland, to determine their sex genetically, by DNA from blood and feather samples. Based on the measurements of DNA-sexed individuals, I developed criteria for morphological sexing of each species. I applied these criteria to sex unsampled birds captured at the same ringing site during several migration seasons in the past, to identify sex differences in their migration timing and the effects of weather on migration. Differential migration in the form of protandry was revealed in both species. The timing of males' passage varied considerably from year to year in Chiffchaff, but less so in Willow Warbler, pointing to a more rigid migration schedule in the latter species. Additionally, temperature appears to influence migration timing and choice of stopover in Chiffchaffs.
Dissecting the nature of subtle phenotypic variation in wing colour elements of Müllerian co-mimics

Abstract: Polymorphism is common in nature, but few Heliconius species are polymorphic for wing colour patterns. Eastern Brazil H. erato phyllis populations are polymorphic for hindwing elements (red raylets) and studies suggest that trait distribution varies seasonally. We carried a 3-y sampling to evaluate the hypothesis that season, wing length and pollen foraging were associated with morph diversity. Individual phenotypes were scored with regards to number of red elements in the dry and in the wet seasons. Co-mimic H. melpomene nanna was also analysed. We scored 432 H. erato and 513 H. melpomene. Our results confirm polymorphism in H. erato, with individuals showing from one to eight elements, with a mode between five and six. We found that H. melpomene is polymorphic for red dots, varying from two to five (mode = 2). Red basal dots were mostly invariant in H. erato. Even though we found a seasonal change in pollen loads, we found no association between individual phenotypes and season, pollen load scores, or wing length. We reject the hypothesis of ecological correlates of morph frequency, and suggest that trait colour variation in the two species is linked to and constrained by effects on mate recognition.
A new genus of Cryphonectriaceae isolated from Lagerstroemia speciosa in southern China

Numerous species in the Cryphonectriaceae have been recorded on the Myrtales and many of these are economically important pathogens of Eucalyptus. Some species have also recently been shown as endophytes of native Myrtaceae and to have undergone host jumps to infect Eucalyptus species established as exotics in plantations. Recent surveys in the GuangDong and HaiNan Provinces of South China reveal the presence of a species of Cryphonectriaceae associated with cankers on trees of Lagerstroemia speciosa (Lythraceae, Myrtales). Fungal structures were observed on the surface of dead bark covering cankers and on branch stubs. The fungus was identified and its pathogenicity to L. speciosa and a Eucalyptus clone was tested. Multigene phylogenetic analyses were conducted based on DNA sequence comparisons of the partial LSU gene, ITS region of the nuclear ribosomal DNA gene and two regions of the β-tubulin (BT) gene. The results revealed the presence of a previously undescribed genus and species in the Cryphonectriaceae. The fungus is described here as Chrysomorbus lagerstroemiae gen. et sp. nov. Inoculation tests showed that it is an aggressive pathogen on L. speciosa and that it can also infect Eucalyptus. This article is protected by copyright. All rights reserved.
Collective decision making in guppies: a cross-population comparison study in the wild

Lay Summary We investigated collective cognition in populations subject to different levels of predation. In a choice experiment, wild guppies had to distinguish an edible from a nonedible but similar-looking object. We found that the guppies under low predation made better decisions when in groups but not those under high predation. This suggests a trade-off in the ability of fish to use collective cognition to detect predators and to detect food, depending on the predation level they face.
How small and constrained is the genome size of angiosperm woody species

Abstract Angiosperm hardwood species are generally considered to show an average smaller genome size with a narrow range of variation than their herbaceous counterparts. Various explanations pertaining to limitations of cell size exerted by wood fibers, the requirement of smaller stomata, longer generation time, large population size, etc., have been put forward to account for their small and constrained genome size. Yet studies done in the past several years show that genomically as well as evolutionarily, hardwoods are as diverse and active as their herbaceous counterparts. This is entirely supported by the presence of well developed inter and intraspecific polyploid series and natural triploidy in many genera. Polyploidy, in some instances has been shown to confer adaptability to arid and salt stress conditions and in colonization of new areas. Moreover, hardwoods also show reasonable amenability to the induced polyploidy which abruptly changes the balance between nuclear and cell size. Polyploidy has been induced in many hardwoods to restore fertility in interspecific hybrids and for the production of triploids. Furthermore, some cases studied show that genome size variation in hardwoods can be as variable as that of herbaceous species. Genome size has been shown to vary remarkably both at homoploid level as well as by polyploidy in certain genera. In the same way, the genome size is not correlated with the habit in certain groups having both herbaceous and woody taxa. This point is further proved by the presence of secondary and insular woody habit in certain cases where either the transition to woodiness is not followed by any diminution in the genome size, or the genome size of insular woody species may be even more than that of the congeneric herbaceous species. This shows that woody habit does not by itself put any constraints on the genome size either at homoploid or at polyploidy levels. The genome size in fact, not only varies significantly in many congeneric woody species but also may not show any correlation with the habit when woody and herbaceous species are compared in some narrow taxonomic groups studied.
Bioinformatics challenges in molecular epidemiology of cancers

Molecular epidemiology is the integration of molecular biologic techniques into epidemiologic study. With the advances in understanding of carcinogenesis and the human genome, there has been an evolution in the field of cancer epidemiology. However, traditional analyses of single genetic variants often fail to identify susceptibility genes for cancer risk. In particular, recent technological evolution has enabled high-throughput analyses for a number of genetic variants and driven accumulation of unprecedentedly large genome data, imposing bioinformatics challenges. These studies aim to inte grate the genetic basis of complex diseases including cancers in which the interplay of multiple genetic and environmental risk factors may play an important role. Here we outline currently available approaches for detecting variants of cancer risk. We also review up-coming bioinformatics challenges and technical aspects in the field of molecular epidemiology, and discuss their future impact on the understanding of carcinogenesis and personalized strategies for cancer prevention and therapy.
Population of the temperate mosquito, Culex pipiens, decreases in response to habitat climatological changes in future

Predictions of the temporal distribution of vector mosquitoes are an important issue for human health because the response of mosquito populations to climate change could have implications for the risk of vector‐borne diseases. To elucidate the effects of climate change on mosquito populations inhabiting temperate regions, we developed a Physiology‐based Climate‐driven Mosquito Population model for temperate regions. For accurately reproducing the temporal patterns observed in mosquito populations, the key factors were identified by implementing the combinations of factors into the model. We focused on three factors: the effect of diapause, the positive effect of rainfall on larval carrying capacity, and the negative effect of rainfall as the washout mortality on aquatic stages. For each model, parameters were calibrated using weekly observation data of a Culex pipiens adult population collected in Tokyo, Japan. Based on its likelihood value, the model incorporating diapause, constant carrying capacity, and washout mortality was the best to replicate the observed data. By using the selected model and applying global climate model data, our results indicated that the mosquito population would decrease and adults’ active season would be shortened under future climate conditions. We found that incorporating the washout effect in the model settings or not caused a difference in the temporal patterns in the projected mosquito populations. This suggested that water resources in mosquito habitats in temperate regions should be considered for predicting the risk of vector‐borne diseases in such regions.
DNA damage and the activation of the p53 pathway mediate alterations in metabolic and secretory functions of adipocytes Running title: DNA damage and p53 in obese adipocytes

Activation of the p53 pathway in adipose tissue contributes to insulin resistance associated with obesity. However, the mechanisms of p53 activation and the impact on adipocyte functions are still elusive. Here we found a higher level of DNA oxidation and a reduction in telomere length in adipose tissue of high-fat diet mice and an increase in DNA damage and activation of the p53 pathway in adipocytes. Interestingly, hallmarks of chronic DNA damage are visible at the onset of obesity. Furthermore, treatment of lean mice with doxorubicin, a DNA damage-inducing drug, increased the expression of chemokines in adipose tissue and promoted its infiltration by pro-inflammatory macrophages and neutrophils together with adipocyte insulin resistance. In vitro, DNA damage in adipocytes increased chemokines expression and triggered the production of chemotactic factors for macrophages and neutrophils. Insulin signaling and effect on glucose uptake and Glut4 translocation were decreased while lipolysis was increased. These events were prevented by p53 inhibition whereas its activation by nutlin-3 reproduced the DNA damage-induced adverse effects. This study reveals that DNA damage in obese adipocyte could trigger p53-dependent signals involved in alteration of adipocyte metabolism and secretory function leading to adipose tissue inflammation, adipocyte dysfunction and insulin resistance.