Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Variability Assessment of Sorghum (Sorghum bicolor (L.) Moench) Germplasm Accessions using Qualitative Morphological Descriptors

Sorghum (Sorghum bicolor (L.) Moench) is considered as the fifth most important cereal crop in the world. It is well adapted to a range of environmental conditions. This study was based on twenty six sorghum germplasm accessions conserved at the seed gene bank of Plant Genetic Resource Center, Gannoruwa, Sri Lanka. The evaluation of the morphological diversity was based on 14 qualitative morphological traits outlined by the International Plant Genetic Resources Institute. Qualitative data recorded from morphological traits were analyzed using PROC CLUSTER procedure of SAS software. The clustering pattern of studied sorghum accessions based on qualitative morphological markers comprised of seven major clusters. Clustering pattern based on the qualitative traits depicts the geographical origin of the studied accessions. This can be explained by the fact that qualitative traits are less influenced by the environment. In principle, qualitative data are expected to provide additional information on hierarchical units. Observation of a considerably high number of clusters consolidates that principle. There were 13 polymorphic qualitative morphological traits with respect to all the studied sorghum germplasm accessions. Cluster I, II, III, IV, V and VI had one or several features shared by all the member accessions those cannot be found in all the members of any other clusters. Also there were unique features restricted to cluster II, III, V and VI. This study reveals sufficient genetic relatedness of studied sorghum germplasm accessions which will meaningful in the conservation and breeding programs of the crops.
The feedstock microbiome selectively steers process stability during the anaerobic digestion of waste activated sludge

Strategies to enhance process performance of anaerobic digestion remain of key importance to achieve further spreading of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e., organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process performance of the digesters fed sterile WAS, with a 92 ± 45 % decrease in methane production, compared to a 42 ± 31 % increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process performance between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L−1. Feedstock sterilisation strongly impacted the microbial community in the digesters. In conclusion, feedstock inoculation can be considered a cheap, yet, disturbance-specific strategy to enhance process stability in full-scale anaerobic digestion processes.
Comparative and Population Genomics of Host-Pathogen Co-Evolution in Birds

Infectious disease produces some of the strongest selective forces on natural populations across the tree of life. The signatures of pathogen-­‐mediated evolution on host genomes have been described for several traditional model organisms, but few studies of more diverse organisms have detected such signatures beyond candidate immune loci. In my dissertation, I combine population and comparative genomics to study the dynamics of pathogen-­‐mediated selection at two evolutionary timescales in wild bird populations. In Chapters 1 and 2, I integrate geographic and temporal sampling to compare the impacts on genomic variability of recent founder events and an epizootic on the House Finch (Haeomorhous mexicanus). House Finches, native to the western US and Mexico, were introduced to the Hawaiian Islands in 1870 and separately to the eastern US in 1940. In 1994, Mycoplasma gallisepticum (MG), previously associated with poultry, jumped to House Finches and caused severe declines. In Chapter 1, I genotype ~2,000 loci in samples collected before and 10 years after the epizootic. I demonstrate that demographic shifts brought about by the founder events have much more profound genomic impacts than pathogen-­‐mediated natural selection. In Chapter 2, I use whole-­‐genome resequencing data in six House Finch populations from three time points. I show that the expansion of the western US population following the last glacial maximum had the largest impact on
Taxonomic status of the extinct Canary Islands Oystercatcher
 Haematopus meadewaldoi

TS performed this work as part of her MSc (Genetics) at University of Aberdeen. TJS is supported by PhD funding from The Sound Approach. DMP's research forms part of the Oystercatcher Conservation Programme and was supported by the National Research Foundation and the University of Cape Town. We thank curatorial staff, Tony Parker at the World Museum, Liverpool and Henry McGhie at Manchester Museum. We thank Amy Bastow for securing material from Eurasian Oystercatcher and Lucie Goodayle for photography of NHM oystercatcher specimen. EST was funded by the Canadian Barcode of Life Network, and ROM Governor’s Fund.
Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates

The culture of pelagic marine invertebrates, especially the ctenophore Mnemiopsis leidyi, has been demonstrated in past studies dating back to the 1960’s, however the mass culture of delicate pelagic invertebrates has remained elusive. By using a pair of acrylic tubes and enabling water diffusion between them, we have been able to reliably and cost effectively mass culture several genera of ctenophores (Pleurobrachia, Hormiphora, Bolinopsis, Mnemiopsis, and Leucothea), one species of siphonophore (Nanomia) and one species of larvacean (Oikopleura). The simple, compact method is effective enough to support two permanent exhibits of ctenophores at the Monterey Bay Aquarium while minimizing live food culture requirements with the potential to support further investigation of pelagic marine invertebrate ontogeny, ecology and genomics.
BioCyc: Online Resource for Genome and Metabolic Pathway Analysis

BioCyc.org is a genomic resource that contains more than 7600 Pathway/Genome Databases (PGDBs) for organisms whose genomes have been completely sequenced. Although most PGDBs are bacterial, PGDBs exist for key experimental organisms, including humans (HumanCyc), yeast (YeastCyc), and Arabidopsis (AraCyc).
Detoured flight direction responses along the southwest coast of Lake Erie by night-migrating birds

ABSTRACT Migratory birds encounter the Great Lakes while moving through eastern North America toward breeding grounds to the North, which offers a good opportunity to study variation in migratory behavior as birds face a potentially influencing topographical feature. Using passive infrared technology, we documented the direction of relatively low-flying, nocturnal, mostly passerine migration in spring along the southern coast of Lake Erie's western basin. We examined the extent to which spring migrants flew across Lake Erie as a continuation of the inland, northeasterly broad front migratory direction, as determined by weather radar and infrared observations, or displayed a tendency to deviate to more closely follow the direction of the coastline. We found that an estimated 62% of all low-flying migrants deviated their flight directions toward the coast of Lake Erie at 2 coastal sites, Cedar Point and Ottawa, which were characterized by northwest–southeast oriented coastlines. Migrants at a third coastal location, Maumee Bay, which has a more east–west oriented coastline, did not display similarly deviated flight directions. We found that even when winds were energetically favorable for a lake crossing, many migrants still routinely displayed deviated flight directions that approached paralleling the coastline. Further, the mean flight direction at one site, Ottawa, shifted more in the direction of the coastline as the night progressed, suggesting that time of night could influence the shift to a more coastal flight direction. The data indicate that the western basin of Lake Erie acts as a salient topographical feature influencing the flight directions of nocturnal migrants. The data further suggest that birds are making active decisions while in flight, based on current environmental and physiological conditions, about whether to continue to cross Lake Erie or take a coastal detour.
Sterol regulatory element binding protein and Sp1 is required for transcriptional activation of a freshwater carnivorous fish (Channa striata) elovl5 elongase

Long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis involves the activities of two groups of enzymes, the fatty acyl desaturases (Fads) and elongases of very long-chain fatty acid (Elovl). Fish are major source of beneficial n-3 LC-PUFA in human diet and there is a considerable interest to elucidate the mechanism and regulatory aspects of LC-PUFA biosynthesis in farmed fish species. The promoter of elovl5 elongase, which catalyze the rate limiting reaction of adding two carbons to the C18 PUFA have been previously described and characterized from several marine and diadromous teleost species. We report here the cloning and characterization of the elovl5 promoter from two freshwater fish species, the carnivorous snakehead fish (Channa striata) and zebrafish. Results show the importance of sterol regulatory element binding protein (Srebp) and the corresponding sterol responsive element (SRE) in the core regulatory region of both promoters. Mutagenesis luciferase and electrophoretic mobility shift assays confirm that SRE is indispensable for basal transcriptional activation in both species. In addition, several Sp1 binding sites located in close proximity with SRE were present in the snakehead promoter, with one having a potential synergy with SRE in regulating elovl5 expression. The core elovl5 promoter fragments of both species also directed in vivo expression in the yolk syncytial layer of developing zebrafish embryos. This study is the first functional promoter analysis of Elovl5 in freshwater teleost.
Resurrection of the sea pen genus Ptilella Gray, 1870 and description of Ptilella grayi n. sp. from the NE Atlantic (Octocorallia: Pennatulacea)

The order Pennatulacea covers a group of specialized and morphologically distinct octocorals found in all oceans from intertidal areas to more than 6000 m in depth. Sea pens constitute an important structural component in marine soft-bottom communities by increasing the complexity of these environments. Despite being both morphologically distinctive and ecologically important, the taxonomy and systematics of sea pens is still poorly understood. Recent molecular studies have shown the existence of convergent morphological features, making the current familial distribution of genera unstable. The genus Pennatula Linnaeus, 1758 was one of the first described octocoral genera. It is the type genus of its family, Pennatulidae. Colonies of this genus have a characteristic morphology. Recent sampling efforts in the northeastern Atlantic have provided a number of colonies initially attributable to the genus Pennatula. Both morphological and molecular (mtMutS, Cox1 and 28S genes) study of this material supports the polyphyletic nature of this genus and the need to resurrect the genus Ptilella Gray, 1870 to accommodate these and other species. A new species, Ptilella grayi n. sp. , is described and illustrated. The species Pennatula bayeri is proposed to be a junior synonym of Pennatula bellissima (here also considered in the genus Ptilella).
The periphery and the core properties explain the omnigenic model in the human interactome

Understanding the connectivity patterns of genes in a localized disease neighborhood or disease module in a molecular interaction network (interactome) is a key step toward advancing the knowledge about molecular mechanisms underlying a complex disease. In this work, we introduce a framework that detects peripheral and core regions of a disease in the human interactome. We leverage gene expression data on 104 diseases and analyze the connectivity of differentially expressed genes (quantified by a p-value < 0.05) and their topological membership in the network to distinguish between peripheral and core genes. Per definition, peripheral and core genes are topologically different and we show that they also differ biologically. Core genes are more enriched for Genome-wide association study (GWAS) and Online Mendelian Inheritance in Man (OMIM) data, whereas peripheral genes are more shared across different disease states and their overlap helps predict disease proximity in the human interactome. Based on this observation, we propose a flower model to explain the organization of genes in the human interactome, with core genes of different diseases as the petals and the peripheral genes as the (shared) stem. We show that this network model is an important step towards finding novel drug targets and improving disease classification. Overall, we were able to demonstrate how perturbations percolate through the human interactome and contribute to peripheral and core regions, an important novel feature of the omnigenic model.
Interactive Effects of Subsidiary Crops and Weed Pressure in the Transition Period to Non-Inversion Tillage, A Case Study of Six Sites Across Northern and Central Europe

Reducing soil tillage can lead to many benefits, but this practice often increases weed abundance and thus the need for herbicides, especially during the transition phase from inversion tillage to non-inversion tillage. We evaluated if subsidiary crops (SCs, e.g., cover crops) can mitigate the effects of non-inversion tillage on weed abundance. Two-year experiments studying SC use, tillage intensity, and nitrogen (N) fertilization level were carried out twice at six sites throughout northern and central Europe. SCs significantly reduced weed cover throughout the intercrop period (−55% to −1% depending on site), but only slightly during the main crops. Overall weed abundance and weed biomass were higher when using non-inversion tillage with SCs compared to inversion tillage without SCs. The effects differed due to site-specific weed pressure and management. With increasing weed pressure, the effect of SCs decreased, and the advantage of inversion over non-inversion tillage increased. N fertilization level did not affect weed abundance. The results suggest that SCs can contribute by controlling weeds but cannot fully compensate for reduced weed control of non-inversion tillage in the transition phase. Using non-inversion tillage together with SCs is primarily recommended in low weed pressure environments.
The dual function receptor kinase, OsWAKL21.2, is involved in elaboration of lipaseA/esterase induced immune responses in rice

Plant pathogens secrete cell wall degrading enzymes (CWDEs) to degrade various components of the plant cell wall. Plants sense this cell wall damage as a mark of infection and induce immune responses. Little is known about the plant functions that are involved in the elaboration of cell wall damage-induced immune responses. Transcriptome analysis revealed that a rice receptor kinase, WALL-ASSOCIATED KINASE-LIKE 21 (OsWAKL21.2), is upregulated following treatment with either Xanthomonas oryzae pv. oryzae (Xoo, a bacterial pathogen) or lipaseA/esterase (LipA: a CWDE of Xoo). Downregulation of OsWAKL21.2 attenuates LipA mediated immune responses. Overexpression of OsWAKL21.2 in rice mimics LipA treatment mediated induction of immune responses and enhanced expression of defence related genes, indicating it could be involved in the perception of LipA induced cell wall damage in rice. OsWAKL21.2 is a dual function kinase having in-vitro kinase and guanylate cyclase (GC) activities. Ectopic expression of OsWAKL21.2 in Arabidopsis also activates plant immune responses. Interestingly, OsWAKL21.2 needs kinase activity to activate rice immune responses while in Arabidopsis it needs GC activity. Our study reveals a novel receptor kinase involved in elaboration of cell wall damage induced rice immune responses that can activate similar immune responses in two different species via two different mechanisms. One sentence Summary A novel rice receptor WAKL21 that sense cell wall damage caused by Xanthomonas secreted cell wall degrading enzyme to induce immune responses.
USE OF dsRNA WSSV VP19 WITH DIFFERENT DOSE FOR INFECTION CONTROL White Spote Syndrome Virus (WSSV) IN VANAME SHRIMP Litopenaeus vannamei

Increased production of lithopanaeus vannamei vannamei shrimp continues to be pursued, one of which is by increasing shrimp immune response to infection with WSSV disease. This study aims to evaluate the best dosage of dsRNA VP19 WSSV in-vitro production to increase the immune response of vannamei shrimp (L. vannamei). The isolation of the VP19 gene and the construction of the VP19 vaccines were carried out using the Megascript kit with VP 19 genomic DNA as a template. Vaccination was carried out by injection method on vannamei shrimp with an average weight of 10.5 ± 3.5 g and a length of 11.05 ± 1.95 cm. The vaccine dose tested was 0.02 μg; 0.2 μg; 2 μg; and as controls are shrimp that are not vaccinated. The study consisted of four vaccine dose treatments with each of two replication and maintained for five days. The challenge test was carried out for five days by injecting the WSSV virus in saline solution (1:3 v/v). The differential hemocyte count (DHC) calculation was carried out before the challenge test and after the challenge test on days 1, 2, and 3. Data analysis was performed statistically by analysis of variance (ANOVA). VP19 gene isolation, construction with T7 promoter, and making of WSSV VP19 dsRNA were successfully carried out, and application of dsRNA vaccine in vannamei shrimp with a dose of dsRNA vaccine of 2.0 μg had a significant effect (P <0.05) on granular hemocytes cells
Poaching creates ecological traps within an iconic protected area

Ecological traps occur when areas preferentially selected by a species harbour an unknown increased mortality risk or reduced fitness for the individuals utilizing them. If animals continue to utilize these habitats, rapid declines may result that threaten the persistence of the population. Both black and white rhinoceroses are plagued by severe, targeted rhino poaching in South Africa that may have population and species‐level consequences in the long term. Poaching can rapidly increase mortality and may create habitats that function as ecological traps for protected populations. We used spatially explicit data of live rhino and poached rhino carcasses in the Kruger National Park, South Africa, to define high‐ and low‐risk states for both black and white rhino species. The proportion of area functioning as ecological trap was similar for both species (black: 37.73%, white: 35.51%), while the proportion of safe harbour was considerably lower for black rhino (black rhino: 32.01%, white rhino: 44.74%). Species‐specific risk areas were condensed into management categories that reflect the actions most likely to be effective for overall rhino protection in those areas. ‘Threat’ area, representing ecological traps for both species, comprised 32.48% of southern Kruger; this represents the highest priority for anti‐poaching interventions. A further 31.03% was identified as ‘haven’, representing safe harbours for both species, which may benefit most from continued rhino monitoring and surveillance. Using these categories, authorities can prioritize the distribution of limited resources and tailor anti‐poaching and biological management actions according to the needs of each area for the concurrent protection of both rhino species. This work illustrates how the conservation of multiple species or taxa within a system can be simultaneously prioritized in vast areas where resources and/or capacity may be insufficient to undertake species‐specific approaches.
Yield and Nutritional Quality of Vesuvian Piennolo Tomato PDO as Affected by Farming System and Biostimulant Application

Scientific investigations are being increasingly devoted to biostimulant effects on vegetable yield and quality, with the perspective of sustainable crop management. Two farming systems (conventional or organic) in factorial combination with two biostimulant treatments (tropical plant extract (PE); legume-derived protein hydrolysate (PH)) plus a non-treated control were compared in terms of tomato fruit yield, yield components, mineral composition, functional and nutritional indicators. PE- and PH-based biostimulants resulted in higher plant biomass, PH even in higher leaf area index, compared to non-treated control. Marketable yield was not significantly affected by farming system. PH and PE gave higher yield than non-treated control. PH treatment led to higher fruit number than the control, whereas PE incurred significant increase in yield only under organic farming. The mean fruit weight attained the highest value upon PE application under conventional management. Colour component a* (redness) was higher with the conventional system compared to the organic one, whereas an opposite trend was shown by the organic acids malate, oxalate and isocitrate. Irrespective of the farming system, the soluble solids, fruit brightness (L*) and redness as well as the target organic acids malate, oxalate, citrate and isocitrate were significantly higher than untreated plants by 10.1%, 16.1%, 19.8%, 18.9%, 12.1%, 13.5% and 26.8%, respectively, with no significant differences between the PH- and PE-based biostimulants. Higher lipophilic activity and total ascorbic acid concentration but lower lycopene were recorded under organic management. PE and PH application resulted in higher total phenol and ascorbic acid as well as in lycopene content, and lipophilic antioxidant activity than the non-treated control. Biostimulants proved to be an effective sustainable tool for enhancing tomato fruit yield and functional quality both under conventional and organic vegetable systems.
Molecular Population Genetics

In the article by S. Casillas and A. Barbadilla (GENETICS 205: 1003–1035) entitled “Molecular Population Genetics,” on page 1010, the references provided in Table 1 were incomplete. For the measure/test vA, the reference to “Castellano et al. (2016), James et al. (2016)” has been removed and changed to “Gossmann et al. (2010). ” Additionally, the reference for the measure/ test Kaþ has been updated to “Gossmann et al. (2010), Castellano et al. (2016). ” Accordingly, Gossmann et al. (2010) has been added to the reference list as such: T. I. Gossmann, B. -H. Song, A. J.Windsor, T.Mitchell-Olds, C.J. Dixon et al., 2010Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol. Biol. Evol. 27: 1822–1832. Additionally, on page 1015, Figure 3 was replaced due to an error in the equation (see below). On pages 1015 and 1018, one equation and several instances of in-text equationswere corrected. Please see below for the full corrected text. “Specifically, mutations enter the population at a rate 2Nm (the mutation rate m is per site per generation, and in a diploid population there are 2N potential chromosomes to mutate) (Figure 3C). Each of these new mutations have a given selection coefficient s that is determined by its fitness effect on the individual (DFE, Figure 3A). All mutations with this s, fðsÞ, have a probability of fixation that depends both on the population census and the effective population size, in addition to the selection coefficient, uðN;Ne; sÞ (thus contributing to the divergence between species) (Kimura 1957; Figure 3B). s potentially ranges from2N to +N (sometimes scaled from21 to 1), so the overall molecular evolutionary rate (K) taking into account all mutations is determined by the general expression: