Miracle-dz/UniFAR-FTUs huggingface dataset:
Peripheral blood and head kidney haematopoietic tissue response to experimental blood loss in mullet (Mugil cephalus)

Abstract Changes in haematological parameters and differential leukocyte counts of peripheral blood and head kidney haematopoietic tissue of mullet were assessed after an experimental anaemia, induced by caudal blood extraction. Thirty fish were used and divided into two groups: Group A (control group n = 20) and Group B (experimental group n = 10). From Group A, 10 fish were sacrificed to obtain head kidney control; from the 10 remaining, blood samples were collected by caudal venipuncture. From Group B, blood samples were collected five times once a week (T0, T1, T2, T3, T4) to induce experimental blood loss. At the end of the experimental period fish were sacrificed and the head kidneys were isolated. For all fish, haemogram and manual differential leukocyte counts were determined in peripheral blood. Reduced red blood cell count (RBC), haematocrit (Hct), haemoglobin (Hb), thrombocyte count (TC), lymphocytes and increased mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), monocytes and neutrophil values were found at T1 with respect to T0. Successively, until T3, RBC, Hct, Hb, TC and lymphocyte values showed an increase in peripheral blood. A decrease of haematological parameters in peripheral blood after the last bleeding time (T4) was observed. Cell identification and differential counts on head kidneys were performed and a significant increase of lymphocytes, monocytes and early unidentified blast cells was observed. A decrease in RBC, neutrophils, eosinophils, TC and a total absence of basophils were found. These results indicated that mullet are able to recover from anaemia caused by various adverse environmental and/or nutritional factors.
Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State

Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
Excellent Cyclic and Rate Performances of SiO/C/Graphite Composites as Li-Ion Battery Anode

The SiO-based composites containing different carbon structures were prepared from asphalt and graphite by the milling, spray drying, and pyrolysis. In the obtained near-spherical composite particles, the refined amorphous SiO plates, which are coated with an amorphous carbon layer, are aggregated with the binding of graphite sheets. The SiO/C/Graphite composites present a maximum initial charge capacity of 963 mAh g−1 at 100 mA g−1, excellent cyclic stability (~950 mAh g−1 over 100 cycles), and rate capability with the charge capacity of 670 mAh g−1 at 1,000 mA g−1. This significant improvement of electrochemical performances in comparison with pristine SiO or SiO/C composite is attributed to the unique microstructure, in which both the graphite sheets and amorphous carbon coating could enhance the conductivity of SiO and buffer the volume change of SiO. The higher pyrolysis temperature causes the denser spherical microstructure and better cycle life. Our work demonstrates the potential of this SiO/C/Graphite composite for high capacity anode of LIBs.
Salt, nonmuscle proteins, and hydrocolloids affecting rigidity changes during gelation of giant squid (Dosidicus gigas)

A thermal scanning rigidity monitor was used to determine how certain nonmuscle proteins and hydrocolloids contribute, separately or in combination, to gelation of giant squid mantle homogenized with 1.5% or 2.5% NaCl. In batters with 1.5% salt, rigidity was higher and peak gelation also took place at a higher temperature. Of all the ingredients tested, only ι-carrageenan contributed significantly to rigidity. Maximum values for batter rigidity and for folding test and work of penetration in cooked gels were attained when ι-carrageenan was added along with starch and a nonmuscle protein, which indicates synergy among the three ingredients. Keywords: Squid muscle; gelation; proteins; hydrocolloids; rheology
SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant

One of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in its ORF3b gene. Here, we show that SARS-CoV-2 ORF3b is a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays revealed that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Furthermore, analyses of more than 15,000 SARS-CoV-2 sequences identified a natural variant, in which a longer ORF3b reading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients, but also describe a possibility of the emergence of natural SARS-CoV-2 quasispecies with extended ORF3b that may exacerbate COVID-19 symptoms. Highlights ORF3b of SARS-CoV-2 and related bat and pangolin viruses is a potent IFN antagonist SARS-CoV-2 ORF3b suppresses IFN induction more efficiently than SARS-CoV ortholog The anti-IFN activity of ORF3b depends on the length of its C-terminus An ORF3b with increased IFN antagonism was isolated from two severe COVID-19 cases
Predicting tissue-specific gene expression from whole blood transcriptome

Machine learning tool TEEBoT predicts an individual’s tissue-specific gene expression from his/her blood transcriptome. Complex diseases are mediated via transcriptional dysregulation in multiple tissues. Thus, knowing an individual’s tissue-specific gene expression can provide critical information about her health. Unfortunately, for most tissues, the transcriptome cannot be obtained without invasive procedures. Could we, however, infer an individual’s tissue-specific expression from her whole blood transcriptome? Here, we rigorously address this question. We find that an individual’s whole blood transcriptome can significantly predict tissue-specific expression levels for ~60% of the genes on average across 32 tissues, with up to 81% of the genes in skeletal muscle. The tissue-specific expression inferred from the blood transcriptome is almost as good as the actual measured tissue expression in predicting disease state for six different complex disorders, including hypertension and type 2 diabetes, substantially surpassing the blood transcriptome. The code for tissue-specific gene expression prediction, TEEBoT, is provided, enabling others to study its potential translational value in other indications.
Formation and properties of Inceptisols (Cambisols) of major agricultural rainfed areas in Jordan

Inceptisols (Cambisols) occupy a large and important part of the agricultural land in Jordan. Rainfed agriculture is practiced there and the soils are used for cultivated field crops. They have sustained agriculture for many decades. Relatively few pedogenic studies have been directed to Inceptisols (Cambisols) in Jordan. Six sites from different precipitation zones were selected where Inceptisols (Cambisols) occur on limestone parent material. The physical and chemical properties of these soils were determined to study the genesis of these soils, to classify them according to the USDA and FAO system and to provide basic information about the soils for agricultural development. Typical Inceptisols (Cambisols) were found on steep slopes and on young geomorphic surfaces. Illuviation, lessivage and pedoturbation processes are relatively active in the studied soils but none of these processes predominate. Weathering was most effective at the surface.
Effects of Early Skip-A-Day Feed Removal and Litter Material on Broiler Live and Processing Performance and Litter Bacterial Levels

This study investigated effects of early skip-a-day feed removal and litter materials on broiler live and processing performance and levels of litter bacteria. A total of 1600 male broilers were evenly distributed in 16 pens. Eight pens were provided feed ad libitum (AL Treatment) and 8 were provided feed ad libitum except for 24 hour removal periods at 6, 8, 10 and 12 days of age (4R Treatment). Half the pens in each feeding treatment were provided used pine shavings and the other half were provided used sand as litter. An increasing photoperiod program was provided which decreased from 23L:1D to 13L:11D at 6 days, then increased 2 hours/week beginning at 13 days and reached 23L:1D at 41 days. Body weight and feed consumption were determined and feed conversions calculated approximately weekly. Mortalities were necropsied and recorded daily. At 47 days, 10 birds from each pen were processed, cut up and deboned to determine carcass and parts weights and yields. Litter samples were collected from 3 locations in each pen the day before chicks were placed, weekly during the rearing period and 9 days after bird removal. Relative to the AL Treatment, 4R body weights were decreased 27% immediately after feed removal, this smaller than expected reduction was likely due to the short photoperiod provided at that time. Body weights of AL and 4R Treatments diverged until partial compensatory growth occurred in the 4R Treatment once 23L:1D was provided. Feed consumption was reduced in the 4R Treatment following the initiation of feed removal, while feed conversion was only transiently reduced. Metabolic and total mortality were reduced by the 4R Treatment. Differences in carcass weights and yields and parts weights were proportional to live weight differences due to feeding treatments. Live production and processing performance were not influenced by litter material. In general, litter bacterial numbers were only influenced slightly by feeding treatments. However, litter type played a more marked role, with sand having lower aerobic, anaerobic and enteric counts than pine shavings.
Gut microbiota impairs insulin clearance during obesity

Hyperinsulinemia can be a cause and consequence of obesity and insulin resistance. Increased insulin secretion and reduced insulin clearance can contribute to hyperinsulinemia. The triggers for changes in insulin clearance during obesity are ill-defined. We found that oral antibiotics mitigated impaired insulin clearance in mice fed a high fat diet (HFD) for 12 weeks or longer. Short-term HFD feeding and aging did not alter insulin clearance in mice. Germ-free mice colonized with microbes from HFD-fed mice had impaired insulin clearance, but not C-peptide clearance, and only after mice were colonized for 6 weeks and then HFD-fed. Five bacterial taxa predicted >90% of the variance in insulin clearance. Our data indicate that gut microbes are an independent and transmissible factor that regulates obesity-induced changes in insulin clearance. A small cluster of microbes may be a target for mitigating defects in insulin clearance and the progression of obesity and Type 2 Diabetes. We propose that a small community in the gut microbiota can impair insulin clearance and increase insulin load and the risk of complications from hyperinsulinemia.
Comparison of Oxidative Processes on Myofibrillar Proteins from Beef during Maturation and by Different Model Oxidation Systems

The aim of this work was to compare the oxidative processes occurring in myofibrillar proteins during meat maturation and after an in vitro exposure to different enzymic and nonenzymic oxidative systems. Myofibrils were prepared from bovine Longissimus lumborum and Diaphragma pedialis at day 1 and day 10 post-mortem. Myofibrillar protein oxidation was measured by the carbonyl content, with the 2,4-dinitrophenylhydrazine (DNPH) method, and by (thiol group) SH content with the 2,2‘-dithiobis(5-nitropyridine) (DTNP) method. Polymerization and/or fragmentation of oxidized proteins were estimated by SDS-PAGE and Western blot analysis using a polyclonal antibody to myosin. Oxidation of myofibrillar proteins is dependent upon the different metal-catalyzed oxidation (MCO) systems. The increase in carbonyl content and also the decrease in SH content of myofibrillar proteins, after maturation of 10 days, were similar to those obtained after a 1 h incubation of myofibrillar proteins in the presence of several MCO sy.
Learning hierarchical sequence representations across human cortex and hippocampus

Sequence learning is tracked across the human brain, and the computational systems used to parse the sequences are highlighted. Sensory input arrives in continuous sequences that humans experience as segmented units, e.g., words and events. The brain’s ability to discover regularities is called statistical learning. Structure can be represented at multiple levels, including transitional probabilities, ordinal position, and identity of units. To investigate sequence encoding in cortex and hippocampus, we recorded from intracranial electrodes in human subjects as they were exposed to auditory and visual sequences containing temporal regularities. We find neural tracking of regularities within minutes, with characteristic profiles across brain areas. Early processing tracked lower-level features (e.g., syllables) and learned units (e.g., words), while later processing tracked only learned units. Learning rapidly shaped neural representations, with a gradient of complexity from early brain areas encoding transitional probability, to associative regions and hippocampus encoding ordinal position and identity of units. These findings indicate the existence of multiple, parallel computational systems for sequence learning across hierarchically organized cortico-hippocampal circuits.
Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

Understanding the contribution of different molecular processes to the evolution and development of divergent phenotypes is crucial for identifying the molecular routes of rapid adaptation. Here, we used RNA-seq data to compare patterns of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into benthic and pelagic ecotypes across multiple independent lakes. We found that genes that were differentially spliced and differentially expressed between the benthic and pelagic ecotypes were mostly independent (<6% overlap) and were involved in different processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were mostly involved in energy metabolism, immunity and growth. Together, these likely explain different axes of divergence between ecotypes in swimming performance and activity. Furthermore, we found that alternative splicing and gene expression are mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7 - 10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks (‘hub genes’) and were annotated to significantly more gene ontology terms compared to non-differentially spliced genes, consistent with a higher level of connectivity and pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary phenotypes important for local adaptation. This study provides novel insights into the importance of contrasting but putatively complementary molecular processes for rapid and parallel adaptive evolution.
Boulders or urchins? Selecting seeding sites for juvenile Haliotis midae along the Namaqualand coast of South Africa

The extent to which the relationship between juvenile abalone Haliotis midae and sea urchins Parechinus angulosus is induced by their physical habitat along the Namaqualand coast of South Africa was investigated. Correlation analyses between the proportion of abalone utilising sea urchins for refuge and the proportion of habitat defined as exposed were computed from 28 experimental seeding sites in Port Nolloth on the north-west coast of South Africa. A highly significant positive correlation was found (r = 0.72, p < 0.05). It was concluded that, along the Namaqualand coast, under-boulder habitat was the most important factor determining the survival of juvenile abalone (size 12–26mm). Site selection should therefore be based on the suitability of the physical substratum to provide shelter for juvenile abalone along that coast.
Low genotyping error rates in wild ungulate faeces sampled in winter

We show that Alpine ibex (Capra ibex) and Corsican mouflon (Ovis musimon) faeces yield useful DNA for microsatellite analysis, however, we detected higher genotyping error rates for spring faeces than for winter faeces. We quantified the genotyping error rate by repeatedly genotyping four microsatellites. Respectively, 99 and 95% of mouflon and ibex genotyping repetitions provided a correct genotype using winter samples, whereas spring samples provided only 52 and 59% correct genotypes. Thus, before starting a noninvasive study, we recommend that researchers conduct a pilot study to quantify genotyping error rates for each season, population and species to be studied.
Fine Structure and Function of Pharynx Cilia in Glossobalanus minutus Kowalewsky (Enteropneusta)

Two kinds of cilia have been observed in the pharynx of Glossobalanus minutus Kowalewsky. From the present study, a ciliary specialization can be found in order to move a determinate substance, i.e. mucus or water. Mucus-moving cilia (type I cilia) have a single basal centriole and poorly developed ciliary rootlets. Their tips are rounded, bearing an inner, asymmetrical cap attached to some tubules. Water-moving cilia (type II cilia) are exclusively located at lateral epithelia of branchial bars, giving rise to the water current through the gills. They have two basal centrioles, proximal and distal, and a complex system of ciliary rootlets made up of a principal rootlet, a secondary or accessory rootlet and a ‘fan’ rootlet. The tips of type II cilia have a long process with some tubules inside. All basal structures are precisely orientated in order to assure a good coordination of ciliary beat. The possible functional significance of ciliary substructure is also discussed. From these observations a model for mucus and water currents through gill slits is postulated.
Long-term effects of prey-availability, partnering and temperature on overall egg capsule output of 'New Zealand flatworms', Arthurdendyus triangulatus.

Summary Arthurdendyus triangulatus is an invasive terrestrial fl atworm that preys on earthworms. To assess A. triangulatus egg capsule production, fl atworms were maintained in ventilated polypropylene tubs (7.5 L) kept in controlled environment (CE) chambers or outdoors in the ground. Controlled environment chambers were maintained at 8°C or 14°C, fl atworms kept singly or paired within tubs and offered Eisenia fetida according to a weight equalling one-eighth or one-half of the mean fl atworm weight, or left unfed. The tubs were a successful method for keeping fl atworms, with some surviving for over one year. The greatest number of egg capsules produced by an individual A. triangulatus was nine over a 16 week period for a fl atworm kept at 14°C and fed at the one-half regime (0.56 egg capsules fl atworm –1 week –1 ). Although the effects of treatments varied with CE chambers, there was some evidence from fl atworms kept outdoors, that feeding affected egg capsule output, with those fl atworms fed at the one-half regime tending to produce more egg capsules (P = 0.057). Flatworms at the oneeighth regime or that were unfed produced progressively lighter egg capsules and substantially declined in weight themselves. Nevertheless, even unfed fl atworms continued to produce egg capsules for 18 weeks. The lightest egg capsule weighed 8 mg, whilst the heaviest was 180 mg. In the CE chambers at 14°C, there was evidence for two different reproductive/survival strategies. Some fl atworms produced cumulatively more egg capsules the longer they survived, whereas others lived longer but produced fewer egg capsules. Flatworms kept without a partner still produced egg capsules up to 35 weeks later. Egg capsules contained a mean of 4.14 (CE chambers) or 4.62 (outdoors) juveniles, with a maximum of 11. Overall, juveniles were 45% of the weight of egg capsules, although larger egg capsules had more juveniles, which comprised a greater proportion of the egg capsule. The conversion of earthworm prey to egg capsule production was estimated at 13%.
Intraspecific competition in larvae of the ant‐lion Morter sp. and interspecific interactions with Macroleon quinquemaculatus

Abstract. 1 Intraspecific competition was investigated in the pit‐digging larvae of the ant‐lion Morter sp. , which normally occurs at low density in a food‐rich habitat. 2 Morter larvae interact by displays, challenges, and sand tossing. Challenges/displays affected pit spacing while sand tossing affected pit size. Pit ownership determined the outcome of contests regardless of the relative sizes or feeding condition of the contestants. 3 Competition had no effect on the pit size of winners but losers showed a density dependent reduction in pit size. Interference competition caused a density dependent reduction in larval growth rates. 4 Macroleon quinquemaculatus (Hagen) always won contests with Morter, even when smaller. Cannibalism occurred in 60% of these contests. 5 Little intraspecific competition occurs in Morter in the field. Morter is more willing to incur energy costs than Macroleon.