Miracle-dz/UniFAR-FTUs huggingface dataset:
Ionic Stress Induced Cytotoxic Effect of Cadmium and Nickel Ions on Roots of Allium cepa L.

The cytotoxic effects of low doses (20 to 100 μM) of nickel ions (Ni) and cadmium ions (Cd) as well as antioxidative enzyme changes in Allium cepa roots were studied. Heavy metal induced oxidative damage showed significant reduction in root length, mitotic index, total protein content and catalase (CAT) activity and increased cell abnormality index as well as proline content. Enhanced antioxidative enzyme activities were noticed to minimize oxidative stress by increasing guaiacol peroxidase (GPX) activity of the tissue. The effect of toxicity was found to be dose dependent in antioxidative enzyme level and more pronounced in root systems. Evans blue uptake by the root cells showed the cell death parameter which served as an indicator of cytotoxicity. Recovery experiments till 48 h showed significant changes in antioxidative enzyme systems of the cells reverting back to normal. Treatment of Ni and Cd led to spindle abnormalities like multipolarity, sticky bridge in anaphase, early separation, clumping of chromosomes, late separation as well as direct chromosomal damage with chromosome break, chromosome erosion, laggard chromosomes. This experiment explains the role of reactive oxygen in heavy metal toxicity and their DNA damage, cell death and adaptive responses to genotoxic challenges of the cells amelioration.
Partitioning protein ParP directly links chemotaxis to biofilm dispersal in Pseudomonas aeruginosa

The recent characterization of partitioning proteins in the localization of chemotaxis signal transduction systems was proposed to have broad implications for polarly-flagellated non-enterobacteriaceae gamma-proteobacteria. These studies showed that the loss of either partitioning protein resulted in equivalent reductions in swimming motility and chemotaxis protein localization and inheritance. However, the role of these chemotaxis partitioning proteins outside of Vibrio spp. remains untested. Our studies on the chemotaxis partitioning proteins in Pseudomonas aeruginosa revealed an unexpected role for the partitioning protein ParP. While the P. aeruginosa ParC and ParP homologs are needed for wild type swimming motility, the loss of ParP results in a greater swimming defect compared to the parC mutant. Our studies revealed that the Par-like proteins directly interact with each other and the chemotaxis system, and ParP interacts with DipA. Deletion of dipA results in a similar defect in swimming motility as the parP mutant. ParP has an interdependence for polar cluster formation, but not localization, with both CheA and DipA, and CheA cluster formation is partially dependent on ParP. Due to the direct interactions and interdependence of cluster formation of ParP and DipA, and the similar phenotypes of the parP and dipA mutants, further investigation into the role of ParP in biofilm dispersion is warranted. Importance Impaired chemotaxis protein cluster formation or inheritance reduces chemotaxis which can have an impact on of the virulence of a bacterium. In some gamma-proteobacteria there are systems in place to ensure that chemotaxis proteins, like chromosomes and plasmids, are localized for optimal chemotaxis and that daughter cells inherit their own clusters for use after cell division. Par-like proteins have been implicated in the partitioning and localization of chemotaxis proteins and the chemotactic ability of Vibrio spp. and Rhodobacter sphaeroides [1–3]. We propose that Par-like proteins can do more than localize chemotaxis proteins to the poles of the cells. In P. aeruginosa, they bring together other key proteins involved in regulating flagellar-based motility, and we propose they function as a critical link between biofilm dispersal and motility.
Neurochemical Cytoarchitecture of the Primate Parabrachial Nucleus

We describe the distribution of calbindin (CAL), cholecystokinin (CCK), dynorphin (DYN), galanin (GAL), neurotensin (NT), somatostatin (SOM), and substance P (SP) immunoreactive elements in the primate parabrachial nucleus (PbN), a pontine structure with a crucial role in autonomic control. This study follows earlier work using calcitonin gene-related peptide (CGRP) as a marker for ascending visceral pathways in the human brain (de Lacalle & Saper, 2000). Our observations were made on horizontal sections through the brainstem from four neurologically normal human individuals and five male Cebus monkeys. Tissue was processed for immunocytochemistry using commercially available antibodies. Which revealed areas of dense peptide immunoreactivity in fibers, as well as in cell bodies. The extreme expansion of the superior cerebellar peduncle has altered the topographical organization of these pathways in the primate. However, using the peduncle as a marker, we found that similarities in the distribution of cell bodies and fibers remain conserved in some areas across species. The PbN of the Cebus monkey contained well defined external lateral and external medial subnuclei. The distribution of CAL-ir , CCK-ir, NT-ir, SOM-ir, and SP-ir elements were very similar in the human and monkey for the external lateral and external medial subnuclei, and DYN-ir elements were found in the external lateral PbN only in both species. GAL-ir elements were present in the central lateral PbN and dorsal medial PbN areas in both species. Our results contribute to define a neurochemical identity for different regions in the primate PbN, thus providing support to the delineation of physiological roles for
Seasonality and species composition of Peristenus (Hymenoptera: Braconidae) species, and Lygus (Hemiptera: Miridae) species parasitism in southern Alberta, Canada

ABSTRACT We report a long-term survey summarising the seasonal variation in species composition of Peristenus species, and their levels of parasitism in an assemblage of Lygus spp. , over more than 10 years in southern Alberta in western Canada. Plants sampled include alfalfa (Medicago sativa L.), canola (Brassica napus L.), and stands of different weed and grass species commonly found on crop field edges. Three native Peristenus species (Peristenus dayi, Peristenus mellipes, and Peristenus howardi) were recorded in 2003–2011 and 2013–2015. In laboratory trials, P. mellipes emerged 13 days earlier than P. howardi. Degree-days for field-collected individuals suggested a sequential occurrence during the growing season: P. dayi appears early in the season, followed by P. mellipes, and later on by P. howardi. Studies of species composition and phenology of native parasitoids of insect pests provide valuable baseline information when considering introduction of exotic agents, and contribute to the management and improvement of conservation biological control by endemic natural enemies in agricultural systems.
Ecological genetic conflict between specialism and plasticity through genomic islands of divergence

There can be genetic conflict between genome elements differing in transmission patterns, and thus in evolutionary interests. We show here that the concept of genetic conflict provides new insight into local adaptation and phenotypic plasticity. Local adaptation to heterogeneous habitats sometimes occurs as tightly linked clusters of genes with among-habitat polymorphism, referred to as genomic islands of divergence, and our work sheds light on their evolution. Phenotypic plasticity can also influence the divergence between ecotypes, through developmental responses to habitat-specificcues. We show that clustered genes coding for ecological specialism and unlinked generalist genes coding for phenotypic plasticity differ in their evolutionary interest. This is an ecological genetic conflict, operating between habitat specialism and phenotypically plastic generalism. The phenomenon occurs both for single traits and for syndromes of co-adapted traits. Using individual-based simulations and numerical analysis, we investigate how among-habitat genetic polymorphism and phenotypic plasticity depend on genetic architecture. We show that for plasticity genes that are unlinked to a genomic island of divergence, the slope of a reaction norm will be steeper in comparison with the slope favored by plasticity genes that are tightly linked to genes for local adaptation.
Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California

Microbial communities control numerous biogeochemical processes critical for ecosystem function and health, particularly in coastal ecosystems. However, comparatively little is known about microbial community structure in coastal regions, such that basic patterns of microbial biodiversity, such as species richness and community composition, are generally understudied. To better understand the global patterns of microbial biodiversity in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites near Puerto Nuevo (Baja California, Mexico) using 16S and 18S rRNA gene amplicon sequencing methods. We found that sediment bacteria, archaea, and eukaryote microbial communities contained approximately 5 × 10^2 fold greater operational taxonomic units (OTUs) than their seawater-based counterparts (p < 0.001). Further, distinct bacterial, archaeal and eukaryal phyla were found in sediment and seawater samples. The phyla Acidobacteria, Chlorobi, and Chloroflexi were found to be abundant and unique to the sediment and Cyanobacteria, Spirochaetae, and Woesearchaeota to the seawater environment. Apicomplexa and Arthropoda were abundant eukaryal phyla found uniquely in the sediment whereas the Cryptomonadales and Protalveolata were detected only in the seawater. Furthermore, bacterial and archaeal communities were statistically different by site (p < 0.05) in both seawater and sediment samples for the Major Outlet site, the site closest to a residential area. In contrast, eukaryal microbial communities were only different among sites in the seawater samples. Overall, these results suggest that our understanding of coastal microbial biodiversity patterns require spatially robust sampling. This study contributes to a growing body of foundational microbial biodiversity and ecology knowledge, providing context to the global change that is induced by urban development.
Citizen science: how high school students can provide scientifically sound data in biogeochemical experiments

Citizen science has proved acutely useful in collecting vast amounts of environmental data at large spatial and temporal scales. However, evidence on successful experimental approaches with citizen scientist involvement is still scarce. We demonstrate that collaborations with high school students in biogeochemical experiments may generate robust and reliable data for scientific analyses. Within an Austrian research-education-cooperation dealing with landuse effects on stream processes, we performed laboratory experiments on P adsorption capacities of stream sediments together with high school students. The students were involved in every step of the procedure, from the planning of the study design to the interpretation of the results. Data quality was checked via comparisons of coefficients of variation among replicates and R2 values of adsorption curves performed by students and scientists. Data generated by students did not differ significantly from those of professionals regarding both absolute values and variability among replicates. Based on our experiences, we discuss preconditions, restrictions, and advantages of collaborating with high school students in scientific laboratory experiments.
Development of an assay for vitamin D in biological samples

II DECLARATION BY AUTHOR . V PUBLICATIONS DURING CANDIDATURE . VI PUBLICATIONS INCLUDED IN THIS THESIS . VII CONTRIBUTIONS BY OTHERS TO THE THESIS . IX STATEMENT OF PARTS OF THE THESIS SUBMITTED TO QUALIFY FOR THE AWARD OF ANOTHER DEGREE . IX RESEARCH INVOLVING HUMAN OR ANIMAL SUBJECTS . X ACKNOWLEDGEMENTS . XI FINANCIAL SUPPORT . XII
Plant competition alters the temporal dynamics of plant‐soil feedbacks

Most studies on plant‐soil feedback (PSF) and plant competition measure the feedback response at one moment only. However, PSFs and competition may both change over time, and how PSF and competition interact over time is unclear. We tested the temporal dynamics of PSF and interspecific competition for the forb Jacobaea vulgaris and the grass Holcus lanatus. We grew both species individually and in interspecific competition in soil that was first conditioned in the greenhouse by J. vulgaris, by H. lanatus or without plant growth. For a period of 11 weeks, we harvested plants twice a week and analysed the fungal and chemical composition of the different soils at the end of the first and second growth phase. During the second growth phase, when grown in isolation, both species produced more biomass in heterospecific conditioned soil than in conspecific conditioned soil. Young J. vulgaris exhibited a strong negative conspecific feedback, but this effect diminished over time and became neutral in older plants. In contrast, when grown in competition, the negative conspecific feedback of J. vulgaris exacerbated over time. Older H. lanatus plants benefited more from heterospecific conditioning when competing with J. vulgaris, then when grown isolated. Fungal community composition and soil chemistry differed significantly between soils but this was mainly driven by differences between plant‐conditioned and unconditioned soils. Remarkably, at the end of the second growth phase, fungal community composition was not explained by the legacy of the species that had been grown in the soil most recently, but still reflected the legacy of the first growth phase. We reexamined plant growth during a third growth phase. Biomass of J. vulgaris was still influenced by the treatments imposed during the first phase, while H. lanatus responded only to the plant growth treatments imposed during the second phase. Synthesis. Our study shows that the direction and magnitude of PSF depends on plant age and competition, and also on soil legacy effects of earlier plant growth. These results highlight the need to incorporate dynamic PSFs in research on plant populations and communities.
Development and characterization of thirty-two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing

The anchovy, Engraulis ringens , is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele’s presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management.
Next-generation sequencing reveals the diversity of benthic diatoms in tidal flats

Copyright © 2018 The Korean Society of Phycology 167 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 Next-generation sequencing reveals the diversity of benthic diatoms in tidal flats Sung Min An, Dong Han Choi, Howon Lee, Jung Ho Lee and Jae Hoon Noh* Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Busan 49111, Korea Department of Marine Biology, University of Science and Technology, Daejeon 34113, Korea Department of Biology Education, Daegu University, Gyeongsan 38453, Korea
Genome-wide analysis of H3K4me3 and H3K27me3 modifications throughout the mouse urogenital ridge at E11.5

In mammals, the adrenal gland, testis and ovary arise from a common progenitor tissue known as the urogenital ridge (UGR). This small population of cells will adopt a number of different cell fates following sex determination, including forming the precursors of somatic cells (such as Sertoli and granulosa cells) and steroidogenic cells. In addition, this tissues also contains the Wolffian and Müllerian ducts that later form components of the reproductive tracts. A potential mechanism to maintain developmental plasticity of the UGR until gonad formation is through the epigenetic modification of histone proteins. In order to provide a resource for future studies, we used chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) for two histone modifications, H3K4me3 and H3K27me3, in the E11.5 mouse UGR. These marks are both known to reflect the active, repressive or a poised chromatin state. We found that enrichment for each histone mark reflected transcriptional activity in precursor cells of the developing gonad. From the analysis of potential enhancer/regulator peak regions for DNA binding motifs, we identified several candidate transcription factors that may contribute to gonadal cell lineage specification. We additionally identified signaling pathway genes that are targeted by both chromatin modifications. Together, these datasets provide a useful resource for investigating gene regulatory networks functioning during UGR development at E11.5.
The unexpected provenance of components in eukaryotic nucleotide-excision-repair and kinetoplast DNA-dynamics from bacterial mobile elements

Background Protein ‘weaponry’ deployed in biological conflicts between selfish elements and their hosts are increasingly recognized as being re-purposed for diverse molecular adaptations in the evolution of several uniquely eukaryotic systems. The anti-restriction protein ArdC, transmitted along with the DNA during invasion, is one such factor deployed by plasmids and conjugative transposons against their bacterial hosts. Results Using sensitive computational methods we unify the N-terminal single-stranded DNA-binding domain of ArdC (ArdC-N) with the DNA-binding domains of the nucleotide excision repair (NER) XPC/Rad4 protein and Trypanosoma Tc-38 (p38) protein implicated in kinetoplast(k) DNA replication and dynamics. We show that the ArdC-N domain was independently acquired twice by eukaryotes from bacterial mobile elements. One gave rise to the ‘beta-hairpin domains’ of XPC/Rad4 and the other to the Tc-38-like proteins in the stem kinetoplastid. Eukaryotic ArdC-N domains underwent tandem duplications to form an extensive DNA-binding interface. In XPC/Rad4, the ArdC-N domain combined with the inactive transglutaminase domain of a peptide-N-glycanase originally derived from an active archaeal version, often incorporated in systems countering invasive DNA. We also show that parallel acquisitions from conjugative elements and bacteriophages gave rise to the Topoisomerase IA, DNA polymerases IB-Ds, and DNA ligases involved in kDNA dynamics. Conclusions We resolve two outstanding questions in eukaryote-biology: 1) origin of the unique DNA lesion-recognition component of NER; 2) origin of the unusual, plasmid-like features of kDNA. These represent a more general trend in the origin of distinctive components of systems involved in DNA dynamics and their links to the ubiquitin system.
Leveraging mutational burden for complex trait prediction in sorghum

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. Though selection keeps deleterious mutations rare, their complete removal from the genome is impeded due to lack of recombination, drift, and their coupling with favorable loci. To study how deleterious mutations impact agronomic phenotypes, we identified putative deleterious mutations among ~5.5M segregating variants of 229 diverse sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that about 33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups; the caudatum shows higher mutation burden while the guinea has lower burden. Across racial groups, the mutation burden correlated negatively with biomass, plant height, Specific Leaf Area (SLA), and tissue starch content, suggesting deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (5.2%). There is no advantage in total heritable variance for SLA and starch. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, our results suggest that including putatively deleterious variants in models do not significantly improve breeding accuracy because of extensive linkage. However, knowledge of deleterious variants could be leveraged for sorghum breeding through genome editing.
Characterization of Neurospora mitochondrial group I introns and the function of tyrosyl-tRNA synthetase in RNA splicing /

Previous studies showed that the Neurospora crassa mitochondrial LSU intron is not self-splicing and is dependent on the mitochondrial tyrosyl-tRNA synthetase (CYT18 protein) for splicing in vitro and in vivo. Here, a comprehensive study of the remaining N. crassa mtDNA group I introns identified two additional introns, cob-12 and the NDl-11, that are completely dependent on CYT-18 for splicing. The other seven introns are not dependent on CYT18 and include five that self-splice and two that do not splice under any conditions examined. None of these seven introns bind CYT-18 in vitro. Six of the introns that do not bind CYT-18 contain large peripheral extensions of the P5 stem that has been show to block CYT-18 binding. Conversely, the J6/6a region in the CYT-18-dependent introns was shown to be an important region for CYT-18 binding. The CYT-18-dependent NDl intron contains a proximal, alternative 3' splice site near the N-terminus of the intron ORF. The use of this 3' splice site brings the intron ORF inframe with the upstream exon and may be the means by which the open reading frame is expressed, and thus conferring mobility to the NDl intron. A 196 nt mini-derivative of the