Miracle-dz/UniFAR-FTUs huggingface dataset:
The vulnerability of reproductively active squaretail coralgrouper (Plectropomus areolatus) to fishing

Squaretail coralgrouper (Plectropomus areolatus) were captured and tagged at a fish spawning aggregation (FSA) site with conventional and acoustic tags to assess their vulnerability to fishing and spatial dynamics during reproductive periods. Males outnumbered females in catch and, on average, were larger than females. Findings revealed a high vulnerability to fishing, particularly during reproductive periods, and most fish were recaptured within the 5-month spawning season and within 10−12 km of the aggregation site. Individual and sex-specific variability in movement to, and residency times at, the FSA site indicates that individual monthly spawning aggregations represent subsets of the total reproductive population. Some individuals appeared to move along a common migratory corridor to reach the FSA site. Sex-specific behavioral differences, particularly longer residency times, appear to increase the vulnerability of reproductively active males to fishing, particularly within a FSA, which could reduce reproductive output. Both fishery-dependent and fishery-independent data indicate that only males were present within the first month of aggregation. The combined results indicate that reproductively active P. areolatus are highly vulnerable to fishing and that FSAs and migratory corridors of reproductively active fish should be incorporated into marine protected areas. The capture of P. areolatus during reproductive periods should be restricted as part of a comprehensive management strateg
Improving and Characterizing the Nutritive Value of Feather Meal Using Rainbow Trout (Oncorhynchus mykiss) as a Biological Model: Insights into Determinants of Digestibility of Proteins

Feather meal (FeM) is a high-protein and cost-effective feed ingredient, made from the steam-hydrolysis of keratin waste products generated by the animal processing industry. Keratins are composed of ~90% indigestible protein highly cross-linked with disulphide bridges. Steam-hydrolysis promotes the disruption of disulphide, peptide, and hydrogen bonds, allowing peptides to become digestible and amino acids absorbable. The variability of the nutritional value of FeM is the result of the use of different raw materials and processing conditions during the production of this ingredient. Variations of heat processing conditions create disparities of disulphide conformers, D-amino acids, and cross-linked amino acids contents, and these affect the nutritional value of protein ingredients. Better understanding of the chemical interactions occurring during the processing of FeM would enable the development of methods to improve and estimate the nutritional value of this ingredient, which could assure the quality of FeM to feed stakeholders. FeMs were hydrolyzed using a novel enzymatic pre-treatment with the aim of better understanding the effects of peptide and disulphide bonds on the digestibility of amino acids and bioavailability of test amino acids (arginine) in this ingredient by rainbow trout. In a first study, a bench-scale trial was carried out to determine the potential of incubating FeM with sodium sulfite and proteases to cleave disulphide and peptide bonds, respectively. Subsequently, a pre-treatment to improve the nutritional value of FeMs was developed. In a second study, the bioavailability of arginine in two FeMs and in their pre-treated counterpart (PTFeM) were assessed through a growth trial using rainbow trout. In follow up studies, the apparent digestibility of amino acids in the same FeMs and PTFeMs were assessed in rainbow trout. The disulphide and cross-linked amino acid contents in the four ingredients were quantified in an attempt to determine the factors affecting their digestibility and bioavailability. Results from this thesis demonstrate that a simple treatment targeting the disruption of disulphide and peptide bonds effectively improves the bioavailability of arginine and the digestibility of amino acids in FeMs. Furthermore, this thesis gives insight on the effect of structural and chemical characteristics of protein on the nutritional value of FeM.
A minority-ruled population coding of kinematics in the striatum

The structure of population activity in the dorsolateral striatum during the performance of motor sequences has not been characterized and it is unclear if striatal ensembles encode (predict) kinematic parameters defining how sequences are executed. Here we analyzed hundreds of striatal spike trains from naive and trained rats performing a running sequence. We found that the population response was composed of a diversity of phasic modulations covering the entire sequence. The accuracy of kinematics encoding by single neurons was around chance level but improved when neuronal ensembles were considered. The distribution of single-neuron contributions to ensemble encoding was highly skewed with a minority of neurons responsible for most of the encoding accuracy. Importantly, running speed ensemble encoding improved after learning. We propose that during motor learning, striatal ensembles adjust their task representation by tuning the activity of a minority of neurons to the kinematic parameters most relevant to motor performance.
Genetics and epigenetic alterations of hexaploid early generation derived from hybrid between Brassica napus and B. oleracea

Good fertility was observed previously in hexaploid derived from hybrid (ACC) between calona ‘Zhongshuang 9’(Brassica napus, 2n = 38, AACC) and kale ‘SWU01’ (B. oleracea var. acephala, 2n = 18, CC). However, the mechanism to underlying the character is unknown. In the present study, genetic and epigenetic alterations of S0, 6 S1, and 18 of their S2 progenies with hexaploid chromosome conformation (20A + 36C) were selected to compare with ACC and their parental species. 13.08% and 26.45% polymorphism alleles different from two parental species were identified in ACC via 58 SSR (simple sequence repeats) and 14 MSAP (methylation sensitive amplified polymorphism), respectively. 33.74% new alleles in DNA methylation, but not in DNA sequence were detected in S0 after chromosome doubling of ACC. DNA profilling revealed a little genetic but much epigenetic differences among S0, S1 and S2 generations. Genetic alteration was relatively stable, because only 8.09% and 3.21% alleles inheriated from ACC were changed in S2 and S1, respectively. While on average of 52.44 ± 5.32% DNA methylation site inherited from ACC were detected in S1, and 41.52 ± 9.04% in S2 due to dramatic epigenetic variance among early generations. New DNA methylation sites occurred in S0 would inheritated into the successive generations, but the frequency was decreased because some new site might be recovered. It demonstrated that much DNA methylation but a little DNA sequence variance was occurred in hexaploid early generation.
The Effect of Docosahexaenoic Acid in a Mouse Model of Neuroinflammation

2.6. 1 Epidemiological studies have linked fish consumption to lower rates of neurological diseases. Fish contain high levels of n-3 PUFA, and several lines of evidence suggest that the n-3 PUFA DHA acts in the brain via anti-apoptotic and neurotrophic pathways. In addition, DHA may act through anti-neuroinflammatory pathways, as DHA possesses anti-inflammatory properties in the periphery. Evidence from animal models has indicated that DHA and its derivatives (resolvin D1 and protectin D1) attenuate colitis, peritonitis and ischemic stroke. n-3 PUFA deprivation in rats decreases brain levels of DHA and increases markers of the brain ARA cascade, a proinflammatory pathway. Thus, chronic low intake of n-3 PUFA may predispose the brain to weak anti-inflammatory, as well as strong proinflammatory signals. Neurological disorders, including Alzheimer’s disease, Parkinson’s disease and major depression, display a neuroinflammatory component. n-3 PUFA supplementation, as well as drugs targeting brain PUFA metabolism, are promising candidates in the prevention and treatment of neurological disorders. Introduction 2.6. 2 Fish consumption has been linked to lower rates of neurological diseases, including Alzheimer's disease (Kalmijn et al 1997; Barberger-Gateau et al 2002; Morris et al 2003), Parkinson's disease (de Lau et al 2005), multiple sclerosis (Swank et al 1952; Agranoff et al 1974), and major and postpartum depression (Hibbeln et al 1995; Hibbeln 2002). Clinical trials investigating the effects of fish oil or n-3 PUFA supplementation on disease progression have been inconsistent, with beneficial effects demonstrated in some (Nemets et al 2002; Peet et al 2002; Su et al 2003; Hallahan et al 2007), but not all (Silvers et al 2005; Grenyer et al 2007), studies of major depression, and some benefits in very mild Alzheimer's disease, but not in mild to moderate
Short-chain fatty acid (SCFA) histone deacetylase inhibitors produced by gut microbiota regulate selected microRNAs to modulate local and systemic antibody responses

Epigenetic marks and factors, such as histone modifications and miRNAs, interact with genetic programs to regulate intrinsic B cell functions and inform antibody responses. As shown by our transcriptome and miRNome analyses, histone deacetylase inhibitors (HDIs) selectively downregulate AID, which is critical for class switch DNA recombination (CSR) and somatic hypermutation (SHM), and Blimp-1, the master transcription factor for B cells differentiation to plasma cells, by selectively upregulating miRNAs that target Aicda and Prdm1 mRNAs. As we have also shown, HDI-mediated impairment of CSR, SHM and plasma cell differentiation blunted T-dependent and T-independent antibody responses in wild type mice and autoantibody responses in lupus-prone mice. Potent HDI activity is displayed by butyrate and propionate, two abundant SCFA molecules generated by gut microbiota through fermentation of dietary fibers. We found that these SCFAs synergistically downregulate AID and Blimp-1 expression through selective miRNA upregulation. Feeding a no-fiber diet, or decreasing the load of SCFA-producing microbiota by treating mice with vancomycin reduced gut and serum SCFAs and resulted in increased IgA and IgG1 titers in serum and feces, and IgA+, IgG1+ B cells and plasma cells in Peyer’s patches, mesenteric lymph nodes and spleen. This outcome was reversed by administration of butyrate and propionate, which also synergistically inhibited CSR to IgG and IgA in purified human and mouse B cells in a dose-dependent fashion. Thus, endogenous HDIs integrate cues from metabolites by gut microbiota and relay them to selective downstream effectors, e.g. miRNAs, thereby modulating B cell differentiation and antibody/autoantibody responses.
Next-Generation Transcriptome Assembly: Strategies and Performance Analaysis

Accurate and comprehensive transcriptome assemblies lay the foundation for a range of analyses, such as differential gene expression analysis, metabolic pathway reconstruction, novel gene discovery, or metabolic flux analysis. With the arrival of next-generation sequencing technologies, it has become possible to acquire the whole transcriptome data rapidly even from non-model organisms. However, the problem of accurately assembling the transcriptome for any given sample remains extremely challenging, especially in species with a high prevalence of recent gene or genome duplications, those with alterna- tive splicing of transcripts, or those whose genomes are not well studied. In this chapter, we provided a detailed overview of the strategies used for transcriptome assembly. We reviewed the different statistics available for measuring the quality of transcriptome assemblies with the emphasis on the types of errors each statistic does and does not detect. We also reviewed simulation protocols to computationally generate RNAseq data that present biologically realistic problems such as gene expression bias and alternative splic- ing. Using such simulated RNAseq data, we presented a comparison of the accuracy, strengths, and weaknesses of nine representative transcriptome assemblers including de novo , genome-guided, and ensemble methods.
JAK3 and TYK2 Serve as Prognostic Biomarkers and Are Associated with Immune Infiltration in Stomach Adenocarcinoma

Background Stomach adenocarcinoma (STAD) is one of the most common malignant tumors. The Janus kinases (JAKs) play a significant part in cellular biological process, inflammation, and immunity. The roles of JAKs in STAD are still not systematically described. Methods A series of bioinformatics tools were used to clarify the role of JAKs in STAD. Results JAK3/TYK2 levels were significantly increased in STAD during subgroup analyses based on gender, tumor grade, cancer stages, and nodal metastasis status. STAD patients with high levels of JAK3/TYK2 had poor overall survival, postprogression survival, and first progression. Immune infiltration revealed a significant correlation between JAK3/TYK2 expression and the abundance of immune cells as well as immune biomarker expression in STAD. JAK3/TYK2 was associated with the adaptive immune response, chemokine signaling pathway, and JAK-STAT signaling pathway. Conclusions JAK3 and TYK2 serve as prognostic biomarkers and are associated with immune infiltration in STAD.
Carotinoide in Zygaena -Arten (Lepidoptera)/ Carotenoids in Zygaena Species (Lepidoptera)

Abstract Species of Zygaena (Lepidoptera) have been fed with leaves of Lathyrus pratensis rich in chlorophylls and carotenoids. The metabolism of the pigments was followed in eggs, larvae, pupae, and imagines of the insects. No chlorophylls, only lutein - the main carotenoid of the food plants - was stored in the animals. Traces of α-zeacarotene, absent in plants, could be found in eggs and larvae
Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients

Background We used bioinformatic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays to investigate the association between plasma microRNAs (miRNAs) and stable warfarin dosage in a Chinese Han population. Methods Bioinformatics analysis was used to screen out potential warfarin dose-associated miRNAs. Three plasma miRNAs were validated in 99 samples by RT-qPCR. Kruskal–Wallis test and multivariate logistic regression were used to compare differences in plasma miRNAs expression levels between three warfarin dosage groups. Results There were significant between-group differences among the three dose groups for hsa-miR-133b expression (p = 0.005), but we observed an “n-shaped” dose-dependent curve rather than a linear relationship. Expression levels of hsa-miR-24-3p (p = 0.475) and hsa-miR-1276 (p = 0.558) were not significantly different in the multivariate logistic regression. Conclusion miRNAs have received extensive attention as ideal biomarkers and possible therapeutic targets for various diseases. However, they are not yet widely used in precision medicine. Our results indicate that hsa-miR-133b may be a possible reference factor for the warfarin dosage algorithm. These findings emphasize the importance of a comprehensive evaluation of complex relationships in warfarin dose prediction models and provide new avenues for future pharmacogenomics studies.
Conserved Non-Coding Element m2de3 Directed Gene Expression During Development

Meis genes are well known for their important roles in gene regulation and development, in combination with other transcription factors such as the Hox and Pbx families. The primary purpose of this study is to gain a better understanding of the genetic mechanisms that control the expression of meis genes during development. The Zerucha lab identified four highly conserved non-coding elements, named m2de1-m2de4 (for meis2 downstream element) that we hypothesize regulate expression of the meis2 gene. I have characterized the m2de3 element to determine if this element is able to direct spatial and temporal gene expression consistent with meis2 expression patterns over different stages of development. Zebrafish (Danio rerio) were used in combination with a Tol2 injection cassette to introduce gene expression constructs containing murine m2de3 through microinjection at single cell stage. In primary transgenic embryos, m2de3 directed expression was observed in a punctate expression pattern along the notochord, within motor neurons along the notochord, around the heart and in developing muscle fibers along the trunk of zebrafish embryos. In addition, a stable m2de3 transgenic zebrafish genetic line was generated through fin clip genome analysis. This transgenic line demonstrates the expression pattern in the heart and along the entire notochord.
Microbial induction of programmed cell death in the gastrointestinal tract

Infection with Helicotmcter pylon and Shigatoxin-producing Escherichia coli is associated with a number of diseases in humans. The mechanisms underlying disease pathophysiology remain unclear. Recent evidence suggests that induction of apoptosis could be a pathogenic trait of specific bacterial pathogens. Therefore, the objectives of this thesis were 1) to determine if gastrointestinal pathogens or their products induce an apoptotic response in epithelial cells following infection and 2) to delineate the rnechanisms by which infection triggers the cell's apoptotic machinery. I determined if infection with the gastric pathogen, H. pylori, induced apoptosis of gastric epithelial cells. In vivo studies documented that infection was associated with an increase in both proliferation and apoptosis of gastric epithelial cells in association with enhanced expression of the tumor supressor p53. These findings indicate that induction of apoptosis occurs during infection and could influence disease outcome. I began to explore the mechanisms responsible for the increase in apoptosis observed during H. pylori infection in vivo. I determined that the bacteria could directly trigger apoptosis of epithelial cells in vitro. In addition, infection with H. pylori increased expression of the Fas death receptor on gastric epithelial cells in association with an increased sensitivity to Fas-triggered cell death. Taken together, these findings indicate that H. pylorkrnediated apoptosis occurs by more than one pathway. The bacterium directly stimulates apoptosis and infiltrating immune cells can induce apoptosis through the Fas signaling pathway. Finally, I demonstrated that epithelial cells expressing globotriaosylceramide undergo apoptosis following incubation with Shigatoxins produced by E. coli. The induction of apoptosis is associated with an alteration in Bcl-2 family rnember expression. Furthermore the toxin-mediated apoptosis can be inhibited by overexpression of the anti-apoptotic homologue BcC2 or by inhibition of downstream caspase activation. Inhibition of the apoptotic cascades defined in these studies could ameliorate the disease complications associated with infection. These findings indicate that bacterial pathogens and their products are capable of inducing apoptosis in epithelial cells. Therefore, the induction of apoptosis could be a common mechanism by which bacteria interact with host cells.
Vertical distribution of mesozooplankton and ichthyoplankton communities in the South-western Atlantic Ocean (23°14′1″S 40°42′19″W)

A study was conducted over eight consecutive days in February 2010 in which daily variations in the vertical distributions of heterotrophic bacteria, mesozooplankton and ichthyoplankton at 1–1200 m in the South-western Atlantic Ocean were investigated. Diurnal and nocturnal samples were collected at an oceanographic station at four regional depths: Tropical Water (TW) (1 m), South Atlantic Central Water (SACW) (250 m), Antarctic Intermediate Water (AAIW) (800 m) and Upper Circumpolar Deep Water (UCDW) (1200 m). Bacterial, mesozooplankton and larval fish densities significantly differed between sample depths but not between sampling tow times. In total, 154 zooplankton species and 18 larval fish species were identified. The highest number of taxa was obtained from the night-time TW trawls. This depth zone had the highest densities of mesozooplankton, larval fish and bacterioplankton (auto and heterotrophic), associated with the highest temperature and salinity and the lowest inorganic nutrient concentrations. Two sample groups were identified based on their mesozooplankton and larval fish compositions: night-time TW and other water masses (daytime TW, SACW, AAIW and UCDW). Thirty-two indicator species were detected in night-time TW. The copepod Nullosetigera impar was, to the best of our knowledge, identified for the first time on the Brazilian coast. Our results showed significant variability in the abundance and vertical distribution of mesozooplankton, bacterioplankton and larval fish along the water column in an oceanic area. We have provided new data and insights on the composition and vertical distribution of mesozooplankton, larval fish and bacterioplankton in deep waters in the South-western Atlantic Ocean.
Assesing the Drivers of Pollinator and Natural Enemy Community in Pigeonpea and Field Bean Crops

Arthropods that have a direct impact on crop production (i.e. pests, natural enemies and pollinators) can be influenced by both local farm management and the context within which these fields occur in the wider landscape. However, the contributions and spatial scales at which these drivers operate and interact are not fully understood, particularly in Africa. The impact of both local management and landscape context on insect pollinators and natural enemy communities and on their capacity to deliver related ecosystem services to an economically important tropical crop, pigeonpea was investigated. The study was conducted in nine paired farms across a gradient of landscape contexts in Kibwezi, Kenya. Results show that proximity of fields to semi-natural habitats negatively affected pollinator and chewing insect abundance. Within fields, pesticide use was a key negative predictor of pollinator, pest and foliar active predator abundance. On the contrary, fertilizer application significantly enhanced pollinator and both chewing and sucking insect pest abundance. At 1 km spatial scale of fields, significant negative effects of number of semi-natural habitat patches within fields dominated by mass flowering pigeonpea on pollinator abundance were found. For service provision, a significant decline in fruit set when insects were excluded from flowers was recorded. This study reveals the interconnections of pollinators and predators with pigeonpea crop. For sustainable yields and to conserve high densities of both pollinators and predators of pests within pigeonpea landscapes, it is crucial to target the adoption of less disruptive farm management practices such as reducing pesticide and fertilizer inputs.