Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-canonical cell death by reassortant reovirus

Triple-negative breast cancer (TNBC) constitutes 12% of all breast cancer and is associated with worse prognosis compared to other subtypes of breast cancer. Current therapies are limited to cytotoxic chemotherapy, radiation, and surgery, leaving a need for targeted therapeutics to improve outcomes for TNBC patients. Mammalian orthoreovirus (reovirus) is a nonenveloped, segmented, dsRNA virus in the Reoviridae family. Reovirus preferentially kills transformed cells and is in clinical trials to assess its efficacy against several types of cancer. We previously engineered a reassortant reovirus, r2Reovirus, that infects TNBC cells more efficiently and induces cell death with faster kinetics than parental reoviruses. In this study, we sought to understand the mechanisms by which r2Reovirus induces cell death in TNBC cells. We show that r2Reovirus infection of TNBC cells of a mesenchymal-stem like (MSL) lineage downregulates the MAPK/ERK pathway and induces non-conventional cell death that is caspase dependent, but caspase 3-independent. Infection of different MSL lineage TNBC cells with r2Reovirus results in caspase 3-dependent cell death. We map the enhanced oncolytic properties of r2Reovirus in TNBC to epistatic interactions between the Type 3 Dearing M2 gene segment and Type 1 Lang genes. These findings suggest that the genetic composition of the host cell impacts the mechanism of reovirus-induced cell death in TNBC. Together, our data show that understanding host and virus determinants of cell death can identify novel properties and interactions between host and viral gene products that can be exploited for the development of improved viral oncolytics. Importance Triple negative breast cancer (TNBC) is unresponsive to hormone therapies, leaving patients afflicted with this disease with limited treatment options. We previously engineered an oncolytic reovirus (r2Reovirus) with enhanced infective and cytotoxic properties in TNBC cells. However, how r2Reovirus promotes TNBC cell death is not known. In this study, we show that reassortant r2Reovirus can promote non-conventional caspase-dependent but caspase 3-independent cell death and that the mechanism of cell death depends on the genetic composition of the host cell. We also map the enhanced oncolytic properties of r2Reovirus in TNBC to interactions between a Type 3 M2 gene segment and Type 1 genes. Our data show that understanding the interplay between the host cell environment and the genetic composition of oncolytic viruses is crucial for the development of efficacious viral oncolytics.
Characterization and In Vivo Hydrolysis of Amylose–Stearic Acid Complex

ABSTRACT Objectives of this study were to compare thermal properties, swelling power, and enzymatic hydrolysis of a type 5 resistant starch (RS5) with that of normal corn starch (NCS) and high-amylose corn starch (HA7). The RS5 was prepared by complexing debranched HA7 with stearic acid (SA). Because of amylose-helical-complex formation with SA, the RS5 starch granules showed restricted swelling at 95°C. The RS5 displayed a larger RS content (67.8%) than the HA7 (33.5%) and NCS (0.8%), analyzed following AOAC method 991.43 (AACC International Approved Method 32-07.01). When the cooked RS5, HA7, and NCS were used to prepare diets for rats with 55% (w/w) starch content, RS contents of the diets were 33.7, 15.8, and 2.6%, respectively. After the diet was fed to the rats in week 1, ≈16% of the starch in the RS5 diet was found in the feces, substantially greater than that of the HA7 diet (≈6%) and NCS diet (0.1%). The percentage of starch not being utilized in the RS5 diet decreased to ≈5% in week 9, which cou.
Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion

The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-minute protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable “open source” design strategy would enable virtually any lab to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment.
ER-directed TREX1 limits cGAS recognition of micronuclei

Chromosomal instability in cancer results in the formation of nuclear aberrations termed micronuclei. Spontaneous loss of micronuclear envelope integrity exposes DNA to the cytoplasm, leading to chromosome fragmentation and innate immune activation. Despite connections to cancer genome evolution and anti-tumor immunity, the mechanisms underlying damage and immune sensing of micronuclear DNA are poorly understood. Here, we use a novel method for the purification of micronuclei and live-cell imaging to show that the ER-associated nuclease TREX1 inhibits cGAS sensing of micronuclei by stably associating with and degrading micronuclear DNA upon micronuclear envelope rupture. We identify a TREX1 mutation, previously associated with autoimmune disease, that untethers TREX1 from the ER, disrupts TREX1 localization to micronuclei, alleviates micronuclear DNA damage, and enhances cGAS recognition of micronuclei. Together, these results establish ER-directed resection of micronuclear DNA by TREX1 as a critical regulator of cytosolic DNA sensing in chromosomally unstable cells and provide a mechanistic basis for the importance of TREX1 ER-tethering in preventing autoimmunity.
An ex vivo model of Toxoplasma recrudescence

Toxoplasma has been a useful parasite model for decades because it is relatively easy to genetically modify and culture, however, attempts to generate and study the recrudescence of tissue cysts have come up short with lab-adapted strains generating low numbers of tissue cysts in vivo. Here we have established a new model of Toxoplasma recrudescence using bradyzoites from an unadapted Type II ME49 strain (ME49EW) isolated from murine brain tissue. Ex vivo bradyzoite infection of fibroblasts and astrocytes produced sequential tachyzoite growth stages; a fast-growing stage was followed by formation of a slower-growing stage. In astrocytes, but not in fibroblasts, bradyzoites also initiated a second recrudescent pathway involving bradyzoite to bradyzoite replication. Intraperitoneal infections of mice with either bradyzoites or the fast-growing tachyzoite stage efficiently disseminated to brain tissue leading to high numbers of tissue cysts, while infections with the slow-growing tachyzoite stage were largely retained in the peritoneum. Poor infection and cyst formation of slow-growing tachyzoites was reversible by serial tissue cyst passage, while the poor tissue cyst formation of lab-adapted tachyzoites was not reversible by these approaches. To distinguish strain developmental competency, we identified Toxoplasma genes highly expressed in ME49EW in vivo tissue cysts and developed a qPCR approach that differentiates immature from mature bradyzoites. In summary, the results presented describe a new ex vivo bradyzoite recrudescence model that fully captures the growth and developmental processes during toxoplasmosis reactivation in vivo opening the door to the further study of these important features of the Toxoplasma intermediate life cycle.
Combined effect of biological and physical stress on artificial production of agarwood oleoresin in Aquilaria malaccensis

Agarwood is the most expensive wood of the world and highly demanded wood in perfumery industry and ritual ceremonies of various religions. Agarwood is the infectious wood part of Aquilaria tree. Naturally, production of agarwood in Aquilaria takes 10-20 years of time and it can develop only in 1-2% of Aquilaria trees. Different types of biological, chemical and physical methods have been developed for artificial production of agarwood to fulfil the rising demand of the market. In the current article, we tried to explore combined effect of physical and biological stress in the form of stick method to improve agarwood production in Aquilaria malaccensis and compared it with well-known artificial fungal infection syringe method. Total 21 fungal strains were applied alone (syringe method) and with bamboo sticks (stick method). We found maximum infection occurred in stick method by fungi Penicillium polonicum AQGGR1.1 with 10 cm infection length. Artificial induction of marker compounds of agarwood, benzyl acetone and anisyl acetone were measured mostly in stick method, induced by 71.4% fungal strains grown on bamboo sticks, while alone only 42.9% fungi can induced in syringe method. Penicillium aethiopicum AQGGR1.2 found highly agarwood oleoresin inducing fungus in stick method and shown high potential agent in stick method for artificial production of agarwood.
Endogenous lysine and other amino acid flows at the terminal ileum of the growing pig (20 kg bodyweight): The effect of protein-free, synthetic amino acid, peptide and protein alimentation

Twenty-four crossbred pigs of 15 kg initial bodyweight were fed four semi-synthetic diets for 10 days according to a completely randomised design. The study aimed to determine the effects of state of body nitrogen balance and the presence of dietary peptides and protein in the digestive tract on the excretion of endogenous amino acids from the ileum of the pig. Endogenous lysine excretion was determined for pigs given a protein-free (PF) diet, an enzymically hydrolysed casein- (EHC), a zein- (ZN) or a synthetic amino acid- (SAA) based diet. Digesta from the EHC-fed animals were centrifuged and ultrafiltered after collection and the precipitate plus retentate fraction was used to determine the endogenous flows. Such processing excludes unabsorbed dietary amino acids from the measure of endogenous loss. ZN is naturally deficient in lysine and tryptophan and these two amino acids were omitted from the synthetic amino acid-based diet to allow direct measurement of endogenous lysine flow. Pigs given the ZN and SAA diets received free lysine and tryptophan orally throughout the study except for the final 2 days of the study, when these amino acids were infused intravenously. Endogenous flows for amino acids other than lysine were determined for pigs given the PF and EHC diets. On the final day of the study the pigs were given their daily dietary allowance hourly and killed 10 h after the start of feeding. Digesta were collected from the terminal ileum (20 cm anterior to the ileo-caecal junction) and endogenous flows were determined by reference to the marker chromic oxide. The mean endogenous ileal lysine flows for the ZN- and EHC-fed pigs were not significantly different (overall mean, 419 mg kg−1 dry matter intake), but were higher (P < 0.05) than those for the PF- and SAA-fed pigs (overall mean, 268 mg kg−1 dry matter intake) whose mean flows were not significantly different from each other. The mean endogenous ileal flows for amino acids other than lysine were higher (P < 0.05) for the EHC-fed pigs compared to the animals on the PF diet, except for proline, glycine and arginine. The similar endogenous ileal lysine excretion for pigs receiving a SAA-based diet and in positive body nitrogen balance, and PF-fed pigs in negative body nitrogen balance, indicates that negative body nitrogen balance per se does not lead to a lowered endogenous ileal excretion. It would appear, however, that the presence of dietary peptides or protein in the gut increases amino acid excretion at the terminal ileum above that found with PF or SAA alimentation. Consequently, endogenous ileal amino acid flow in the pig may be underestimated when determined by the traditional PF method.
A Purkinje cell model that simulates complex spikes

Purkinje cells are the principal neurons of the cerebellar cortex. One of their distinguishing features is that they fire two distinct types of action potential, called simple and complex spikes, which interact with one another. Simple spikes are stereotypical action potentials that are elicited at high, but variable, rates (0 – 100 Hz) and have a consistent waveform. Complex spikes are composed of an initial action potential followed by a burst of lower amplitude spikelets. Complex spikes occur at comparatively low rates (~ 1 Hz) and have a variable waveform. Although they are critical to cerebellar operation a simple model that describes the complex spike waveform is lacking. Here, a novel single-compartment model of Purkinje cell electrodynamics is presented. The simpler version of this model, with two active conductances and a leak channel, can simulate the features typical of complex spikes recorded in vitro. If calcium dynamics are also included, the model can capture the pause in simple spike activity that occurs after complex spike events. Together, these models provide an insight into the mechanisms behind complex spike spikelet generation, waveform variability and their interactions with simple spike activity.
Fast response of freshwater consumers to a new trophic resource: Predation on the recently introduced Asian bivalve Limnoperna fortunei in the lower Paraná river, South America

Comparison of Limnoperna fortunei numbers and biomass in screened (5, 15 and 40 mm) and unscreened cages deployed for 18 months in the lower Parana delta indicates that predators harvest 26-79% (numbers), or 20-85% (biomass) of the mussel population. Predation impact decreases with mussel size. On average, 6 kg of whole live mussel ¥ m -2 ¥ year -1 (0.36 g of dry mussel tissue ¥ m -2 ¥ day -1 ) were eliminated from the unscreened cages. Cages with 15 and 40 mm screens lost between 1 and 2 kg ¥ m -2 ¥ year -1 . Aquatic mammals, birds, and especially fish, are probably the main consumers of large mussels. Small L. fortunei are most probably eaten by fish and also by several invertebrates, including crustaceans, leeches and gastropods. It is suggested that L. fortunei intercepts a significant fraction of the organic carbon that the Parana-Uruguay rivers flush into the ocean, locally boosting numbers of benthophagous animals, deposit feeders and, indirectly, higher level predators. Our results indicate that only 15 years after its first introduction in South America this invasive species is very actively consumed by local predators, but predatory suppression of the mussel seems very unlikely. Comparisons with the effects reported for the zebra mussel (Dreissena polymorpha) in Europe and North America suggest that L. fortunei is consumed more actively and that its negative impact on the local fauna is more restricted. These differences are attributed to the fact that while D. polymorpha feeds chiefly on plankton, a limited resource, L. fortunei feeds on detrital particulate organic matter, whose supply in these large South American rivers largely exceeds consumption.
EVALUATION OF WHOLE PLANT FABABEAN FORAGE IN RUMINANT RATIONS

Feeding trials were conducted to evaluate nutritive value of whole plant fababean (FB) silages. A growth trial with dairy heifers resulted in higher consumption (P 0.05) in average daily gain (ADG). Lactating Holstein cows were fed four diets, 1-GL + high grain (HG) (control diet), 2-direct cut FB (33% DM) + HG, 3-wilted FB (37% DM) + HG and 4-wilted FB + medium grain (MG), in a Lucas design. Consumption of the direct cut FB silage was higher (P < 0.05) than that of grass silage, and reducing the level of grain feeding from 56 to 43% of the diet resulted in an increase (P < 0.05) in FB silage consumption. Wintering calves were fed five silages (1-FB, 2-GL, 3-barley-clover (BC), 4-corn or 5-barley) plus 1 kg grain supplement for 93 days. Calves receiving FB or GL silage consumed more (P < 0.05) DM than animals on the other treatments. In trial 2, beef calves were fed four silages (early FB, frosted FB, corn or GL) or two types of.
Molecular cloning, nucleotide sequence and gene expression of a transferrin gene from the rice stem borer, Chilo suppressalis Walker (Lepidoptera: Crambidae)

Chilo suppressalis transferrin cDNA was cloned by reverse transcription polymerase chain reaction (RT-PCR). The clone (2,248 bp) encodes a protein of 644 amino acids with a calculated molecular weight of 71,805 Da. The deduced amino acid sequence showed significant homology with known insect transferrins from Bombyx mori (82%), Manduca sexta (77%), Blaberus discoidalis (43%), Riptortus clavatus (42%), Aedes aegypti (36%), Sarcophaga peregrina (32%), Drosophila melanogaster (33%) and D. silvestris (32%). Transferrin expression was examined by RNA gel blot analysis using diapausing and non-diapausing larvae of C. suppressalis. As a result, higher levels of expression were observed in diapausing larvae.
Monitoring Texas Wood Ducks With a Cooperative Nest-Box Program

Abstract We analyzed 8 years of data from the Texas Cooperative Nest Box Program initiated in 1988 by Texas Parks and Wildlife, USA, as a means of involving private cooperators in statewide wood duck (Aix sponsa) management. Cooperators operated ≤9 boxes and most reported nest-box data for only 1 year (56.5%) and 2 years (20.6%) over the 8-year life of the project. Mean nest-box use differed among ecological regions of the state (F = 4.23, df = 6, P = 0.001) but did not exceed 30% in any region. Mean nest-box success ranged between 74–91% across ecological regions during 1988–1995, but annual estimates of nest-box success lacked precision (CVs >30%) in most years for all regions. Our project was unsuccessful as a management tool for monitoring wood duck demographics. Future efforts should focus on improving the amount and quality of data collected from box-nesting wood ducks.
Association of soil organic carbon with physically separated soil fractions in different land uses of Costa Rica

Studies on soil organic carbon (SOC) storage and stability require the separate assessment of soil fractions in relation to protection against loss. This on-farm study assessed the role of primary (sand, silt, and clay) and secondary (micro- and macroaggregates) particle size fractions on the physical protection of SOC to 30-cm depth of nine agricultural and three forest land uses within three contrasting ecoregions of Costa Rica (i.e., Isthmian-Atlantic moist, Pacific dry, and Montane forest). Specific objectives were to: (1) determine the effect of land use in each ecoregion on particulate organic matter carbon (POM-C), silt plus clay-associated carbon (S+C-C), and micro- and macroaggregate associated water-stable aggregate carbon (WSA-C), and (2) establish the relationships among aggregate properties and SOC concentration. Aggregate stability was characterized by studying the WSA, mean weight diameter (MWD), and tensile strength (TS). Soils under coffee (Coffea arabica), oil palm (Elaeis guineensis), and pineapple (Ananas comosus) plantations had high clay contents to 30-cm depth (ranging between 42.9 and 60.7%), which indicated a high potential for SOC storage. In comparison to less disturbed forest soils, micro- and macroaggregation was not strongly affected by agricultural land use. At coffee and pasture land uses, POM-C concentration was significantly lower (ranging between 0.4 and 2.0 g C kg−1). Between 58 and 98% of SOC was associated with S+C fractions indicating the importance of these particle size fractions to SOC storage. The S+C-C and micro- and macroaggregate-C concentrations differed mainly among pineapple, mango (Mangifera indica), pasture, and other land uses within ecoregions. Further, there was no general tendency of higher C concentrations in the macro- vs. the microaggregate fractions in contrast to the aggregate hierarchy theory. The MWD was affected by land use only for pineapple and organic farming, and it decreased for mango and coffee with increase in soil depth. Correlations among SOC, texture, and TS were site-specific. Silt content was more important than the other particle size fractions in explaining SOC contents. In summary, the amount of physically separated soil fractions and their C storage and stability to 30-cm depth differed mainly among pineapple, mango, pasture, and coffee in specific ecoregions. Well-designed long-term field experiments in Costa Rica are needed to develop management practices for enhancing SOC storage and stabilization in physically separated soil fractions.
Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data

The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 16 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively in the reference population. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed, and offer a perspective on implementing this data in considered breed management strategies.
Lack of mitochondrial gene flow between populations of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis inhabiting Amami-oshima Island

: The Ryukyu-ayu, Plecoglossus altivelis ryukyuensis, is an amphidromous fish that is endemic to Amami-oshima Island in southernmost Japan. Its abundance, however, has been appreciably reduced during the last two decades such that the subspecies is now considered to be endangered. The variation of the mitochondrial DNA control region was investigated among specimens of the extant populations in the eastern and western parts of Amami-oshima Island (Sumiyo Bay and Yakeuchi Bay areas, respectively), using restriction fragment length polymorphism analysis in order to estimate the extent of gene flow between the two areas. Of a total of 165 fish including temporally different samples, four haplotypes were detected and each area possessed the two haplotypes. However, the common haplotypes shared between these areas were not observed, which indicates that recent gene flow has not occurred between these populations. The nucleotide divergence between populations was much higher than the nucleotide diversity within each population, and the neighbor-joining phylogram among haplotypes showed that the haplotypes are associated with their geographic area. These results suggest that the two populations of Ryukyu-ayu on Amami-oshima Island have been historically formed.