Miracle-dz/UniFAR-FTUs huggingface dataset:
Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

Abstract This study is the first large‐scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4–26°S and 33–48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale—across national borders.
Discrimination of Tomato Plants (Solanum lycopersicum) Grown under Anaerobic Baffled Reactor Effluent, Nitrified Urine Concentrates and Commercial Hydroponic Fertilizer Regimes Using Simulated Sensor Spectral Settings

We assess the discriminative strength of three different satellite spectral settings (HyspIRI, the forthcoming Landsat 9 and Sentinel 2-MSI), in mapping tomato (Solanum lycopersicum Linnaeus) plants grown under hydroponic system, using human-excreta derived materials (HEDM), namely, anaerobic baffled reactor (ABR) effluent and nitrified urine concentrate (NUC) and commercial hydroponic fertilizer mix (CHFM) as main sources of nutrients. Simulated spectral settings of HyspIRI, Landsat 9 and Sentinel 2-MSI were resampled from spectrometric proximally sensed data. Discriminant analysis (DA) was applied in discriminating tomatoes grown under these different nutrient sources. Results showed that the simulated spectral settings of HyspIRI sensor better discriminate tomatoes grown under different fertilizer regimes when compared to Landsat 9 OLI and Sentinel-2 MSI spectral configurations. Using the DA algorithm, HyspIRI exhibited high overall accuracy (OA) of 0.99 and a kappa statistic of 0.99 whereas Landsat OLI and Sentinel-2 MSI exhibited OA of 0.94 and 0.95 and 0.79 and 0.85 kappa statistics, respectively. Simulated HyspIRI wavebands 710, 720, 690, 840, 1370 and 2110 nm, Sentinel 2-MSI bands 7 (783 nm), 6 (740 nm), 5 (705 nm) and 8a (865 nm) as well as Landsat bands 5 (865 nm), 6 (1610 nm), 7 (2200 nm) and 8 (590 nm), in order of importance, were selected as the most suitable bands for discriminating tomatoes grown under different fertilizer regimes. Overall, the performance of simulated HyspIRI, Landsat 9 OLI-2 and Sentinel-2 MSI spectral bands seem to bring new opportunities for crop monitoring.
Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars

Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
Even obligate symbioses show signs of ecological contingency: Impacts of symbiosis for an invasive stinkbug are mediated by host plant context

Abstract Many species interactions are dependent on environmental context, yet the benefits of obligate, mutualistic microbial symbioses to their hosts are typically assumed to be universal across environments. We directly tested this assumption, focusing on the symbiosis between the sap‐feeding insect Megacopta cribraria and its primary bacterial symbiont Candidatus Ishikawaella capsulata. We assessed host development time, survival, and body size in the presence and absence of the symbiont on two alternative host plants and in the insects' new invasive range. We found that association with the symbiont was critical for host survival to adulthood when reared on either host plant, with few individuals surviving in the absence of symbiosis. Developmental differences between hosts with and without microbial symbionts, however, were mediated by the host plants on which the insects were reared. Our results support the hypothesis that benefits associated with this host–microbe interaction are environmentally contingent, though given that few individuals survive to adulthood without their symbionts, this may have minimal impact on ecological dynamics and current evolutionary trajectories of these partners. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.kg4bc56
CHAPTER 14. The Piscine Erythrocyte Micronucleus Cytome Assay

Technological advancements introduce several genotoxic chemicals that adversely affect the health status of aquatic organisms and may eventually pose a risk to human health via the contaminated food chain. Biomarkers of genotoxicity such as micronuclei (MN) and other nuclear abnormalities can be measured by the erythrocyte micronucleus assay, a relatively simple technique that is highly useful in assessing the health conditions of biota and their surrounding ecosystems. This chapter briefly describes the micronucleus assay in fish and highlights DNA damage detection using this method under laboratory and in situ conditions. Plausible mechanisms of the formation of nuclear and cytoplasmic abnormalities upon exposure to mutagenic agents, literature evidence on the occurrence of MN and other cellular abnormalities and a simplified protocol for conducting the assay in fish peripheral erythrocytes are also described. Ample evidence for renaming the assay as the erythrocyte MN cytome assay (EMNCA) are presented based on the advantage of measuring MN together with other nuclear anomalies in identifying biomarker profiles specific to physical and chemical genotoxin exposures in fish.
Mutational Crosstalk between Nuclear Driver Genes and Mitochondrial DNA in Gingivobuccal Oral Cancer

Somatic alterations in nuclear and mitochondrial genomes are known to play important role in the initiation and progress of tumours. However, crosstalk between these two genomic components in tumours have not been well investigated till date. We have excavated evidence of such crosstalk in gingivobuccal oral cancer. We have identified significant correlation between somatic mutations in nuclear driver genes and mitochondrial genes in 89 gingivobuccal oral cancer patients. Strong positive correlation between nuclear driver genes CASP8, NOTCH1, USP9X, TRPM3 and mitochondrial genes has been observed. Patients having mutations in nuclear driver genes except TP53, were also shown to harbour higher mitochondrial mutation load. TP53 mutations were shown to be negatively correlated with somatic mutations in mitochondrial 12S rRNA and ATP6. Also, TP53 mutations were negatively correlated with mutations in NOTCH1, HRAS and USP9X. We have identified a number of nuclear genes coexpressed with mitochondrial genes, although their association with tumorigenesis could not be established. Our observations suggest that in the absence of mutations in TP53, mutations in mtDNA and other driver genes might aid in the progression of cancer in a complementary fashion.
Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC

Achieving reproducible, stable, and high-level transgene expression in mammalian cells remains problematic. Previously, we attained copy-number-dependent, chromosome-position-independent expression of reporter minigenes by embedding them within a BAC containing the mouse Msh3-Dhfr locus (DHFR BAC). Here we extend this “BAC TG-EMBED” approach. First, we report a toolkit of endogenous promoters capable of driving transgene expression over a 0.01-5 fold expression range relative to the CMV promoter, allowing fine-tuning of relative expression levels of multiple reporter genes expressed on a single BAC. Second, we show small variability in both the expression level and long-term expression stability of a reporter gene embedded in BACs containing either transcriptionally active or inactive genomic regions, making choice of BACs more flexible. Third, we describe an intriguing phenomenon in which BAC transgenes are maintained as episomes in a large fraction of stably selected clones. Finally, we demonstrate the utility of BAC TG-EMBED by simultaneously labeling three nuclear compartments in 94% of stable clones using a multi-reporter DHFR BAC, constructed with a combination of synthetic biology and BAC recombineering tools. Our extended BAC TG-EMBED method provides a versatile platform for achieving reproducible, stable simultaneous expression of multiple transgenes maintained either as episomes or stably integrated copies.
The Quantification of Antibody Elements and Receptors subunit expression using qPCR: The Design of VH, VL, CH, CL, FcR subunits primers for a more holistic view of the immune system

The expression levels of Immunoglobulin elements and their receptors are important markers for health and disease. Within the immunoglobulin locus, the constant regions and the variable region families are associated with certain pathologies, yet a holistic view of the interaction between the expression of the multiple genes remain to be fully characterized. There is thus an important need to quantify antibody elements, their receptors and the receptor subunits in blood (PBMC cDNA) for both screening and detailed studies of such associations. Leveraging on qPCR, we designed primers for all Vκ 1-6, VH1-7, Vλ1-11, nine CH isotypes, Cκ, Cκ, Cλ1 &3, FcεRI α,β, and γ subunits, all three FcγR and their subunits, and FcαR. Validating this on a volunteer PBMC cDNA, we show a qPCR primer set repertoire that can quantify the relative expression of all the above genes to GAPDH housekeeping gene, with implications and uses in both clinical monitoring and research.
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics

The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. The HPO is frequently used to create a set of terms that accurately describe the observed clinical abnormalities of an individual being evaluated for suspected rare genetic disease. This profile is compared with computational disease profiles in the HPO database with the aim of identifying genetic diseases with comparable phenotypic profiles. The computational analysis can be coupled with the analysis of whole‐exome or whole‐genome sequencing data through applications such as Exomiser. This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc.
Result Analysis of Efficient MIMO Framework for NOMA Downlink and Uplink Transmission based on Signal Alignment

In this paper, we aim to combine the schemes of multiuser applied in multiple-input multiple-output (MIMO) scheme with NOMA downlink communication systems. As multiple techniques can achieve multi-stream beam-forming coding diversity, the use of MIMO techniques brings flexible dimension for performance improvements. On the other hand, based on zero-forcing (ZF) technique, low complexity linear precoding scheme can reduce inter-interference when channel transmission. In particular, aiming to significantly enhance spectrum efficiency, we need to tackle the interference issue, which is exacerbated in heterogeneous network due to ultra dense node deployment as well as heterogeneity nature of various nodes. Specifically, we first study an optimal intra-cell inter-tier cooperation to mitigate interference between high power nodes and low power nodes.
Functional divergence of two duplicated Fertilization Independent Endosperm genes in rice with respect to seed development

Fertilization Independent Endosperm (FIE) is an essential member of Polycomb Repression Complex 2 (PRC2) that plays important roles in the developmental regulation of plants. OsFIE1 and OsFIE2 are two FIE homologs in the rice genome. Here, we showed that OsFIE1 probably duplicated from OsFIE2 after the origin of the tribe Oryzeae, but has a specific expression pattern and methylation landscape. During evolution, OsFIE1 underwent a less intensive purifying selection than did OsFIE2. The mutant osfie1 produced smaller seeds and displayed reduced dormancy, indicating that OsFIE1 predominantly functions in late seed development. Ectopic expression of OsFIE1, but not OsFIE2, was deleterious to vegetative growth in a dosage-dependent manner. The newly evolved N-terminal tail of OsFIE1 was probably not the cause of the adverse effects on vegetative growth. The CRISPR/Cas9-derived mutant osfie2 exhibited impaired cellularization of the endosperm, which suggested that OsFIE2 is indispensable for early seed development as a positive regulator of cellularization. Autonomous endosperm was observed in both OsFIE2+− and osfie1/OsFIE2+− but at a very low frequency. Although OsFIE1-PRC2 exhibited H3K27me3 methyltransferase ability in plants, OsFIE1-PRC2 is likely to be less important for development in rice than is OsFIE2-PRC2. Our findings revealed the functional divergence of OsFIE1 and OsFIE2 and shed light on their distinct evolution following duplication.
The complete chloroplast genome of Paeonia lactiflora Pall. (Paeoniaceae)

Abstract The complete chloroplast genome sequence of Paeonia lactiflora was obtained by de novo assembly using next-generation sequencing. The circular molecule of the genome constituted of four parts, with 152,731 bp in the complete chloroplast genome, including a large single-copy (LSC) region of 84,402 bp, a small single-copy (SSC) region of 16,969 bp, and two inverted repeat (IRa and IRb) regions of 25,680 bp each. The genome annotation predicted a total of 111 genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis showed the close taxonomical relationship to P. veitchii.
The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae)

Abstract The complete mitogenome of Japalura splendida (16,673 bp in length) is determined and analyzed in this study. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding regions. All the genes in J. splendida are distributed on the H-strand, except for the ND6 gene and seven tRNA genes which are encoded on the L-strand. The phylogenetic tree suggests that J. splendida and Japalura flaviceps formed a sister group and reveals the order ((((Acanthosaura lepidogaster, Acanthosaura armata), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with substantial support for the monophyly.
Contrast invariant tuning in human perception of image content

Higher levels of visual processing are progressively more invariant to low-level visual factors such as contrast. Although this invariance trend has been well documented for simple stimuli like gratings and lines, it is difficult to characterize such invariances in images with naturalistic complexity. Here, we use a generative image model based on a hierarchy of learned visual features—a Generative Adversarial Network—to constrain image manipulations to remain within the vicinity of the manifold of natural images. This allows us to quantitatively characterize visual discrimination behaviour for naturalistically complex, non-linear image manipulations. We find that human tuning to such manipulations has a factorial structure. The first factor governs image contrast with discrimination thresholds following a power law with an exponent between 0.5 and 0.6, similar to contrast discrimination performance for simpler stimuli. A second factor governs image content with approximately constant discrimination thresholds throughout the range of images studied. These results support the idea that human perception factors out image contrast relatively early on, allowing later stages of processing to extract higher level image features in a stable and robust way.
Investigation of Virus Diseases and Molecular Detection of Little Cherry Virus 1 on Cherry Plants at Niğde Province

To investigate the virus infections of sour and sweet cherries, various locations of Niğde province were examined during 2017. Ninety sweet and sour cherry leaf samples showing suspicious virus symptoms were collected and screened with virus-specific primers: Little cherry virus 1 (LChV1), Cherry necrotic rusty mottle virus (CNRMV), Prune dwarf virus (PDV), Prune necrotic ring spot virus (PNRSV), Apple mosaic virus (ApMV), Cherry green ring mottle virus (CGRMV), Cherry leaf roll virus (CLRV), Cherry mottle leaf virus (CMLV), Plum bark necrotic stem pitting associated virus (PBNSPaV), Cherry twisted leaf virus (CTLV), Apple stem grooving virus (ASGV), Little cherry virus 2 (LChV2), Cherry rusty leaf virus (CRLV), Apple stem pitting virus (ASPV), Apple chlorotic leaf spot virus (ACLSV). Based on RT-PCR analysis, no amplification was observed except LChV1 amplifications, dsRNA analysis resulted in one suspicious profile. To validate those results, more sensitive TaqMan Real-Time PCR analysis and sequence analysis were conducted and LChV1 was detected on 7 samples. It can be concluded that only a low quantity of LChV1 infections was observed on some of the screened cherry samples.
Complete chloroplast genome of the plant Stahlianthus Involucratus (Zingiberaceae)

Abstract The first complete chloroplast genome of Stahlianthus involucratus (Zingiberaceae) was reported in this study. The S. involucratus chloroplast genome was 163,300 bp in length and consisted of one large single copy (LSC) region of 87,498 bp, one small single copy (SSC) region of 15,568 bp, and a pair of inverted repeat (IR) regions 30,117 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species) and 8 rRNA genes (4 rRNA species). The phylogenetic analysis based on single nucleotide polymorphisms strongly supported that S. involucratus, Curcuma roscoeana and Curcuma longa formed a cluster in group CurcumaII within family Zingiberaceae.
New records of nine ciliates (Protozoa: Ciliophora) from Korea: Brief descriptions and remarks

Since the study of Korean ciliates began, around 420 species have been reported in South Korea (Dovgal and Pešić, 2014; Jung et al., 2017b; Kim and Jung, 2018; Park et al., 2017). This number constitutes only about 10% of the total number of free-living ciliate species estimated worldwide in 2008 (Foissner, 2008). Thus, many Korean species are likely still awaiting discovery. From a project to discover Korean indigenous species, we identified nine previously unrecorded ciliate species from South Korea. Herein we provide and morphological descriptions of these nine species.
Live cell kinetic analysis of the LMO2/LDB1 leukemogenic protein complex reveals a hierarchy of turnover with implications for complex assembly

Multisubunit protein complexes operate in many cellular functions. The LMO2/LDB1 macromolecular complex has been posited to be critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as bHLH and GATA transcription factors. We analyzed the steady state abundance and kinetic stability of LMO2 and its partners via Halo protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stability, with half lives in descending order: LDB1>SSBP>LMO2>TAL1. Importantly, LDB1’s turnover was markedly prolonged and LDB1 conferred enhanced stability upon each and every subunit component thereby nucleating the formation of the multisubunit protein complex. Our studies provide significant insights into LMO2/LDB1 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.