Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation and development of freshwater invertebrate metabarcoding COI primers for Environmental Impact Assessment

10 A central challenge in the present era of biodiversity loss is to assess and manage human impacts on 11 freshwater ecosystems. Macroinvertebrates are an ideal group for Environmental Impacts Assessment 12 (EIA). However, generating accurate macroinvertebrate inventories based on larval morphology is 13 difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to 14 accurately identify invertebrates in bulk samples at the species level, has been demonstrated in 15 several case studies. However, DNA based identification is often limited by primer bias, potentially 16 leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an 17 emerging technique for EIA critically relies on carefully evaluating primers. 18 We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) 19 sequence data for the 15 most globally relevant freshwater invertebrate groups in EIAs. Using these 20 sequence alignments, we developed four primer combinations optimized for freshwater 21 macrozoobenthos. All primers were evaluated by sequencing ten mock community samples each 22 consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the 23 literature and the developed primers were tested in silico against the 15 relevant invertebrate groups. 24 The developed primers varied in amplification efficiency and the number of detected taxa, yet 25 all detected more taxa than standard ‘Folmer’ barcoding primers. Two new primer combinations 26 showed more consistent amplification than a previously tested ribosomal marker (16S) and detected 27 all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical 28 design flaws in some commonly used primers from the literature. We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in 32 silico primer evaluation. We further demonstrate that some primers currently used in metabarcoding studies may not be suitable for amplification of insect and freshwater taxa. Therefore, careful primer evaluation and more region / ecosystem specific primers are needed before DNA metabarcoding can be used for routine EIA of freshwater ecosystems.
Evaluation of yeasts in gel larval diet for Queensland fruit fly, Bactrocera tryoni

Queensland fruit fly, Bactrocera tryoni (“Q‐fly”), is Australia’s most economically important insect pest of horticultural and commercial crops especially in the eastern regions. The sterile insect technique (SIT) has been adopted as an environmentally benign and sustainable approach for management of Q‐fly outbreaks. High‐performance larval diets are required to produce the millions of flies needed each week for SIT. Yeast products contribute amino acids (protein) to fruit fly larval diets, as well as carbohydrate, fat and micronutrients, but there can be substantial variation in the nutritional composition and suitability of yeast products for use in larval diets. Gel larval diets have recently been developed for large‐scale rearing of Q‐fly for SIT, and composition of these diets requires optimization for both performance and cost, including choice of yeast products. We assessed performance of Q‐flies reared on gel larval diets that contained debittered brewer’s yeast (Lallemand LBI2240), hydrolysed yeast (Lallemand FNILS65), inactivated brewer’s yeast (Lallemand LBI2250) and inactivated torula yeast (Lallemand 2160‐50), including blends. Q‐flies performed poorly when reared on diets containing only or mostly hydrolysed yeast in terms of pupal number, pupal weight and percentage of fliers. Performance was also poor on diets containing high proportions of torula yeast. Overall, debittered brewer’s yeast is recommended as the best option for Q‐fly gel larval diet, as it is cheap, readily available, and produces flies with good performance in quality control assays. Inactivated brewer’s yeast produced flies of comparable quality with only a modest increase in cost and would also serve as an effective alternative.
Multivariate Analysis of Deboning Data for Classifying Hanwoo (Korean Native Cattle) by Gender

Gender is an important factor in determining the market price of Hanwoo, but its discrimination is impossible after deboning. This study aims at identifying the variables in Hanwoo deboning data that could be used for gender identification and classification. Deboning data of Hanwoo were analysed by discriminant function analysis. Seven pre-deboning and 24 post-deboning variables were identified and showed 91.3% and 98.9% accuracy in gender identification respectively. Discriminant power was 98.9% on using all 31 deboning variables. This result suggests that physical characteristics of meat parts are suitable factors for classification of beef by gender.
Transcription factor and growth factor requirements for thymus vascularization

Scientists and philosophers have marveled over the complex nature of the vascular system for many centuries. In this dissertation work, we were interested in unraveling the molecular mechanisms driving the structuring and organization of this elaborate network in the thymus. Specifically, our aim was to elucidate the possible contributions of a number of thymus-specific transcription factors and growth factors to vascular network formation. The thymus is a specialized microenvironment responsible for the development of self-tolerant and self-restricted T cells. In this dissertation, we used an allelic series of the thymic epithelial cell (TEC)-specific transcription factor Foxn1 to define normal thymic vascular development and to investigate a potential role for Foxn1-dependent TEC differentiation in the formation of the thymic vasculature. We show that endothelial cells initially enter the wild-type thymus at E13.5, with PDGFR-β mesenchymal cells following at E14.5. These events are delayed by 1-2 days in Foxn1 mice, and were accompanied by an apparent loss of capillaries. In Foxn1 mice, endothelial cells could not be detected in the thymus until E15.5, and never enter in Foxn1 null mutants. VEGF-A and PDGF-B expression are reduced at E13.5 and E15.5 in Foxn1 mice compared with controls. Further, empty collagen IV sleeves (collagen IV CD31) were present throughout the mutant thymus. Additionally, we tested the requirement for TEC-derived Shh, VEGF-A, and BMP4 for thymus vascularization. Deletion of these genes in TECs using Foxn1Cre resulted in no observable delay in initial thymus vascularization suggesting that they may be dispensable for thymus vascularization. Together, these data suggest that Foxn1 is required in TECs to produce the cellular and molecular environment needed for normal thymic vascularization, and may mediate a novel TEC-mesenchyme-endothelial form of crosstalk required for fetal thymus organogenesis.
Soil erosion alters soil chemical properties and limits grassland plant establishment on an oceanic island even after goat eradication

Soil erosion after vegetation degradation induced by disturbance by feral goats, an invasive mammal, can lead to loss or accumulation of soil at a local scale and can alter soil chemical properties. This alteration of soil properties can in turn affect the establishment of plant species. We evaluated relationships among the extent of soil erosion, soil chemical properties, and the distribution of plant species in grassland ecosystems after goat eradication on Nakodo‐jima Island in the northwestern Pacific. In 105 1 × 1–m quadrats, changes were measured in the position of topsoil over 2 years. Surface soils were sampled for analysis of chemical properties, and plant species in the quadrat were recorded. Changes in the position of topsoil were related to the area of bare ground. Soil loss occurred at sites where areas of bare ground were extremely large. Significantly higher values of soil exchange acidity and smaller amounts of available phosphorus, total carbon, and total nitrogen were detected in soils at sites with large soil losses. Most of the 11 dominant plant species were absent from sites with large losses of soil. The presence of eight species was significantly negatively related to soil exchange acidity, and three species were significantly positively related to available phosphorus. Our results indicated that exposure of subsoils at the soil surface after vegetation degradation can increase soil loss, which can alter soil chemical properties, and this alteration can continue to limit the establishment of plant species, even long after goat eradication.
EVALUATION OF INFESTATION IN PARASITOIDS ON Metisa plana Walker (LEPIDOPTERA: PSYCHIDAE) IN THREE OIL PALM PLANTATIONS IN PENINSULAR MALAYSIA

The bagworm, Metisa plana Walker (Lepidoptera: Psychidae) is one of the most dominant pest species on oil palm plantations in Malaysia which can cause high yield loses up to 43% over two years after a serious infestation. Parasitoids play an important role as natural enemies to reduce bagworm’s population. The interaction of this pest and parasitoids are highly influenced by the availability of bagworms as a host. Highly infested oil palm plantation in Banting, Selangor, Tapah, Perak and Yong Peng, Johor were chosen as sampling sites. This study represented parasitoids species that associated with Metisa plana namely Cotesia metesae (51%: 70 individuals), Brachymeria carinata (21%: 28 individuals), Buysmania oxymora (13%: 18 individuals), Goryphus bunoh (8%: 11 individuals), Pediobius sp. (5%: 7 individuals) and Eupelmus cotoxanthae (2%: 3 individuals) in highly infested oil palm plantation in Peninsular Malaysia. It is known that parasitoid species Cotesia metesae recorded the highest number of emergence among all parasitoids and presence in all sampling sites. The information regarding parasitoids species in oil palm plantation is crucial in order to regulate the bagworms population.
New Dryocosmus Giraud species associated with Cyclobalanopsis and non-Quercus host plants from the Eastern Palaearctic (Hymenoptera, Cynipidae, Cynipini)

Our knowledge about gall wasps associated with the diverse East Asian oaks, Castanopsis and Cyclobalanopsis, is limited due to the lack of extensive field studies. Here, we describe twelve new oak gall wasp species, Dryocosmus cannoni Schwéger & Tang, D. caputgrusi Tang & Schwéger, D. crinitus Schwéger & Tang, D. harrisonae Melika & Tang, D. hearni Melika &Tang, D. hualieni Schwéger & Tang, D. konradi Tang & Melika, D. liyingi Melika & Tang, D. moriius Tang & Melika, D. quadripetiolus Schwéger & Tang, D. salicinai Schwéger & Tang, and D. taitungensis Tang & Melika, from Taiwan and mainland China. Seven newly described species induce galls on Quercus subgenus Cyclobalanopsis and five on other Fagaceae genus, Castanopsis. All of the new species concepts are supported by morphological and molecular data. We provide descriptions, diagnoses, host associations for the new species and an illustrated identification key to Eastern Palaearctic Dryocosmus species. We represent natural language phenotypes in a semantic format supported by biomedical ontologies to increase the accessibility of morphological data. JHR 53: 77–162 (2016) doi: 10.3897/jhr.53. 9890 http://jhr.pensoft. net Copyright Chang-Ti Tang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. RESEARCH ARTICLE Chang-Ti Tang et al. / Journal of Hymenoptera Research 53: 77–162 (2016) 78
High-resolution seafloor mapping to describe coastal denning habitat of a Canadian species at risk: Atlantic wolffish (Anarhichas lupus)

The Atlantic wolffish (Anarhichas lupus) is listed by Canada’s Species at Risk Act as a species of special concern. Effective conservation strategies rely on accurate knowledge of habitat requirements, distribution, and vulnerabilities; however, current management plans cite lack of wolffish habitat data as a key limitation. For this study, coastal Atlantic wolffish denning habitat was characterized and mapped with high-resolution multibeam data and seafloor video in Conception Bay, Newfoundland. Four Atlantic wolffish dens, used for feeding, spawning, and egg-guarding, were surveyed and mapped. On the basis of the geomorphology and substrate of these dens, a supervised classification was applied to the multibeam bathymetry and backscatter data to identify other potential denning areas. Predicted denning habitat, limited by the occurrence of suitable rocky substrate, is most prevalent in shallow waters (<22 m) distributed over 1.6 km2 (5.9%) of the study area. Shallow denning habitat is exposed to seasona.
Nutritional Value of African Indigenous Whole Grain Cereals Millet and Sorghum

Worldwide population growth expectations increase the pressure to find ways to increase agro-food production in a sustainable manner, be it by increasing production capacity, cultivating currently natural areas or changing crop consumption patterns. Cereals are staple foods and the most frequently consumed are maize, wheat and rice. However, the production of these cereals may become insufficient for the growing needs. Millet and sorghum are traditional cereal crops, able to growth in adverse drought conditions, and do not need many resources to be harvested. Furthermore, they reveal very interesting nutritional profiles, including macro and micronutrients and bioactive compounds. We would like to highlight their fiber content, since fiber inadequacy is a worldwide condition and its adverse effects on health are well described. Over time, these indigenous cultures have become less popular than other cereals, due to their organoleptic and technological proprieties. However, techniques like bio-fortification, fortification, genetic improvement, fermentation, malting, and germination among others can be used to improve their technological properties and enhance their nutritional profile.
fMRI repetition suppression reveals no sensitivity to trait judgments from faces along the ventral visual stream or in the theory-of-mind network

The human face cues a wealth of social information, but the neural mechanisms that underpin social attributions from faces are not well known. In the current fMRI experiment, we used repetition suppression to test the hypothesis that populations of neurons in face perception and theory-of-mind neural networks would show sensitivity to faces that cue distinct trait judgments. Although faces were accurately discriminated based on associated traits, our results showed no evidence that face or theory-of-mind networks showed repetition suppression for face traits. Thus, we do not provide evidence for population coding models of face perception that include sensitivity to high and low trait features. Due to aspects of the experimental design, which bolstered statistical power and sensitivity, we have reasonable confidence that we could detect effects of a moderate size, should they exist. The null findings reported here, therefore, add value to models of neural organisation in social perception by showing instances where effects are absent or small. To test the generalisability of our findings, future work should test different types of trait judgment and different types of facial stimuli, in order to further probe the neurobiological bases of impression formation based on facial appearance.
Diet Determined by Next Generation Sequencing Reveals Pest Consumption and Opportunistic Foraging by Bats in Macadamia Orchards in South Africa

Recent studies have documented the economically significant impact of bats as predators of agricultural pest insects. We used Next Generation Sequencing (NGS) of the cytochrome oxidase I gene to elucidate the diet of six species of bats based on faecal pellets collected from individuals and roosts in macadamia orchards at Levubu, Limpopo Province, South Africa. For five of these species, we compared the molecular data with published results from microscopic analysis of faecal pellets, culled parts and stomach contents. We provide the first description of the molecular diet of the large African molossid bat, Mops midas. Expectations from skull morphology and a single limited study of stomach contents were that this species should be a beetle-specialist. However, NGS revealed that the diet of M. midas contained a much higher prevalence and diversity of lepidopteran (81 taxa from 17 families) compared to coleopteran (two taxa) prey. While this result is predicted by the allotonic frequency hypothesis for a bat species with low echolocation frequency, it could also be explained by unequal PCR amplification, a constraint of amplicon sequencing. Apart from the above-mentioned species where our sample was probably unbiased (24 pellets from multiple roosts and occasions), sample sizes of the other five species were very low and therefore potentially biased (1–6 pellets). Nevertheless, these samples revealed for each bat species surprisingly many prey taxa spanning several insect orders, indicating that individual bats were capable of consuming a wide diversity of prey during one or two nights of foraging. Contrary to expectations, bats of all foraging groups (clutter, clutteredge and open-air) fed opportunistically on mostly-flightless cockroaches (Order Blattodea). About one third of all faecal pellets tested from five species of bats of all foraging groups contained DNA from the significant macadamia pest species, Nezara viridula (Order Heteroptera), indicating the value of intact bat communities in the biological control of pest stink bugs in macadamia orchards. Contrary to the general expectations of the allotonic frequency hypothesis, all six bat species studied fed predominantly on tympanate versus non-tympanate species of moths (57–75% of lepidopteran prey taxa), even those ‘non-allotonic’ bat species having intermediate echolocation peak frequencies that encompass the frequency sensitivity of hearing (tympanate) moths.
Amino acid composition and antioxidative properties of hydrolysed pumpkin (Cucurbita pepo L.) oil cake protein

ABSTRACT Pumpkin oil cake protein isolate (POCPI) was hydrolysed using two food-grade enzymes alcalase and trypsin. Alcalase-hydrolysed POCPI (POCPH1) was selected as the optimum treatment based on the DPPH radical scavenging, total antioxidative, and ferrous ion chelating activities. Amino acid composition showed a direct relationship between the antioxidative activity of POCPH1 and the amount of hydrophobic amino acids that formed 33.49% of its total amino acids. Surface hydrophobicity decreased as a result of hydrolysis and potent thermal and pH stability was observed in POCPH1 (p ˂ 0.05). In terms of molecular weight distribution, size exclusion chromatogram indicated that the majority of peptides possessed molecular weight less than 6.5 kDa. Based on the results, POCPH1 could be employed as a natural antioxidative agent with strong pH and thermal stability.
Assessment of resistances to multiple pathogens in experimental sweet pepper hybrids

The aim of this study was to assess resistance to major sweet pepper pathogens ( Phytophthora capsici, Pepper yellow mosaic virus – PepYMV and Meloidogyne incognita ) in a group of experimental hybrids and their respective parental lines, and to identity hybrids possibly resistant to all three pathogens. Ten parental breeding lines, thirty experimental hybrids and seven commercial controls (Konan-R, Magali-R, Martha-R, Stephany, Mallorca, Magnata Super and Criollo de Morelos-334) were used. Each experiment was set up in a randomized complete block design with three replications. For assessment of resistance to P. capsici and PepYMV, the percent of asymptomatic plants was considered. In evaluating reactions to M. incognita, both the nematode reproduction index and the nematode reproduction factor were calculated. Five hybrids were found with resistant to all three pathogens. For all three pathogens, there was evidence that hybrids with two resistant parental lines showed slightly higher levels of pathogen resistance than those with only one resistant parental line.
Characterizing physiological and genetic differences in the early immune response to Haemonchus contortus in resistant and susceptible sheep

This dissertation compares immune responses of resistant and susceptible sheep to infection with Haemonchus contortus during the peri-parturient period and larval stage of infection. Identification of immunological events resulting in parasite resistance in St. Croix hair sheep may provide better targets for differential gene expression analysis and eventual discovery of selectable markers for parasite resistance. Antibody levels of hair ewes and composite Dorset x Finnsheep-Rambouillet wool ewes were measured during breeding and again after parturition. Results demonstrated that hair ewes had higher levels immunoglobulin-A after infection and maintained a higher level of circulating antigen-specific antibody when compared to wool ewes. To characterize immune responses to the larval stage of infection, hair and wool lambs were sacrificed at 0, 3, 5, and 7 d after infection with H. contortus. Neutrophil migration to abomasal mucosa and lymph node development were higher in hair sheep than in wool sheep. Gene expression analysis indicated no difference in the abomasal lymph node as both breeds expressed a general T-helper cell type 2 (TH2) response. However, profound differences in TH2 responses were observed in the abomasal mucosa, where hair sheep expressed more IL-4, -13 and -33 than wool sheep. These data thus document the presence of immunological differences between the breeds. Immune responses to larval parasite infection in wool sheep are generally suppressed and may increase the magnitude and duration of infection whereas immune responses to larval infection in hair sheep was more robust and more strongly polarized towards a TH2 response.
Sex population structure of Macrobrachium felicinum and Macrobrachium vollenhovenii in the Akor river, Ibere Ikwuano, Abia State

Akor River Ibere was sampled for 24 months during September 2012 – October 2014 using the Area density method. The river was delineated into three stations for sampling purposes namely Station A, B and C. Station A is located at Obuoro, Station B is located at Elemaga while Station C is located at Itunta where the prawns were all collected from. In the three stations, females predominated over the male with overall prawn species of 4,859 individuals out of which 3302 were females and 1551 were males giving a ratio of 1:2.07. A total number of 1,239 Macrobrachium felicinum were caught out of which 370 individuals were males and 869 individuals were females giving a ratio of 1:2 which was significantly different (p<0.05) from expected ratio of 1:1, 3,620 Macrobrachium vollenhovenii samples were caught in the three stations out of which 1,187 were males and 2,433 were females giving a ratio of 1:2 which showed no significant difference (p>0.05) though a ratio of 1:1 is expected. There were significant differences in number of shrimps caught between seasons (p<0.05). There were two peaks of abundance of male shrimps. The first peak was in July Aug 2013, the highest numbers of females were obtained in September 2013, the peak of the rainy season whiles another peak occurred in July and September 2014. The presence of both sexes of Macrobrachium in Akor River suggests that there is possibility of prawn larval production for aquaculture practice.