Miracle-dz/UniFAR-FTUs huggingface dataset:
Delineation of the SUMO-Modified Proteome Reveals Regulatory Functions Throughout Meiosis

Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of homologous recombination. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism.
Temporal variation of regional bird assemblages in highly dynamic fluvial wetlands: seasonality and influence of water level and habitat availability

Study of temporal variation of bird assemblages may be particularly important in highly dynamic ecosystems as fluvial wetlands to identify the factors that influence and contribute to the maintaining of regional diversity. We study temporal variation in regional bird species composition and richness and the factors that drive it in the fluvial system of the Paraná River in Argentina. We sampled birds on a regional scale by performing surveys during 2 years (2011-2013; 16 total surveys) at 60 sites located along the fluvial system. We recorded a total of 162 species and 12,738 individuals, with a mean of 72.7 ± 1.9 species and 796.1 ± 41 individuals per survey. Temporal beta diversity accounted for 57% of regional species richness. Bird composition varied seasonally because of the turnover (and not nestedness) of species between autumn-winter and spring-summer periods; migrant species contributed to but did not account for all these differences. Difference in bird composition between years was caused primarily by turnover of species within autumn-winter periods; that turnover was related to changes in water levels. Temporal variation in availability of habitats across the regional extent of the fluvial system accounted for the highest proportion of temporal beta diversity. Species richness did not vary seasonally nor was it related to fluctuations in water level or habitats. Our results showed that climatic seasonality and environmental dynamics of the fluvial system, as a function of water-level fluctuations and of variations in habitat availability, jointly influence regional composition of birds through temporal turnover of species. These variations in regional composition were not related to variations in regional species richness. These results show the importance of the natural dynamic of the fluvial system to conserve the processes that maintain the regional assemblage of birds.
Biometric relationships between body size and otolith size in 15 demersal marine fish species from the northern Brazilian coast

The relationships between fish size and sagitta otolith measurements were calculated for the first time for 15 species belonging to six families from the northern Brazilian coast. A total of 220 fish were sampled from the bycatch landed by the bottom-trawl industrial shrimp-fishing fleet between August and September 2016. All species had strong relationships between otolith measurements and fish total length with the coefficient of determination (r2) ranging between 0.71 and 0.99. The variable most strongly related to fish total length was found to be the sagittal otolith length (OL) with 98% of the variability. These relationships are a useful tool to estimate length and mass of preyed fish from otoliths found in stomach contents of marine predators.
Cucurbita maxima Duch. population analysis: relationship between Tunisian and Italian germplasm

ABSTRACT Cucurbita maxima Duch. is one of the most diversified Cucurbita species worldwide. The objective of this study was to evaluate the genetic relationship between and within Tunisian and Italian Cucurbita maxima germplasm collections using morphological and molecular markers. The phenotypic parameters showed a large qualitative variability, primarily according to fruit-related traits, for both collections. The RAPD, ISSR and SRAP molecular marker systems used turned out to be effective in discriminating all the accessions. Among the Tunisian collection, the polymorphic information content (PIC) and genetic diversity (H) values were of 0.461 and 0.50 respectively, with a total of 96% of polymorphism detected. The Italian collection revealed a PIC and H values of 0.454 and 0.50 respectively and 90% of polymorphism. Population structure analysis reflected the geographical origin of the accessions and helped to classify the Tunisian collection into two populations and to group all the Italian accessions into one. The results suggest that the combination of morphological and molecular approaches is a highly reliable technique in studying and evaluating Cucurbita maxima germplasm which represents an important genetic resource to be preserved and used in breeding programs.
Environmental variables determining the presence of an avian parasite: the case of the Philornis torquans complex (Diptera: Muscidae) in South America

Philornis flies are exclusive of birds and their nests, being some of them of conservation concern. Despite many studies addressed different aspects of this problem, none have focused on the geographical distribution of these species. In this study, besides providing a model map of environmental suitability of the P. torquans complex in South America, we also contributed with data on the constraints of its abiotic niche. We provided baseline data (supplementary information) on sites where P. torquans complex is present in southern South America, valuable for future Philornis distribution modelling efforts. According to our results, the P. torquans complex is potentially distributed across central-eastern Argentina, mostly restricted to the Pampean and Chaco (eastern Chaco district) biogeographical provinces. The potential distribution of the P. torquans complex mainly relates to the “minimum temperature of the coldest month” and “mean temperature of warmest quarter”. In addition, moisture/aridity seems to be exerting additional constraints. Our work is the first one to identify macro-environmental variables driving the geographical distribution of a Philornis species by evaluating their contribution to its’ environmental niche. Besides the relevance of our model as a tool for bird’s conservation, it integrates the most up-to-date methodological recommendations to predict a robust ecological niche; thus representing a methodological reference for future work on the distribution of this group of parasites.
Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria

The evolution of bacterial regulatory networks has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations faster than TGs. This hypothesis is supported by several lab evolution studies which found TFs, especially global regulators, to be frequently mutated. Despite these studies, the contribution of point mutations in TFs to the evolution of regulatory network is poorly understood. We tested if TFs show greater genetic variation than their TGs using whole-genome sequencing data from a large collection of E coli isolates. We found TFs to be less diverse, across natural isolates, due to their regulatory roles. TFs were enriched in mutations in multiple adaptive lab evolution studies but not in mutation accumulation. However, over long-term evolution, relative frequency of mutations in TFs showed a gradual decay after a rapid initial burst. Our results suggest that point mutations, conferring large-scale expression changes, may drive the early stages of adaptation but gene regulation is subjected to stronger purifying selection post adaptation.
Regulation of yeast RPL22B splicing depends on intact pre-mRNA context of the intron

Yeast RPL22A and RPL22B genes form an intergenic regulatory loop modulating the ratio of paralogous transcripts in response to changing levels of proteins. Gabunilas and Chanfreau (Gabunilas and Chanfreau, PLoS Genet 12, e1005999, 2016) and our group (Abrhámová et al., PLoS ONE 13, e0190685, 2018) described that Rpl22 proteins bound to the divergent introns of RPL22 paralogs and inhibited splicing in dosage dependent manner. Here, we continued to study the splicing regulation in more detail and designed constructs for in vivo analyses of splicing efficiency. We also tested Rpl22 binding to RPL22B intron in three-hybrid system. We were able to confirm the findings reported originally by Gabunilas and Chanfreau on the importance of a stem loop structure within the RPL22B intron. Mutations which lowered the stability of the structure abolished Rpl22-mediated inhibition. In contrast, we were not able to confirm the sequence specificity with respect to either Rpl22 binding or splicing inhibition within this region, which they reported. We contradict their results that the ‘RNA internal loop’ of RPL22Bi (nt 178CCCU181 and 221UGAA224) is crucial for mediating the Rpl22 effects. We assume that this discrepancy reflects the difference in constructs, as the reporters used by Gabunilas and Chanfreau lacked the alternative 5’ splice site as well as surrounding exons. Our own comparison confirms that deleting the sequence spanning alternative 5’ splice site lowers splicing efficiency, hinting to possible disturbances of the regulatory mechanism. We argue that the structural context of the ‘regulatory element’ may reach across the intron or into the surrounding sequences, similarly to what was found previously for other genes, such as RPL30. Apparently, more detailed analyses are needed to discern this intriguing example of splicing regulation.
GROWTH OF BUCKWHEAT (Fagopyrum esculentum Moench) SEED-LINGS AND THE ACCUMULATION OF PRIMARY AND SECONDARY METABOLITES UNDER VARIOUS MINERAL NUTRITION CONDI-TIONS

to the unique nutritional characteristics, it is characterized by the formation of various phenolic compounds including rutin widely used in medicine. The study of the various metabolites formation at the initial growth stages as well as those under the different conditions of mineral nutrition is important for estimation of plant potential productivity and adaptation to environmental conditions. In this paper, we showed the regula- tory effect of macro- and microelements on the growth and accumulation of primary and secondary metabolites in buckwheat plants. For the first time, the formation of primary and secondary metabo- lites in the aerial parts of a new and promising Russian buckwheat variety Dasha (approved by the State Register of the Russian Federation in 2018) has been characterized. The aim of this work was to study the initial stages of F. esculentum ontogenesis, including the assessment of the morphophysi- ological characteristics of seedlings under various mineral nutrition conditions, as well as the accumulation of photosynthetic pigments, sugars, and phenolic compounds in cotyledon leaves. Studies were conducted using two varieties of this culture included in the State Register of the Russian Federation in 2004 and 2018 (Devyatka and Dasha, respectively). Plant cultivation was carried out by a roll method in water (control) and Hoagland-Arnon nutrient medium (sample) at 24  C and 16- hour illumination in laboratory conditions. In the seedlings, the height of the hypocotyls, the length of the roots, and the mass of cotyledon leaves was determined. The water content of the plant material was analyzed after it was dried to constant weight at 70  C. The spectrophotometric method was used to de-termine the amount of chlorophylls a and b (  = 665 nm and  = 649 nm), carotenoids (  = 440 nm), sugars (  = 490 nm), the total amount of soluble phenolic compounds (  = 725 nm), flavonoids (  = 415 nm) and phenylpropanoids (  = 330 nm) in ethanol extracts from cotyledon leaves of seedlings of different ages. The cultivation of buckwheat on Hoagland-Arnon nutrient medium
In Vitro Regeneration of Coral Tree from Three Different Explants Using Thidiazuron

The coral tree (Erythrina variegata) is a multipurpose horticultural plant with a plethora of medicinally important alkaloids. Regeneration via tissue culture can provide an efficient alternative to seed-grown plantlets and reduce the cost of the plant significantly. Thidiazuron (TDZ) is an efficient plant growth regulator and is effective in numerous species. However, the response to it varies with the type and position of the tissue on the plantlet treated. This study was carried out to ascertain the best tissue types for micropropagation of the coral tree using TDZ. Three tissue types (shoot tip, nodal, and hypocotyl), originating from different strata of the plantlet were evaluated. Adventitious shoots were observed in all three explants at the tested concentrations. However the quality and the shoot number varied significantly with the type of explant. Explants with a meristematic zone (shoot tip and nodal) were more responsive to the treatment compared with hypocotyl tissue lacking preexisting meristem. Nodal explants produced the maximum number of shoots (about eight) per explant after 4 weeks of culture, whereas shoot tips produced about only five shoots per explant at an equimolar concentration (1.5 µm). Approximately three shoots were observed in hypocotyl explants. Moreover, growth and rooting of the regenerated shoots was influenced by the origin of the explants. The molecular characterization of the regenerants using intersimple sequence repeat (ISSR) markers revealed genetic homogeneity among regenerants. An efficient micropropagation method for the coral tree is described.
In vitro and In vivo Antiplasmodial of Stem Bark Extract of Garcinia husor

Garcinia husor is one of the folk medicines in Maluku-Indonesia. This species has been used for the treatmet of Malaria disease. The phytochemical contents and antiplasmodial activity not reported yet. In this study we evaluated the quantitative phytochemicals, in vitro and in vivo antiplasmodial activity of stem bark ethyl acetate extract. In vitro assay was done using P. falciparum 3D7 strain sensitive of chloroquine. For in vivo analysis, four groups of M. musculus were infected by P. berghei and their parasitemia levels were for 7 days of treatment with ethyl acetate extract; hematological and biochemical parameter were analyzed at the end of experiment. The result showed ethyl acetate extract with the TPC (169.47 mg GAE/100 g ±0.61) and TPC (167.37 mg QE/100 g ±1.05) was active against P. falciparum 3D7 strain (IC50 value of 0.31±0.43 μg/ml). The animal treated with extract showed suppression of parasitemia to 87.57±1.41% compared with the P. berghei infected-mice (negative control), ED50 value of 22.30 mg/kg BW. The dose of extract in 200 mg/kg BW was reduce parasitemia of infected mice with P. berghei more potential. The ethyl acetate of the stem bark G. husor with has antiplasmodial properties and future investigation are necessary to elucidate its mechanism of action.
Valuing Carbon Stocks across a Tropical Lagoon after Accounting for Black and Inorganic Carbon: Bulk Density Proxies for Monitoring

ABSTRACT Gallagher, J.B. ; Chew, S. -T. ; Madin, J., and Thorhaug, A. , 2020. Valuing carbon stocks across a tropical lagoon after accounting for black and inorganic carbon: Bulk density proxies for monitoring. Journal of Coastal Research, 36(5), 1029–1039. Coconut Creek (Florida), ISSN 0749-0208. Total organic carbon (TOC) stocks of seagrass and mangroves across a Southeast Asian lagoon were measured and valued after correcting for black carbon (BC) and calcareous carbon equivalents (PICequiv) in mitigating CO2 emissions, along with sediment dry bulk densities (DBDs), as a cost-effective means of estimating carbon stock concepts. Overall, seagrass and mangrove TOC densities ranged from 15.3 ± 4.3 and 124.3 ± 21.1 Mg C ha–1, respectively, across the lower lagoon and 175.2 ± 46.9 and 103.2 ± 19.0 Mg C ha–1 for seagrass and 355.0 ± 24.8 and 350.3 ± 35.2 Mg C ha–1 for mangroves across the two upper lagoon branches. Only mangrove biomass made significant additional contributions, ranging from 178.5 ± 62.3 to 120.7 ± 94.8 Mg C ha–1 for lower and upper regions, respectively. The difference between the lagoon's seagrass and mangrove TOC total stock (5.98 ± 0.69 and 390 ± 33.22 Gg C, respectively) was further amplified by the larger mangrove area. When corrected for BC and PICequiv, the carbon stock mitigation service was reduced by a moderate 14.2%. Across the lagoon the sedimentary DBD showed strong (R2 = 0.85, p < 0.001) to moderate (R2 = 0.67, p < 0.001) linear correlations with seagrass and mangrove [TOC], respectively and moderate correlations with seagrass [PIC] (R2 = 0.6, p < 0.001). There was an invariant and relatively constant response to mangrove [PIC] (2.7 ± 0.07 kg m–3). Valuations were worth on average US$0.44 million y–1 over 20 years, and less than the total income of the indigenous custodians (US$1.8 and US$7.4 million y–1).
Chronic Mcm10 deficiency causes defects in telomere maintenance in human cells

Minichromosome maintenance protein 10 (Mcm10) is essential for eukaryotic DNA replication initiation and fork stability. Recently, a compound heterozygous MCM10 mutation was identified in a patient who presented with natural killer (NK) cell deficiency. To understand the mechanism of disease, we modeled this mutation in human cell lines. We demonstrate that Mcm10 deficiency causes chronic replication stress that reduces cell viability due to increased genomic instability and telomere maintenance defects. Our data suggests that Mcm10 deficiency constrains telomerase-dependent telomere extension. This limitation can be overcome by increasing telomerase activity, although defects in telomere replication persist. We propose that stalled replication forks in Mcm10-deficient cells arrest terminally, especially within hard-to-replicate regions, and require nuclease processing involving Mus81, as MCM10:MUS81 double mutants displayed decreased viability and accelerated telomere erosion. Our results reveal that Mcm10 is critical for telomere replication and provide insights into how MCM10 mutations cause NK cell deficiency.
Phosphorus dynamics in a subtropical coastal lake in Southern Brazil

Temporal and spatial variations of organic and inorganic forms of phosphorus in the sediments of a subtropical oligo-mesotrophic shallow lake were investigated in relation to water column parameters, sediment characteristics and benthic fauna. The main results found were: 1) Phosphorus (P) concentration varied seasonally, with organic P and total P increasing in the sediments in warmer periods; 2) Sediment spatial variation, in terms of grain size composition and organic matter content, influenced P concentrations; 3) quantities and qualities of P in the sediments were positively correlated with water parameters, especially DO and NO3, Chl-a, water temperature, pH, and total P. Negative correlations were observed between %OP and DO in sites 1, 3 and 4, and with NO3 in sites 2, 3 and 4; 4) benthic functional feeding groups showed significant relationships with temporal variation in sediment P concentration, including gathering-collectors, shredders, filterers and filtering-collectors. The results suggest a high importance of temperature mediated control of sediment-P release, both directly, through its direct effects on primary production and decomposition rates, and indirectly through its effects on other water and sediment parameters, especially dissolved oxygen concentration.
Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB

Title: Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible with ARB Authors: DeSantis, T.Z. 1 Hugenholtz, P. 2 Larsen, N. 3 Rojas, M. 4 Brodie, E.L. 1 Keller, K. 5 Huber, T. 6 Dalevi, D. 7 Hu, P. 1 Andersen, G.L. 1 Center for Environmental Biotechnology Lawrence Berkeley National Laboratory 1 Cyclotron Road, Mail Stop 70A-3317 Berkeley, CA 94720 USA Microbial Ecology Program DOE Joint Genome Institute 2800 Mitchell Drive Bldg 400-404 Walnut Creek, CA 94598 USA Danish Genome Institute Gustav Wieds vej 10 C DK-8000 Aarhus C Denmark Department of Bioinformatics Baylor University P.O. Box 97356, 1311 S. 5th St. Waco, TX 76798-7356 USA Department of Bioengineering University of California Berkeley, CA 94720 USA Departments of Biochemistry and Mathematics The University of Queensland Brisbane Qld 4072 Australia Department of Computer Science Chalmers University of Technology
Breast Cancer Risk Assessment and Level of Knowledge in Women With Low Levels of Education

Bulgular: Olgularin Gail modeliyle yapilan hesaplamasinda yuksek risk saptanmadi. Saglik Bakanligi’nin risk degerlendirme formuna gore sadece iki olguda orta risk bulundu. Duzenli olarak doktora giden ve muayene olan kadinlarin sayisi %60’in altindaydi. Kadinlarin kendi kendine muayene yapanlarin orani %67 idi. Meme kanserinin en sik goruldugunu bilenler %81 oraninda olup bilgilerin cogunlugu televizyondaki saglik programlarindandir.
Diversification in trophic morphology and a mating signal are coupled in the early stages of sympatric divergence in crossbills

Understanding the mechanisms generating diversity in mating signals is critical to understanding the process of speciation. One mechanism of mating signal diversification occurs when phenotypes that experience divergent ecological selection also affect the production of mating signals, resulting in a coupling between ecological diversification and mating signal diversification. Here, we present evidence that rapid diversification in bill size has resulted in the diversification of some components of song structure in a young adaptive radiation of seed-eating finches (red crossbill, Loxia curvirostra complex). Specifically, we find that larger-billed ecotypes sing songs with lower minimum frequencies, lower syllable repetition rates and greater vocal deviation (i.e. lower performance) than smaller-billed ecotypes for pure tonal syllables. In contrast, bill size was not correlated with maximum frequency or frequency bandwidth, and we found no relationship between bill size and any song parameters in buzzy syllables. Furthermore, we found no evidence for a relationship between the degree of bill size divergence and the potential for song discrimination between sympatric ecotypes. Because bill size is correlated with some features of pure tonal syllables (which appear to be most important for courtship in crossbills) in crossbill song, our results suggest that there was an early-evolving link between ecological and mating signal diversification that may have influenced the rapid evolution of reproductive isolation between sympatric ecotypes.